Starting phenix.real_space_refine on Sun Aug 24 17:39:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dkm_46962/08_2025/9dkm_46962.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dkm_46962/08_2025/9dkm_46962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dkm_46962/08_2025/9dkm_46962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dkm_46962/08_2025/9dkm_46962.map" model { file = "/net/cci-nas-00/data/ceres_data/9dkm_46962/08_2025/9dkm_46962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dkm_46962/08_2025/9dkm_46962.cif" } resolution = 3.4 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= 0.052 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 13656 2.51 5 N 3619 2.21 5 O 3960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21339 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 18190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2333, 18190 Classifications: {'peptide': 2333} Incomplete info: {'truncation_to_alanine': 196} Link IDs: {'PTRANS': 64, 'TRANS': 2268} Chain breaks: 13 Unresolved non-hydrogen bonds: 684 Unresolved non-hydrogen angles: 849 Unresolved non-hydrogen dihedrals: 551 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLU:plan': 38, 'GLN:plan1': 7, 'ASN:plan1': 11, 'TRP:plan': 1, 'PHE:plan': 8, 'TYR:plan': 3, 'ASP:plan': 22, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 392 Chain: "B" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 359 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'HIS:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 4, 'ASP:plan': 3, 'TYR:plan': 2, 'GLN:plan1': 4, 'TRP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 108 Chain: "C" Number of atoms: 2677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2677 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 15, 'TRANS': 327} Chain breaks: 4 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 5, 'PHE:plan': 1, 'ASP:plan': 6, 'GLN:plan1': 2, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 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: 5.31, per 1000 atoms: 0.25 Number of scatterers: 21339 At special positions: 0 Unit cell: (100.92, 140.36, 168.2, 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 3960 8.00 N 3619 7.00 C 13656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5240 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 26 sheets defined 54.6% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 1433 through 1461 Processing helix chain 'A' and resid 1471 through 1494 Processing helix chain 'A' and resid 1511 through 1521 removed outlier: 4.022A pdb=" N SER A1521 " --> pdb=" O LYS A1517 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1534 Processing helix chain 'A' and resid 1535 through 1540 Processing helix chain 'A' and resid 1541 through 1551 Processing helix chain 'A' and resid 1557 through 1567 removed outlier: 3.541A pdb=" N PHE A1561 " --> pdb=" O GLN A1557 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LYS A1563 " --> pdb=" O SER A1559 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LYS A1564 " --> pdb=" O LYS A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1632 removed outlier: 3.955A pdb=" N TRP A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A1616 " --> pdb=" O ASP A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1641 removed outlier: 3.913A pdb=" N VAL A1639 " --> pdb=" O ASP A1635 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER A1641 " --> pdb=" O GLU A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1665 Processing helix chain 'A' and resid 1669 through 1688 removed outlier: 4.148A 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: 3.624A pdb=" N ALA A1724 " --> pdb=" O THR A1720 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1788 removed outlier: 4.159A pdb=" N GLN A1788 " --> pdb=" O ASP A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1813 Processing helix chain 'A' and resid 1827 through 1842 removed outlier: 3.566A pdb=" N GLN A1840 " --> pdb=" O VAL A1836 " (cutoff:3.500A) Processing helix chain 'A' and resid 1850 through 1853 removed outlier: 3.643A 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: 3.719A pdb=" N SER A1862 " --> pdb=" O LEU A1858 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA A1863 " --> pdb=" O SER A1859 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN A1864 " --> pdb=" O ALA A1860 " (cutoff:3.500A) Processing helix chain 'A' and resid 1909 through 1914 Processing helix chain 'A' and resid 1925 through 1938 removed outlier: 3.546A pdb=" N ILE A1929 " --> pdb=" O GLN A1925 " (cutoff:3.500A) Processing helix chain 'A' and resid 1942 through 1959 Processing helix chain 'A' and resid 1969 through 1981 removed outlier: 3.638A pdb=" N LEU A1973 " --> pdb=" O GLY A1969 " (cutoff:3.500A) Processing helix chain 'A' and resid 1982 through 1986 removed outlier: 3.533A pdb=" N SER A1985 " --> pdb=" O PRO A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1990 through 2003 removed outlier: 4.231A 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: 3.997A 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 2143 through 2148 removed outlier: 3.706A pdb=" N LYS A2146 " --> pdb=" O GLY A2143 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN A2147 " --> pdb=" O THR A2144 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER A2148 " --> pdb=" O PHE A2145 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2143 through 2148' Processing helix chain 'A' and resid 2159 through 2164 Processing helix chain 'A' and resid 2166 through 2171 Processing helix chain 'A' and resid 2203 through 2208 Processing helix chain 'A' and resid 2221 through 2236 Processing helix chain 'A' and resid 2246 through 2257 removed outlier: 3.504A pdb=" N ASP A2251 " --> pdb=" O ASP A2247 " (cutoff:3.500A) Processing helix chain 'A' and resid 2258 through 2271 removed outlier: 4.006A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP A2271 " --> pdb=" O THR A2267 " (cutoff:3.500A) Processing helix chain 'A' and resid 2283 through 2299 removed outlier: 3.631A pdb=" N ALA A2287 " --> pdb=" O LYS A2283 " (cutoff:3.500A) Processing helix chain 'A' and resid 2300 through 2302 No H-bonds generated for 'chain 'A' and resid 2300 through 2302' Processing helix chain 'A' and resid 2306 through 2327 Processing helix chain 'A' and resid 2331 through 2346 Processing helix chain 'A' and resid 2381 through 2385 removed outlier: 3.822A pdb=" N VAL A2385 " --> pdb=" O ALA A2382 " (cutoff:3.500A) Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2423 through 2434 removed outlier: 4.081A pdb=" N ASN A2434 " --> pdb=" O