Starting phenix.real_space_refine on Fri Sep 19 08:16:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9djz_46941/09_2025/9djz_46941.cif Found real_map, /net/cci-nas-00/data/ceres_data/9djz_46941/09_2025/9djz_46941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9djz_46941/09_2025/9djz_46941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9djz_46941/09_2025/9djz_46941.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9djz_46941/09_2025/9djz_46941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9djz_46941/09_2025/9djz_46941.map" } resolution = 3.9 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= 0.031 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 111 5.16 5 C 15338 2.51 5 N 4045 2.21 5 O 4409 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23913 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 18155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2335, 18155 Classifications: {'peptide': 2335} Incomplete info: {'truncation_to_alanine': 198} Link IDs: {'PTRANS': 65, 'TRANS': 2269} Chain breaks: 11 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 721 Unresolved non-hydrogen angles: 886 Unresolved non-hydrogen dihedrals: 588 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 13, 'TRP:plan': 2, 'GLU:plan': 43, 'PHE:plan': 5, 'ASP:plan': 22, 'TYR:plan': 1, 'ARG:plan': 13, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 435 Chain: "C" Number of atoms: 2811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2811 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 16, 'TRANS': 339} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'HIS:plan': 1, 'ARG:plan': 1, 'ARG%COO:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2834 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 339} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 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: 5.48, per 1000 atoms: 0.23 Number of scatterers: 23913 At special positions: 0 Unit cell: (112.52, 155.44, 191.4, 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 111 16.00 P 9 15.00 Mg 1 11.99 O 4409 8.00 N 4045 7.00 C 15338 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.2 microseconds 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5806 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 29 sheets defined 50.0% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 1443 through 1461 Processing helix chain 'A' and resid 1471 through 1488 Processing helix chain 'A' and resid 1512 through 1523 Processing helix chain 'A' and resid 1523 through 1534 removed outlier: 4.052A pdb=" N PHE A1534 " --> pdb=" O GLN A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1538 Processing helix chain 'A' and resid 1541 through 1551 Processing helix chain 'A' and resid 1558 through 1561 Processing helix chain 'A' and resid 1562 through 1567 Processing helix chain 'A' and resid 1603 through 1632 removed outlier: 3.557A pdb=" N TRP A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1640 removed outlier: 4.048A pdb=" N VAL A1639 " --> pdb=" O ASP A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1665 Processing helix chain 'A' and resid 1669 through 1688 Processing helix chain 'A' and resid 1691 through 1717 removed outlier: 3.859A pdb=" N GLU A1704 " --> pdb=" O ALA A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1731 Processing helix chain 'A' and resid 1772 through 1788 removed outlier: 4.135A pdb=" N GLN A1788 " --> pdb=" O ASP A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1814 Processing helix chain 'A' and resid 1830 through 1842 Processing helix chain 'A' and resid 1849 through 1853 removed outlier: 3.910A pdb=" N LEU A1853 " --> pdb=" O PHE A1850 " (cutoff:3.500A) Processing helix chain 'A' and resid 1854 through 1875 Processing helix chain 'A' and resid 1909 through 1914 Processing helix chain 'A' and resid 1925 through 1938 removed outlier: 3.690A 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 1988 removed outlier: 4.032A pdb=" N SER A1981 " --> pdb=" O LEU A1977 " (cutoff:3.500A) Proline residue: A1982 - end of helix removed outlier: 4.045A pdb=" N SER A1985 " --> pdb=" O SER A1981 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLU A1986 " --> pdb=" O PRO A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1990 through 2003 removed outlier: 3.903A 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 Processing helix chain 'A' and resid 2031 through 2046 Processing helix chain 'A' and resid 2050 through 2067 removed outlier: 3.819A pdb=" N THR A2066 " --> pdb=" O TYR A2062 " (cutoff:3.500A) Processing helix chain 'A' and resid 2079 through 2096 Processing helix chain 'A' and resid 2110 through 2115 Processing helix chain 'A' and resid 2128 through 2140 removed outlier: 3.518A pdb=" N ASP A2140 " --> pdb=" O ARG A2136 " (cutoff:3.500A) Processing helix chain 'A' and resid 2144 through 2146 No H-bonds generated for 'chain 'A' and resid 2144 through 2146' Processing helix chain 'A' and resid 2159 through 2165 Processing helix