ASN A2430 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2458 removed outlier: 3.770A pdb=" N ILE A2454 " --> pdb=" O THR A2450 " (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: 3.629A pdb=" N ARG A2586 " --> pdb=" O PRO A2583 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N SER A2587 " --> pdb=" O GLU A2584 " (cutoff:3.500A) Processing helix chain 'A' and resid 2588 through 2607 Processing helix chain 'A' and resid 2618 through 2635 removed outlier: 3.918A pdb=" N LEU A2622 " --> pdb=" O SER A2618 " (cutoff:3.500A) Processing helix chain 'A' and resid 2640 through 2657 Processing helix chain 'A' and resid 2662 through 2681 Processing helix chain 'A' and resid 2708 through 2727 removed outlier: 3.713A pdb=" N LEU A2712 " --> pdb=" O ASN A2708 " (cutoff:3.500A) Processing helix chain 'A' and resid 2735 through 2750 Processing helix chain 'A' and resid 2765 through 2777 Processing helix chain 'A' and resid 2791 through 2808 removed outlier: 3.601A pdb=" N PHE A2795 " --> pdb=" O ASN A2791 " (cutoff:3.500A) Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 3.628A pdb=" N LEU A2828 " --> pdb=" O GLU A2824 " (cutoff:3.500A) Processing helix chain 'A' and resid 2846 through 2864 Processing helix chain 'A' and resid 2869 through 2884 Processing helix chain 'A' and resid 2896 through 2904 Processing helix chain 'A' and resid 2905 through 2911 removed outlier: 3.545A 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 2949 through 2953 Processing helix chain 'A' and resid 2960 through 2980 removed outlier: 3.867A pdb=" N ALA A2964 " --> pdb=" O THR A2960 " (cutoff:3.500A) Processing helix chain 'A' and resid 2989 through 3034 Processing helix chain 'A' and resid 3290 through 3299 removed outlier: 3.557A pdb=" N LEU A3299 " --> pdb=" O LEU A3295 " (cutoff:3.500A) Processing helix chain 'A' and resid 3299 through 3319 removed outlier: 4.487A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3333 Processing helix chain 'A' and resid 3334 through 3337 removed outlier: 4.009A pdb=" N LEU A3337 " --> pdb=" O PHE A3334 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3334 through 3337' Processing helix chain 'A' and resid 3338 through 3356 removed outlier: 3.884A 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 3413 through 3423 Processing helix chain 'A' and resid 3435 through 3447 Processing helix chain 'A' and resid 3454 through 3458 removed outlier: 3.625A pdb=" N PHE A3458 " --> pdb=" O GLY A3455 " (cutoff:3.500A) Processing helix chain 'A' and resid 3459 through 3461 No H-bonds generated for 'chain 'A' and resid 3459 through 3461' Processing helix chain 'A' and resid 3462 through 3468 Processing helix chain 'A' and resid 3506 through 3511 Processing helix chain 'A' and resid 3521 through 3538 Processing helix chain 'A' and resid 3538 through 3572 Processing helix chain 'A' and resid 3583 through 3605 Processing helix chain 'A' and resid 3607 through 3639 removed outlier: 3.629A pdb=" N PHE A3611 " --> pdb=" O PHE A3607 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ILE A3620 " --> pdb=" O GLU A3616 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ILE A3621 " --> pdb=" O GLU A3617 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3659 removed outlier: 3.702A 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 3728 Processing helix chain 'A' and resid 3742 through 3753 Processing helix chain 'A' and resid 3755 through 3767 removed outlier: 4.141A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.529A 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 removed outlier: 3.602A pdb=" N LEU A3800 " --> pdb=" O GLY A3796 " (cutoff:3.500A) Processing helix chain 'A' and resid 3818 through 3836 Processing helix chain 'A' and resid 3844 through 3846 No H-bonds generated for 'chain 'A' and resid 3844 through 3846' Processing helix chain 'A' and resid 3847 through 3861 removed outlier: 3.687A pdb=" N LEU A3855 " --> pdb=" O VAL A3851 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N HIS A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A3861 " --> pdb=" O LYS A3857 " (cutoff:3.500A) Processing helix chain 'A' and resid 3885 through 3891 removed outlier: 3.661A pdb=" N ARG A3891 " --> pdb=" O PRO A3887 " (cutoff:3.500A) Processing helix chain 'A' and resid 3902 through 3913 Processing helix chain 'A' and resid 3923 through 3944 removed outlier: 3.916A pdb=" N ARG A3944 " --> pdb=" O THR A3940 " (cutoff:3.500A) Processing helix chain 'A' and resid 3957 through 3975 removed outlier: 3.562A 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 4090 removed outlier: 4.072A pdb=" N ILE A4070 " --> pdb=" O PRO A4066 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 369 Processing sheet with id=AA1, first strand: chain 'A' and resid 1569 through 1574 removed outlier: 3.524A pdb=" N SER A1571 " --> pdb=" O ARG A1583 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N SER A1578 " --> pdb=" O GLU A1594 " (cutoff:3.500A) removed outlier: 11.189A pdb=" N GLU A1594 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR A1580 " --> pdb=" O LEU A1592 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1733 through 1734 Processing sheet with id=AA3, first strand: chain 'A' and resid 1817 through 1821 removed outlier: 6.405A pdb=" N GLY A1792 " --> pdb=" O ILE A1896 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU A1898 " --> pdb=" O GLY A1792 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N PHE A1794 " --> pdb=" O LEU A1898 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY A1791 " --> pdb=" O ARG A1917 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE A1919 " --> pdb=" O GLY A1791 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N CYS A1793 " --> pdb=" O PHE A1919 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1878 through 1881 removed outlier: 3.552A pdb=" N LEU A1881 " --> pdb=" O GLU A1884 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2099 through 2104 removed outlier: 3.662A pdb=" N GLY A2074 " --> pdb=" O THR A2196 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA A2069 " --> pdb=" O GLY A2211 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LEU A2213 " --> pdb=" O ALA A2069 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE A2071 " --> pdb=" O LEU A2213 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N PHE A2215 " --> pdb=" O ILE A2071 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL A2073 " --> pdb=" O PHE A2215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2116 through 2118 Processing sheet with id=AA7, first strand: chain 'A' and resid 2175 through 2177 Processing sheet with id=AA8, first strand: chain 'A' and resid 2358 through 2360 Processing sheet with id=AA9, first strand: chain 'A' and resid 2438 through 2444 removed outlier: 6.300A pdb=" N ASP A2439 " --> pdb=" O VAL A2483 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE A2485 " --> pdb=" O ASP A2439 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL A2441 " --> pdb=" O PHE A2485 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP A2487 " --> pdb=" O VAL A2441 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE A2443 " --> pdb=" O ASP A2487 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLY A2413 " --> pdb=" O ALA A2555 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU A2557 " --> pdb=" O GLY A2413 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE A2415 " --> pdb=" O LEU A2557 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2462 through 2465 Processing sheet with id=AB2, first strand: chain 'A' and resid 2516 through 2517 removed outlier: 3.584A pdb=" N LYS A2522 " --> pdb=" O LYS A2517 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2696 through 2697 removed outlier: 3.557A pdb=" N LYS A2705 " --> pdb=" O SER A2697 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2780 through 2782 removed outlier: 6.285A pdb=" N LYS A2780 " --> pdb=" O CYS A2814 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE A2816 " --> pdb=" O LYS A2780 " (cutoff:3.500A) removed outlier: 6.850A 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: 6.289A pdb=" N THR A2813 " --> pdb=" O HIS A2886 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL A2888 " --> pdb=" O THR A2813 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU A2815 " --> pdb=" O VAL A2888 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N THR A2890 " --> pdb=" O LEU A2815 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE A2817 " --> pdb=" O THR A2890 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N HIS A2755 " --> pdb=" O ILE A2913 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ASN A2915 " --> pdb=" O HIS A2755 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N MET A2757 " --> pdb=" O ASN A2915 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3426 through 3430 removed outlier: 6.444A pdb=" N VAL A3450 " --> pdb=" O PHE A3495 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N HIS A3497 " --> pdb=" O VAL A3450 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE A3452 " --> pdb=" O HIS A3497 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL A3404 " --> pdb=" O ARG A3514 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL A3516 " --> pdb=" O VAL A3404 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N PHE A3406 " --> pdb=" O VAL A3516 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3471 through 3473 removed outlier: 4.551A pdb=" N VAL A3477 " --> pdb=" O VAL A3488 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A3481 " --> pdb=" O HIS A3484 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A3484 " --> pdb=" O ILE A3481 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3813 through 3815 Processing sheet with id=AB8, first strand: chain 'A' and resid 4020 through 4021 removed outlier: 3.854A pdb=" N LEU A4021 " --> pdb=" O ILE A4029 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 161 through 163 Processing sheet with id=AC1, first strand: chain 'B' and resid 201 through 207 removed outlier: 3.781A pdb=" N SER B 203 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE B 231 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N SER B 248 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL B 233 " --> pdb=" O ILE B 246 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 150 through 153 removed outlier: 4.337A pdb=" N CYS C 150 " --> pdb=" O VAL C 491 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL C 491 " --> pdb=" O CYS C 150 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS C 488 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY C 484 " --> pdb=" O LYS C 488 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL C 481 " --> pdb=" O ASP C 465 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AC4, first strand: chain 'C' and resid 201 through 208 removed outlier: 6.739A pdb=" N ALA C 225 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N MET C 204 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL C 223 " --> pdb=" O MET C 204 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL C 206 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL C 221 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU C 220 " --> pdb=" O TRP C 236 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER C 226 " --> pdb=" O GLN C 230 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLN C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 247 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LYS C 235 " --> pdb=" O GLN C 245 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLN C 245 " --> pdb=" O LYS C 235 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL C 237 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N PHE C 243 " --> pdb=" O VAL C 237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 256 through 263 removed outlier: 3.549A pdb=" N ALA C 258 " --> pdb=" O CYS C 273 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP C 262 " --> pdb=" O HIS C 269 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE C 293 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS C 291 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASP C 283 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER C 289 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 300 through 306 removed outlier: 7.026A pdb=" N GLY C 313 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE C 303 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE C 311 " --> pdb=" O ILE C 303 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL C 305 " --> pdb=" O TYR C 309 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU C 321 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN C 328 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 340 through 345 removed outlier: 3.741A pdb=" N SER C 377 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N THR C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU C 386 " --> pdb=" O CYS C 409 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS C 409 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 420 through 426 removed outlier: 4.009A pdb=" N ASP C 422 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER C 432 " --> pdb=" O ARG C 440 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) 1210 hydrogen bonds defined for protein. 