chain 'A' and resid 2166 through 2171 removed outlier: 3.609A pdb=" N LEU A2170 " --> pdb=" O MET A2166 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP A2171 " --> pdb=" O ASN A2167 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2166 through 2171' Processing helix chain 'A' and resid 2203 through 2210 Processing helix chain 'A' and resid 2221 through 2236 Processing helix chain 'A' and resid 2246 through 2257 removed outlier: 3.557A pdb=" N PHE A2257 " --> pdb=" O ILE A2253 " (cutoff:3.500A) Processing helix chain 'A' and resid 2258 through 2270 removed outlier: 3.771A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) Processing helix chain 'A' and resid 2279 through 2282 Processing helix chain 'A' and resid 2283 through 2299 removed outlier: 3.739A pdb=" N GLN A2289 " --> pdb=" O GLU A2285 " (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 2347 Processing helix chain 'A' and resid 2370 through 2374 Processing helix chain 'A' and resid 2381 through 2387 removed outlier: 3.703A pdb=" N MET A2386 " --> pdb=" O HIS A2383 " (cutoff:3.500A) Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2423 through 2434 removed outlier: 3.587A pdb=" N ASN A2434 " --> pdb=" O ASN A2430 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2461 removed outlier: 4.108A pdb=" N ILE A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS A2461 " --> pdb=" O ALA A2457 " (cutoff:3.500A) Processing helix chain 'A' and resid 2501 through 2512 Processing helix chain 'A' and resid 2547 through 2552 removed outlier: 3.689A pdb=" N THR A2551 " --> pdb=" O SER A2547 " (cutoff:3.500A) Processing helix chain 'A' and resid 2563 through 2580 Processing helix chain 'A' and resid 2582 through 2587 removed outlier: 3.620A pdb=" N PHE A2585 " --> pdb=" O VAL A2582 " (cutoff:3.500A) removed outlier: 5.686A 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: 3.806A pdb=" N LEU A2622 " --> pdb=" O SER A2618 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR A2635 " --> pdb=" O THR A2631 " (cutoff:3.500A) Processing helix chain 'A' and resid 2640 through 2657 removed outlier: 3.509A pdb=" N ALA A2657 " --> pdb=" O TRP A2653 " (cutoff:3.500A) Processing helix chain 'A' and resid 2662 through 2681 Processing helix chain 'A' and resid 2708 through 2727 Processing helix chain 'A' and resid 2735 through 2751 removed outlier: 3.895A pdb=" N GLN A2751 " --> pdb=" O ARG A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2766 through 2777 Processing helix chain 'A' and resid 2791 through 2808 removed outlier: 3.656A pdb=" N PHE A2795 " --> pdb=" O ASN A2791 " (cutoff:3.500A) Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 3.815A 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 2910 removed outlier: 3.711A pdb=" N ASN A2910 " --> pdb=" O PRO A2906 " (cutoff:3.500A) Processing helix chain 'A' and resid 2921 through 2934 removed outlier: 3.596A pdb=" N ASP A2934 " --> pdb=" O ASN A2930 " (cutoff:3.500A) Processing helix chain 'A' and resid 2949 through 2953 Processing helix chain 'A' and resid 2960 through 2980 Processing helix chain 'A' and resid 2989 through 3039 Processing helix chain 'A' and resid 3285 through 3318 removed outlier: 3.918A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3333 removed outlier: 3.514A pdb=" N SER A3327 " --> pdb=" O ASN A3323 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A3332 " --> pdb=" O SER A3328 " (cutoff:3.500A) Processing helix chain 'A' and resid 3334 through 3337 removed outlier: 4.094A 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 Processing helix chain 'A' and resid 3365 through 3371 Processing helix chain 'A' and resid 3372 through 3383 removed outlier: 3.690A pdb=" N GLY A3383 " --> pdb=" O TRP A3379 " (cutoff:3.500A) Processing helix chain 'A' and resid 3387 through 3398 Processing helix chain 'A' and resid 3413 through 3423 removed outlier: 3.812A pdb=" N VAL A3417 " --> pdb=" O HIS A3413 " (cutoff:3.500A) Processing helix chain 'A' and resid 3424 through 3426 No H-bonds generated for 'chain 'A' and resid 3424 through 3426' Processing helix chain 'A' and resid 3435 through 3447 Processing helix chain 'A' and resid 3454 through 3458 removed outlier: 3.598A pdb=" N PHE A3457 " --> pdb=" O ASP A3454 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A3458 " --> pdb=" O GLY A3455 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3454 through 3458' 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 3571 removed outlier: 3.692A pdb=" N GLN A3542 " --> pdb=" O ASN A3538 " (cutoff:3.500A) Processing helix chain 'A' and resid 3580 through 3606 removed outlier: 3.775A pdb=" N GLU A3606 " --> pdb=" O SER A3602 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3618 removed outlier: 4.079A pdb=" N PHE A3611 " --> pdb=" O PHE A3607 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP A3612 " --> pdb=" O PHE A3608 " (cutoff:3.500A) Processing helix chain 'A' and resid 3619 through 3637 Processing helix chain 'A' and resid 3645 through 3659 removed