3546 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: 6.48 Time building geometry restraints manager: 2.64 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: 6871 1.34 - 1.46: 5025 1.46 - 1.58: 9721 1.58 - 1.70: 11 1.70 - 1.82: 146 Bond restraints: 21774 Sorted by residual: bond pdb=" C THR A2518 " pdb=" N PRO A2519 " ideal model delta sigma weight residual 1.336 1.368 -0.032 1.20e-02 6.94e+03 6.95e+00 bond pdb=" CB ASN A2198 " pdb=" CG ASN A2198 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.74e+00 bond pdb=" CA ASN A2198 " pdb=" CB ASN A2198 " ideal model delta sigma weight residual 1.534 1.554 -0.020 1.76e-02 3.23e+03 1.34e+00 bond pdb=" C LEU A2491 " pdb=" N PRO A2492 " ideal model delta sigma weight residual 1.331 1.344 -0.013 1.20e-02 6.94e+03 1.20e+00 bond pdb=" C4 ADP A4102 " pdb=" C5 ADP A4102 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.16e+00 ... (remaining 21769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 29169 2.03 - 4.06: 327 4.06 - 6.10: 49 6.10 - 8.13: 7 8.13 - 10.16: 3 Bond angle restraints: 29555 Sorted by residual: angle pdb=" C ASN A2490 " pdb=" N LEU A2491 " pdb=" CA LEU A2491 " ideal model delta sigma weight residual 120.09 125.07 -4.98 1.25e+00 6.40e-01 1.59e+01 angle pdb=" C LYS A2809 " pdb=" N GLU A2810 " pdb=" CA GLU A2810 " ideal model delta sigma weight residual 122.46 127.58 -5.12 1.41e+00 5.03e-01 1.32e+01 angle pdb=" CB MET A2831 " pdb=" CG MET A2831 " pdb=" SD MET A2831 " ideal model delta sigma weight residual 112.70 122.48 -9.78 3.00e+00 1.11e-01 1.06e+01 angle pdb=" CG1 ILE A2689 " pdb=" CB ILE A2689 " pdb=" CG2 ILE A2689 " ideal model delta sigma weight residual 110.70 101.12 9.58 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CA TRP A2084 " pdb=" CB TRP A2084 " pdb=" CG TRP A2084 " ideal model delta sigma weight residual 113.60 119.20 -5.60 1.90e+00 2.77e-01 8.70e+00 ... (remaining 29550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.47: 12747 34.47 - 68.94: 216 68.94 - 103.41: 20 103.41 - 137.88: 0 137.88 - 172.35: 1 Dihedral angle restraints: 12984 sinusoidal: 4937 harmonic: 8047 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 -96.11 -172.35 1 2.00e+01 2.50e-03 4.78e+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 91.55 175.65 -84.10 1 2.00e+01 2.50e-03 2.15e+01 dihedral pdb=" CA ASP A3459 " pdb=" C ASP A3459 " pdb=" N PRO A3460 " pdb=" CA PRO A3460 " ideal model delta harmonic sigma weight residual -180.00 -162.70 -17.30 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 12981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2669 0.049 - 0.099: 595 0.099 - 0.148: 149 0.148 - 0.198: 3 0.198 - 0.247: 3 Chirality restraints: 3419 Sorted by residual: chirality pdb=" CB ILE A2222 " pdb=" CA ILE A2222 " pdb=" CG1 ILE A2222 " pdb=" CG2 ILE A2222 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILE A2689 " pdb=" CA ILE A2689 " pdb=" CG1 ILE A2689 " pdb=" CG2 ILE A2689 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB ILE A3415 " pdb=" CA ILE A3415 " pdb=" CG1 ILE A3415 " pdb=" CG2 ILE A3415 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 3416 not shown) Planarity restraints: 3718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A2618 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO A2619 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A2619 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A2619 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1981 " -0.033 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO A1982 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A1982 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1982 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A2936 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A2937 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A2937 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A2937 " 0.027 5.00e-02 4.00e+02 ... (remaining 3715 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 211 2.63 - 3.20: 18240 3.20 - 3.77: 33164 3.77 - 4.33: 44650 4.33 - 4.90: 75780 Nonbonded interactions: 172045 Sorted by model distance: nonbonded pdb=" O3B ADP A4104 " pdb="MG MG A4105 " model vdw 2.065 2.170 nonbonded pdb=" O2B ADP A4104 " pdb="MG MG A4105 " model vdw 2.071 2.170 nonbonded pdb=" OG1 THR A1803 " pdb="MG MG A4105 " model vdw 2.201 2.170 nonbonded pdb=" OG SER A3832 " pdb=" O GLY A3837 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR A2615 " pdb=" OE1 GLU A2665 " model vdw 2.246 3.040 ... (remaining 172040 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.080 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: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 0.035 21774 Z= 0.143 Angle : 0.562 10.161 29555 Z= 0.291 Chirality : 0.044 0.247 3419 Planarity : 0.004 0.058 3718 Dihedral : 14.190 172.346 7744 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: 0.42 (0.16), residues: 2704 helix: 1.26 (0.13), residues: 1378 sheet: 0.27 (0.30), residues: 335 loop : -1.09 (0.18), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A4028 TYR 0.017 0.001 TYR A2571 PHE 0.019 0.001 PHE A3708 TRP 0.022 0.001 TRP A2084 HIS 0.005 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00330 (21774) covalent geometry : angle 0.56219 (29555) hydrogen bonds : bond 0.14385 ( 1210) hydrogen bonds : angle 5.89841 ( 3546) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.848 Fit side-chains REVERT: A 1556 ASP cc_start: 0.8220 (m-30) cc_final: 0.7911 (t0) REVERT: A 1866 GLN cc_start: 0.8809 (tp-100) cc_final: 0.8133 (tm-30) REVERT: A 1873 GLN cc_start: 0.8305 (tt0) cc_final: 0.8056 (tt0) REVERT: A 2019 SER cc_start: 0.8407 (m) cc_final: 0.8092 (p) REVERT: A 2301 TRP cc_start: 0.6155 (m-90) cc_final: 0.5770 (m-90) REVERT: A 2797 MET cc_start: 0.8374 (ttt) cc_final: 0.8069 (mtt) REVERT: A 2829 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7395 (tm-30) REVERT: A 2950 LYS cc_start: 0.8433 (ttmm) cc_final: 0.8015 (ttpt) REVERT: A 3355 LYS cc_start: 0.8144 (ttmt) cc_final: 0.7783 (tppt) REVERT: A 3377 MET cc_start: 0.8329 (tpp) cc_final: 0.7579 (mmp) REVERT: A 3485 GLU cc_start: 0.8490 (pt0) cc_final: 0.8215 (pt0) REVERT: A 3491 ASP cc_start: 0.7880 (t0) cc_final: 0.7541 (t70) REVERT: A 3890 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8399 (mp10) REVERT: C 299 TRP cc_start: 0.5048 (p-90) cc_final: 0.4027 (p-90) REVERT: C 407 PHE cc_start: 0.7280 (m-10) cc_final: 0.6893 (m-80) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.1526 time to fit residues: 67.4243 Evaluate side-chains 222 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1530 