outlier: 3.659A pdb=" N VAL A3656 " --> pdb=" O CYS A3652 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) Processing helix chain 'A' and resid 3669 through 3687 removed outlier: 3.867A pdb=" N GLU A3673 " --> pdb=" O THR A3669 " (cutoff:3.500A) Processing helix chain 'A' and resid 3691 through 3711 Processing helix chain 'A' and resid 3712 through 3727 Processing helix chain 'A' and resid 3742 through 3753 Processing helix chain 'A' and resid 3755 through 3768 removed outlier: 4.312A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS A3764 " --> pdb=" O LEU A3760 " (cutoff:3.500A) Processing helix chain 'A' and resid 3773 through 3780 Processing helix chain 'A' and resid 3796 through 3807 Processing helix chain 'A' and resid 3818 through 3836 removed outlier: 4.030A pdb=" N ILE A3834 " --> pdb=" O SER A3830 " (cutoff:3.500A) Processing helix chain 'A' and resid 3847 through 3859 removed outlier: 5.511A pdb=" N HIS A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LYS A3857 " --> pdb=" O THR A3853 " (cutoff:3.500A) Processing helix chain 'A' and resid 3885 through 3892 Processing helix chain 'A' and resid 3903 through 3913 Processing helix chain 'A' and resid 3922 through 3945 removed outlier: 3.793A pdb=" N ARG A3944 " --> pdb=" O THR A3940 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU A3945 " --> pdb=" O ALA A3941 " (cutoff:3.500A) Processing helix chain 'A' and resid 3945 through 3950 Processing helix chain 'A' and resid 3957 through 3974 removed outlier: 3.801A pdb=" N PHE A3961 " --> pdb=" O ASN A3957 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3992 Processing helix chain 'A' and resid 4000 through 4015 Processing helix chain 'A' and resid 4037 through 4052 Processing helix chain 'A' and resid 4057 through 4062 Processing helix chain 'A' and resid 4066 through 4091 removed outlier: 3.765A pdb=" N ILE A4070 " --> pdb=" O PRO A4066 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU A4091 " --> pdb=" O GLN A4087 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'B' and resid 362 through 369 Processing sheet with id=AA1, first strand: chain 'A' and resid 1569 through 1575 removed outlier: 6.226A pdb=" N PHE A1575 " --> pdb=" O ILE A1579 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE A1579 " --> pdb=" O PHE A1575 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A1596 " --> pdb=" O ILE A1579 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1733 through 1736 removed outlier: 3.611A pdb=" N PHE A1748 " --> pdb=" O TYR A1735 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1817 through 1821 removed outlier: 6.007A pdb=" N GLY A1845 " --> pdb=" O PHE A1895 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR A1897 " --> pdb=" O GLY A1845 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE A1847 " --> pdb=" O THR A1897 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A1792 " --> pdb=" O VAL A1894 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS A1793 " --> pdb=" O ARG A1917 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1878 through 1881 removed outlier: 3.864A pdb=" N LEU A1881 " --> pdb=" O GLU A1884 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2098 through 2104 removed outlier: 6.119A pdb=" N ALA A2098 " --> pdb=" O ARG A2149 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N TRP A2151 " --> pdb=" O ALA A2098 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL A2100 " --> pdb=" O TRP A2151 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL A2153 " --> pdb=" O VAL A2100 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR A2102 " --> pdb=" O VAL A2153 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A2070 " --> pdb=" O ILE A2192 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A2074 " --> pdb=" O THR A2196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2116 through 2119 removed outlier: 3.639A pdb=" N LEU A2119 " --> pdb=" O GLU A2124 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU A2124 " --> pdb=" O LEU A2119 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2175 through 2177 Processing sheet with id=AA8, first strand: chain 'A' and resid 2438 through 2440 removed outlier: 3.937A pdb=" N VAL A2483 " --> pdb=" O ASP A2439 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLY A2413 " --> pdb=" O ALA A2555 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU A2557 " --> pdb=" O GLY A2413 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE A2415 " --> pdb=" O LEU A2557 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2462 through 2464 removed outlier: 3.697A pdb=" N PHE A2515 " --> pdb=" O VAL A2524 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2696 through 2697 Processing sheet with id=AB2, first strand: chain 'A' and resid 2780 through 2782 removed outlier: 5.815A pdb=" N LYS A2780 " --> pdb=" O CYS A2814 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE A2816 " --> pdb=" O LYS A2780 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL A2782 " --> pdb=" O ILE A2816 