GLN A1605 GLN ** A3845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.147964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.116378 restraints weight = 26955.680| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.71 r_work: 0.3024 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21774 Z= 0.140 Angle : 0.498 7.086 29555 Z= 0.258 Chirality : 0.041 0.159 3419 Planarity : 0.004 0.049 3718 Dihedral : 6.225 172.700 2981 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.45 % Allowed : 6.89 % Favored : 92.66 % 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: 1.10 (0.16), residues: 2704 helix: 1.90 (0.14), residues: 1396 sheet: 0.24 (0.28), residues: 357 loop : -0.84 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3655 TYR 0.019 0.001 TYR A2571 PHE 0.018 0.001 PHE A2404 TRP 0.021 0.001 TRP A2084 HIS 0.007 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00330 (21774) covalent geometry : angle 0.49822 (29555) hydrogen bonds : bond 0.03864 ( 1210) hydrogen bonds : angle 4.30503 ( 3546) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 250 time to evaluate : 0.767 Fit side-chains REVERT: A 1556 ASP cc_start: 0.8316 (m-30) cc_final: 0.7920 (t0) REVERT: A 1866 GLN cc_start: 0.8838 (tp-100) cc_final: 0.8205 (tm-30) REVERT: A 2019 SER cc_start: 0.8413 (m) cc_final: 0.8209 (p) REVERT: A 2797 MET cc_start: 0.8528 (ttt) cc_final: 0.8136 (mtt) REVERT: A 2829 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7714 (tm-30) REVERT: A 3355 LYS cc_start: 0.8288 (ttmt) cc_final: 0.7893 (tppt) REVERT: A 3485 GLU cc_start: 0.8553 (pt0) cc_final: 0.8259 (pt0) REVERT: A 3491 ASP cc_start: 0.7790 (t0) cc_final: 0.7490 (t70) REVERT: A 3754 LYS cc_start: 0.7983 (mmpt) cc_final: 0.7671 (mmtp) REVERT: A 3831 LYS cc_start: 0.8621 (ttmt) cc_final: 0.8378 (ttmm) REVERT: A 3890 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8343 (mp10) REVERT: C 294 GLN cc_start: 0.6176 (mt0) cc_final: 0.5159 (pp30) REVERT: C 299 TRP cc_start: 0.5347 (p-90) cc_final: 0.4223 (p-90) REVERT: C 407 PHE cc_start: 0.7246 (m-10) cc_final: 0.6817 (m-80) outliers start: 10 outliers final: 6 residues processed: 255 average time/residue: 0.1504 time to fit residues: 61.2352 Evaluate side-chains 235 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 229 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2105 ASP Chi-restraints excluded: chain A residue 2275 ILE Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3951 SER Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 315 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 151 optimal weight: 0.0770 chunk 237 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 134 optimal weight: 0.4980 chunk 176 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 250 optimal weight: 10.0000 chunk 239 optimal weight: 0.4980 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3387 ASN ** A3845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.148527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.117212 restraints weight = 27008.218| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.70 r_work: 0.3045 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21774 Z= 0.111 Angle : 0.466 8.808 29555 Z= 0.240 Chirality : 0.040 0.154 3419 Planarity : 0.003 0.046 3718 Dihedral : 6.097 171.296 2981 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.72 % Allowed : 9.01 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.38 (0.16), residues: 2704 helix: 2.19 (0.14), residues: 1397 sheet: 0.12 (0.28), residues: 369 loop : -0.72 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3655 TYR 0.016 0.001 TYR C 429 PHE 0.013 0.001 PHE A2404 TRP 0.020 0.001 TRP A2084 HIS 0.005 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00254 (21774) covalent geometry : angle 0.46587 (29555) hydrogen bonds : bond 0.03413 ( 1210) hydrogen bonds : angle 4.01495 ( 3546) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 241 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: A 1556 ASP cc_start: 0.8296 (m-30) cc_final: 0.7909 (t0) REVERT: A 1866 GLN cc_start: 0.8828 (tp-100) cc_final: 0.8177 (tm-30) REVERT: A 2019 SER cc_start: 0.8400 (m) cc_final: 0.8195 (p) REVERT: A 2044 ARG cc_start: 0.8357 (ttp-110) cc_final: 0.8110 (mtm110) REVERT: A 2797 MET cc_start: 0.8497 (ttt) cc_final: 0.8090 (mtt) REVERT: A 2829 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7744 (tm-30) REVERT: A 3330 TYR cc_start: 0.9024 (OUTLIER) cc_final: 0.8040 (t80) REVERT: A 3355 LYS cc_start: 0.8239 (ttmt) cc_final: 0.7839 (tppt) REVERT: A 3485 GLU cc_start: 0.8510 (pt0) cc_final: 0.8224 (pt0) REVERT: A 3491 ASP cc_start: 0.7742 (t0) cc_final: 0.7482 (t70) REVERT: A 3890 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8371 (mp10) REVERT: C 294 GLN cc_start: 0.6158 (mt0) cc_final: 0.5177 (pp30) REVERT: C 299 TRP cc_start: 0.5293 (p-90) cc_final: 0.4596 (p-90) REVERT: C 407 PHE cc_start: 0.6987 (m-10) cc_final: 0.6661 (m-80) outliers start: 16 outliers final: 9 residues processed: 248 average time/residue: 0.1493 time to fit residues: 59.0247 Evaluate side-chains 229 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 219 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2105 ASP Chi-restraints excluded: chain A residue 2275 ILE Chi-restraints excluded: chain A residue 3011 GLN Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3951 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 480 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 247 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 143 optimal weight: 0.6980 chunk 261 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 208 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 230 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3387 ASN A3845 GLN C 298 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.149532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.117930 restraints weight = 26744.878| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.74 r_work: 0.3041 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21774 Z= 0.127 Angle : 0.479 9.525 29555 Z= 0.245 Chirality : 0.041 0.215 3419 Planarity : 0.003 0.044 3718 Dihedral : 6.064 170.760 2981 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.04 % Allowed : 10.41 % Favored : 88.56 % 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: 1.45 (0.16), residues: 2704 helix: 2.30 (0.14), residues: 1398 sheet: 0.05 (0.27), residues: 368 loop : -0.73 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3655 TYR 0.017 0.001 TYR A2571 PHE 0.015 0.001 PHE A3638 TRP 0.020 0.001 TRP A2084 HIS 0.005 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00298 (21774) covalent geometry : angle 0.47904 (29555) hydrogen bonds : bond 0.03389 ( 1210) hydrogen bonds : angle 3.91274 ( 3546) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 228 time to evaluate : 0.875 Fit side-chains REVERT: A 1556 ASP cc_start: 0.8344 (m-30) cc_final: 0.7939 (t0) REVERT: A 1866 GLN cc_start: 0.8875 (tp-100) cc_final: 0.8176 (tm-30) REVERT: A 2019 SER cc_start: 0.8315 (m) cc_final: 0.8027 (p) REVERT: A 2301 TRP cc_start: 0.6255 (m-90) cc_final: 0.5978 (m-90) REVERT: A 2465 VAL cc_start: 0.9050 (p) cc_final: 0.8835 (m) REVERT: A 2736 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7787 (mm-30) REVERT: A 2797 MET cc_start: 0.8480 (ttt) cc_final: 0.8048 (mtt) REVERT: A 2839 ASP cc_start: 0.8622 (p0) cc_final: 0.8340 (p0) REVERT: A 3330 TYR cc_start: 0.9056 (OUTLIER) cc_final: 0.8171 (t80) REVERT: A 3355 LYS cc_start: 0.8268 (ttmt) cc_final: 0.7819 (tppt) REVERT: A 3485 GLU cc_start: 0.8547 (pt0) cc_final: 0.8291 (pt0) REVERT: A 3491 ASP cc_start: 0.7794 (t0) cc_final: 0.7505 (t70) REVERT: A 3754 LYS cc_start: 0.8144 (mmpt) cc_final: 0.7750 (mmtp) REVERT: A 3890 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8358 (mp10) REVERT: C 299 TRP cc_start: 0.5331 (p-90) cc_final: 0.4606 (p-90) REVERT: C 407 PHE cc_start: 0.7039 (m-10) cc_final: 0.6716 (m-80) REVERT: C 450 LEU cc_start: 0.7503 (mt) cc_final: 0.7253 (pp) outliers start: 23 outliers final: 17 residues processed: 239 average time/residue: 0.1543 time to fit residues: 58.7615 Evaluate side-chains 232 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 1886 THR Chi-restraints excluded: chain A residue 1937 MET Chi-restraints excluded: chain A residue 1964 ASN Chi-restraints excluded: chain A residue 2105 ASP Chi-restraints excluded: chain A residue 2275 ILE Chi-restraints excluded: chain A residue 2544 ILE Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3438 LYS Chi-restraints excluded: chain A residue 3951 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 480 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 27 optimal weight: 0.0980 chunk 123 optimal weight: 2.9990 chunk 239 optimal weight: 0.8980 chunk 268 optimal weight: 8.9990 chunk 244 optimal weight: 7.9990 chunk 242 optimal weight: 4.9990 chunk 29 optimal weight: 0.0000 chunk 40 optimal weight: 0.3980 chunk 94 optimal weight: 0.0040 chunk 117 optimal weight: 0.5980 chunk 166 optimal weight: 2.9990 overall best weight: 0.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1554 HIS A3318 GLN C 245 GLN C 298 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.152382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.119991 restraints weight = 26504.291| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.61 r_work: 0.3084 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 21774 Z= 0.085 Angle : 0.443 8.611 29555 Z= 0.227 Chirality : 0.039 0.217 3419 Planarity : 0.003 0.043 3718 Dihedral : 5.828 167.105 2981 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.81 % Allowed : 11.80 % Favored : 87.39 % 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: 1.68 (0.17), residues: 2704 helix: 2.51 (0.14), residues: 1397 sheet: 0.13 (0.27), residues: 368 loop : -0.65 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3655 TYR 0.015 0.001 TYR C 429 PHE 0.014 0.001 PHE A2972 TRP 0.018 0.001 TRP A2084 HIS 0.003 0.000 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00174 (21774) covalent geometry : angle 0.44325 (29555) hydrogen bonds : bond 0.02904 ( 1210) hydrogen bonds : angle 3.73698 ( 3546) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 247 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 1556 ASP cc_start: 0.8251 (m-30) cc_final: 0.7922 (t0) REVERT: A 2019 SER cc_start: 0.8310 (m) cc_final: 0.8051 (p) REVERT: A 2044 ARG cc_start: 0.8312 (ttp-110) cc_final: 0.7980 (mtm110) REVERT: A 2085 LYS cc_start: 0.8587 (ttmm) cc_final: 0.8365 (mttm) REVERT: A 2167 ASN cc_start: 0.8814 (m-40) cc_final: 0.8589 (m110) REVERT: A 2797 MET cc_start: 0.8414 (ttt) cc_final: 0.8048 (mtt) REVERT: A 3330 TYR cc_start: 0.9022 (OUTLIER) cc_final: 0.8161 (t80) REVERT: A 3355 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7797 (tppt) REVERT: A 3360 TYR cc_start: 0.7519 (p90) cc_final: 0.7289 (p90) REVERT: A 3754 LYS cc_start: 0.7856 (mmpt) cc_final: 0.7552 (mmtp) REVERT: A 3890 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8386 (mp10) REVERT: C 294 GLN cc_start: 0.6450 (mt0) cc_final: 0.5301 (pp30) REVERT: C 299 TRP cc_start: 0.5027 (p-90) cc_final: 0.4530 (p-90) REVERT: C 407 PHE cc_start: 0.6964 (m-10) cc_final: 0.6635 (m-80) outliers start: 18 outliers final: 10 residues processed: 255 average time/residue: 0.1540 time to fit residues: 62.7083 Evaluate side-chains 234 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 223 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2105 ASP Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3011 GLN Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3951 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 480 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 51 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 240 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 chunk 196 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 142 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1554 HIS C 478 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.146793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.116153 restraints weight = 26989.752| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.79 r_work: 0.3022 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21774 Z= 0.142 Angle : 0.491 10.725 29555 Z= 0.249 Chirality : 0.041 0.174 3419 Planarity : 0.003 0.046 3718 Dihedral : 5.930 168.326 2981 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.08 % Allowed : 12.93 % Favored : 85.99 % 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: 1.59 (0.17), residues: 2704 helix: 2.45 (0.14), residues: 1396 sheet: 0.07 (0.27), residues: 366 loop : -0.70 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2771 TYR 0.019 0.001 TYR A2571 PHE 0.019 0.001 PHE A3638 TRP 0.021 0.001 TRP A2084 HIS 0.007 0.001 HIS A2971 Details of bonding type rmsd covalent geometry : bond 0.00341 (21774) covalent geometry : angle 0.49092 (29555) hydrogen bonds : bond 0.03388 ( 1210) hydrogen bonds : angle 3.78954 ( 3546) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 225 time to evaluate : 0.887 Fit side-chains REVERT: A 1556 ASP cc_start: 0.8418 (m-30) cc_final: 0.7960 (t0) REVERT: A 1866 GLN cc_start: 0.8763 (tp-100) cc_final: 0.8081 (tm-30) REVERT: A 2019 SER cc_start: 0.8326 (m) cc_final: 0.8016 (p) REVERT: A 2044 ARG cc_start: 0.8485 (ttp-110) cc_final: 0.8134 (mtm110) REVERT: A 2064 GLN cc_start: 0.8656 (pp30) cc_final: 0.8265 (pp30) REVERT: A 2797 MET cc_start: 0.8456 (ttt) cc_final: 0.8008 (mtt) REVERT: A 3330 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.8343 (t80) REVERT: A 3355 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7773 (tppt) REVERT: A 3377 MET cc_start: 0.8393 (tpp) cc_final: 0.7715 (mmp) REVERT: A 3754 LYS cc_start: 0.8110 (mmpt) cc_final: 0.7587 (mmmm) REVERT: A 4087 GLN cc_start: 0.7794 (mp-120) cc_final: 0.7410 (mp10) REVERT: C 299 TRP cc_start: 0.5322 (p-90) cc_final: 0.4603 (p-90) REVERT: C 372 TYR cc_start: 0.6238 (m-80) cc_final: 0.5722 (m-10) REVERT: C 407 PHE cc_start: 0.7175 (m-10) cc_final: 0.6638 (m-80) REVERT: C 480 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7400 (tpp) outliers start: 24 outliers final: 16 residues processed: 234 average time/residue: 0.1515 time to fit residues: 56.7462 Evaluate side-chains 231 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 1964 ASN Chi-restraints excluded: chain A residue 2105 ASP Chi-restraints excluded: chain A residue 2275 ILE Chi-restraints excluded: chain A residue 2544 ILE Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3011 GLN Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3438 LYS Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3951 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 478 GLN Chi-restraints excluded: chain C residue 480 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 97 optimal weight: 0.1980 chunk 100 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 137 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 92 optimal weight: 0.0070 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.148703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.116089 restraints weight = 26770.722| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.70 r_work: 0.3024 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21774 Z= 0.105 Angle : 0.464 9.582 29555 Z= 0.235 Chirality : 0.040 0.157 3419 Planarity : 0.003 0.045 3718 Dihedral : 5.861 167.348 2981 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.08 % Allowed : 13.20 % Favored : 85.72 % 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: 1.66 (0.17), residues: 2704 helix: 2.52 (0.14), residues: 1397 sheet: 0.03 (0.27), residues: 365 loop : -0.66 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3655 TYR 0.014 0.001 TYR A2571 PHE 0.013 0.001 PHE A2972 TRP 0.020 0.001 TRP A2084 HIS 0.005 0.001 HIS A2971 Details of bonding type rmsd covalent geometry : bond 0.00240 (21774) covalent geometry : angle 0.46386 (29555) hydrogen bonds : bond 0.03106 ( 1210) hydrogen bonds : angle 3.73030 ( 3546) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 228 time to evaluate : 0.898 Fit side-chains REVERT: A 1556 ASP cc_start: 0.8381 (m-30) cc_final: 0.8021 (t0) REVERT: A 1866 GLN cc_start: 0.8729 (tp-100) cc_final: 0.8091 (tm-30) REVERT: A 2019 SER cc_start: 0.8334 (m) cc_final: 0.8073 (p) REVERT: A 2044 ARG cc_start: 0.8383 (ttp-110) cc_final: 0.8048 (mtm110) REVERT: A 2167 ASN cc_start: 0.8934 (m-40) cc_final: 0.8681 (m-40) REVERT: A 2797 MET cc_start: 0.8471 (ttt) cc_final: 0.8064 (mtt) REVERT: A 3330 TYR cc_start: 0.9005 (OUTLIER) cc_final: 0.8324 (t80) REVERT: A 3355 LYS cc_start: 0.8227 (ttmt) cc_final: 0.7811 (tppt) REVERT: A 3556 ARG cc_start: 0.6698 (mtt90) cc_final: 0.6082 (mtt180) REVERT: A 3754 LYS cc_start: 0.8055 (mmpt) cc_final: 0.7703 (mmtp) REVERT: A 4087 GLN cc_start: 0.7842 (mp-120) cc_final: 0.7448 (mp10) REVERT: C 230 GLN cc_start: 0.6648 (pt0) cc_final: 0.6321 (pt0) REVERT: C 299 TRP cc_start: 0.5401 (p-90) cc_final: 0.4723 (p-90) REVERT: C 372 TYR cc_start: 0.6334 (m-80) cc_final: 0.5811 (m-10) REVERT: C 407 PHE cc_start: 0.7219 (m-10) cc_final: 0.6710 (m-80) REVERT: C 480 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7493 (tpp) outliers start: 24 outliers final: 18 residues processed: 239 average time/residue: 0.1620 time to fit residues: 61.4369 Evaluate side-chains 237 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 217 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 1886 THR Chi-restraints excluded: chain A residue 1964 ASN Chi-restraints excluded: chain A residue 2105 ASP Chi-restraints excluded: chain A residue 2275 ILE Chi-restraints excluded: chain A residue 2544 ILE Chi-restraints excluded: chain A residue 2609 THR Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3011 GLN Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3438 LYS Chi-restraints excluded: chain A residue 3637 GLN Chi-restraints excluded: chain A residue 3951 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 480 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 48 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 255 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 205 optimal weight: 0.5980 chunk 215 optimal weight: 0.5980 chunk 159 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 GLN C 478 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.149798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.116951 restraints weight = 26744.771| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.69 r_work: 0.3024 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21774 Z= 0.115 Angle : 0.476 9.079 29555 Z= 0.242 Chirality : 0.040 0.167 3419 Planarity : 0.003 0.043 3718 Dihedral : 5.853 167.045 2981 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.26 % Allowed : 13.65 % Favored : 85.09 % 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: 1.64 (0.17), residues: 2704 helix: 2.50 (0.14), residues: 1397 sheet: 0.03 (0.27), residues: 365 loop : -0.66 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3655 TYR 0.018 0.001 TYR C 429 PHE 0.015 0.001 PHE A3638 TRP 0.020 0.001 TRP A2084 HIS 0.005 0.001 HIS A2971 Details of bonding type rmsd covalent geometry : bond 0.00268 (21774) covalent geometry : angle 0.47569 (29555) hydrogen bonds : bond 0.03189 ( 1210) hydrogen bonds : angle 3.72738 ( 3546) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 0.884 Fit side-chains REVERT: A 1556 ASP cc_start: 0.8391 (m-30) cc_final: 0.7990 (t0) REVERT: A 1866 GLN cc_start: 0.8703 (tp-100) cc_final: 0.8077 (tm-30) REVERT: A 2019 SER cc_start: 0.8346 (m) cc_final: 0.8077 (p) REVERT: A 2044 ARG cc_start: 0.8406 (ttp-110) cc_final: 0.8077 (mtm110) REVERT: A 2797 MET cc_start: 0.8446 (ttt) cc_final: 0.8060 (mtt) REVERT: A 3330 TYR cc_start: 0.9007 (OUTLIER) cc_final: 0.8323 (t80) REVERT: A 3355 LYS cc_start: 0.8179 (ttmt) cc_final: 0.7772 (tppt) REVERT: A 3556 ARG cc_start: 0.6672 (mtt90) cc_final: 0.6102 (mtt180) REVERT: A 3754 LYS cc_start: 0.8041 (mmpt) cc_final: 0.7648 (mmmm) REVERT: A 3890 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8320 (mp10) REVERT: A 4076 LEU cc_start: 0.8314 (mt) cc_final: 0.8099 (mm) REVERT: A 4087 GLN cc_start: 0.7833 (mp-120) cc_final: 0.7411 (mm-40) REVERT: C 299 TRP cc_start: 0.5403 (p-90) cc_final: 0.4724 (p-90) REVERT: C 372 TYR cc_start: 0.6366 (m-80) cc_final: 0.5825 (m-10) REVERT: C 407 PHE cc_start: 0.7205 (m-10) cc_final: 0.6709 (m-80) REVERT: C 480 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7553 (tpp) outliers start: 28 outliers final: 19 residues processed: 239 average time/residue: 0.1646 time to fit residues: 62.4149 Evaluate side-chains 240 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 1886 THR Chi-restraints excluded: chain A residue 1964 ASN Chi-restraints excluded: chain A residue 2105 ASP Chi-restraints excluded: chain A residue 2252 LEU Chi-restraints excluded: chain A residue 2275 ILE Chi-restraints excluded: chain A residue 2544 ILE Chi-restraints excluded: chain A residue 2609 THR Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3011 GLN Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3951 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 478 GLN Chi-restraints excluded: chain C residue 480 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 211 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 259 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 207 optimal weight: 0.0470 chunk 146 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1464 ASN C 478 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.148157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.116110 restraints weight = 26808.763| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.69 r_work: 0.3050 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21774 Z= 0.111 Angle : 0.475 8.964 29555 Z= 0.242 Chirality : 0.040 0.177 3419 Planarity : 0.003 0.043 3718 Dihedral : 5.837 166.700 2981 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.04 % Allowed : 14.23 % Favored : 84.73 % 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: 1.67 (0.17), residues: 2704 helix: 2.52 (0.14), residues: 1400 sheet: 0.04 (0.27), residues: 365 loop : -0.66 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3476 TYR 0.016 0.001 TYR C 429 PHE 0.012 0.001 PHE A2972 TRP 0.020 0.001 TRP A2084 HIS 0.005 0.001 HIS A2971 Details of bonding type rmsd covalent geometry : bond 0.00258 (21774) covalent geometry : angle 0.47524 (29555) hydrogen bonds : bond 0.03149 ( 1210) hydrogen bonds : angle 3.71515 ( 3546) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 225 time to evaluate : 0.890 Fit side-chains REVERT: A 1556 ASP cc_start: 0.8375 (m-30) cc_final: 0.7972 (t0) REVERT: A 1866 GLN cc_start: 0.8716 (tp-100) cc_final: 0.8067 (tm-30) REVERT: A 2019 SER cc_start: 0.8333 (m) cc_final: 0.8054 (p) REVERT: A 2044 ARG cc_start: 0.8415 (ttp-110) cc_final: 0.8095 (mtm110) REVERT: A 2091 MET cc_start: 0.7884 (mtt) cc_final: 0.7615 (mtt) REVERT: A 2797 MET cc_start: 0.8422 (ttt) cc_final: 0.8025 (mtt) REVERT: A 3002 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8083 (tt) REVERT: A 3330 TYR cc_start: 0.9012 (OUTLIER) cc_final: 0.8326 (t80) REVERT: A 3355 LYS cc_start: 0.8149 (ttmt) cc_final: 0.7722 (tppt) REVERT: A 3377 MET cc_start: 0.8335 (tpp) cc_final: 0.7680 (mmp) REVERT: A 3556 ARG cc_start: 0.6674 (mtt90) cc_final: 0.6125 (mtt180) REVERT: A 3754 LYS cc_start: 0.8047 (mmpt) cc_final: 0.7601 (mmmm) REVERT: A 3890 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8347 (mp10) REVERT: A 4076 LEU cc_start: 0.8220 (mt) cc_final: 0.7996 (mm) REVERT: A 4087 GLN cc_start: 0.7812 (mp-120) cc_final: 0.7347 (mm-40) REVERT: C 299 TRP cc_start: 0.5259 (p-90) cc_final: 0.4677 (p-90) REVERT: C 372 TYR cc_start: 0.6389 (m-80) cc_final: 0.5825 (m-10) REVERT: C 407 PHE cc_start: 0.7204 (m-10) cc_final: 0.6700 (m-80) REVERT: C 480 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7486 (tpp) outliers start: 23 outliers final: 17 residues processed: 235 average time/residue: 0.1588 time to fit residues: 59.1573 Evaluate side-chains 237 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 217 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1640 VAL Chi-restraints excluded: chain A residue 1886 THR Chi-restraints excluded: chain A residue 2063 MET Chi-restraints excluded: chain A residue 2105 ASP Chi-restraints excluded: chain A residue 2252 LEU Chi-restraints excluded: chain A residue 2275 ILE Chi-restraints excluded: chain A residue 2544 ILE Chi-restraints excluded: chain A residue 2609 THR Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3002 LEU Chi-restraints excluded: chain A residue 3011 GLN Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3951 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 304 ASP Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 480 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.5817 > 50: distance: 13 - 38: 31.233 distance: 21 - 49: 36.667 distance: 25 - 55: 35.864 distance: 33 - 38: 30.326 distance: 34 - 63: 32.825 distance: 38 - 39: 49.866 distance: 39 - 42: 36.696 distance: 40 - 41: 39.109 distance: 40 - 49: 40.167 distance: 42 - 43: 41.639 distance: 43 - 44: 40.356 distance: 44 - 45: 18.303 distance: 45 - 46: 37.775 distance: 46 - 47: 20.266 distance: 46 - 48: 21.645 distance: 49 - 50: 39.577 distance: 50 - 53: 40.908 distance: 51 - 52: 46.127 distance: 51 - 55: 56.267 distance: 53 - 54: 57.263 distance: 55 - 56: 36.668 distance: 56 - 59: 21.626 distance: 57 - 58: 40.536 distance: 57 - 63: 39.617 distance: 59 - 60: 4.100 distance: 60 - 61: 45.846 distance: 60 - 62: 23.272 distance: 63 - 64: 39.905 distance: 65 - 66: 40.637 distance: 65 - 67: 39.882 distance: 68 - 69: 39.716 distance: 69 - 75: 56.104 distance: 72 - 73: 41.242 distance: 72 - 74: 25.061 distance: 76 - 77: 38.424 distance: 76 - 79: 49.891 distance: 77 - 80: 69.507 distance: 80 - 81: 55.831 distance: 81 - 82: 15.026 distance: 81 - 84: 22.923 distance: 82 - 83: 43.831 distance: 82 - 88: 15.087 distance: 84 - 85: 21.080 distance: 85 - 87: 56.628 distance: 89 - 92: 40.113 distance: 90 - 91: 40.907 distance: 90 - 96: 56.677 distance: 92 - 93: 39.434 distance: 93 - 94: 39.050 distance: 97 - 98: 37.505 distance: 97 - 100: 3.619 distance: 99 - 125: 34.619 distance: 100 - 101: 39.574 distance: 104 - 105: 57.352 distance: 104 - 107: 39.820 distance: 105 - 112: 34.265 distance: 106 - 132: 34.675 distance: 107 - 108: 44.816 distance: 108 - 109: 43.543