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N THR A2813 " --> pdb=" O HIS A2886 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL A2888 " --> pdb=" O THR A2813 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU A2815 " --> pdb=" O VAL A2888 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N THR A2890 " --> pdb=" O LEU A2815 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE A2817 " --> pdb=" O THR A2890 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3427 through 3430 removed outlier: 6.389A pdb=" N VAL A3450 " --> pdb=" O PHE A3495 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N HIS A3497 " --> pdb=" O VAL A3450 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE A3452 " --> pdb=" O HIS A3497 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A3496 " --> pdb=" O PRO A3405 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3471 through 3473 removed outlier: 3.689A pdb=" N ALA A3473 " --> pdb=" O ARG A3476 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A3476 " --> pdb=" O ALA A3473 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A3479 " --> pdb=" O VAL A3486 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A3486 " --> pdb=" O VAL A3479 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE A3481 " --> pdb=" O HIS A3484 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS A3484 " --> pdb=" O ILE A3481 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3812 through 3814 removed outlier: 6.373A pdb=" N LYS A3812 " --> pdb=" O LEU A3840 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE A3839 " --> pdb=" O PHE A3874 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N TYR A3785 " --> pdb=" O ASP A3893 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N VAL A3895 " --> pdb=" O TYR A3785 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR A3787 " --> pdb=" O VAL A3895 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 4020 through 4021 Processing sheet with id=AB7, first strand: chain 'C' and resid 150 through 153 removed outlier: 4.599A pdb=" N LYS C 488 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL C 481 " --> pdb=" O LEU C 464 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU C 464 " --> pdb=" O VAL C 481 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY C 483 " --> pdb=" O ASN C 462 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 161 through 163 removed outlier: 3.582A pdb=" N VAL C 172 " --> pdb=" O TYR C 180 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 201 through 208 removed outlier: 6.724A pdb=" N ALA C 225 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET C 204 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL C 223 " --> pdb=" O MET C 204 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL C 206 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL C 221 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEU C 220 " --> pdb=" O TRP C 236 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP C 236 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS C 232 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE C 231 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N SER C 248 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C 233 " --> pdb=" O ILE C 246 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 256 through 263 removed outlier: 3.524A pdb=" N ALA C 258 " --> pdb=" O CYS C 273 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 300 through 306 removed outlier: 3.815A pdb=" N SER C 302 " --> pdb=" O GLY C 313 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG C 320 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER C 331 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N HIS C 323 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY C 329 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 340 through 346 removed outlier: 7.163A pdb=" N ALA C 376 " --> pdb=" O GLU C 341 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL C 343 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL C 374 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N PHE C 345 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N TYR C 372 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER C 377 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLU C 386 " --> pdb=" O CYS C 409 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N CYS C 409 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 423 through 426 removed outlier: 3.728A pdb=" N HIS C 451 " --> pdb=" O CYS C 441 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASP C 443 " --> pdb=" O CYS C 449 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N CYS C 449 " --> pdb=" O ASP C 443 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 150 through 153 Processing sheet with id=AC6, first strand: chain 'B' and resid 158 through 163 removed outlier: 6.919A pdb=" N ALA B 173 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL B 161 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N PHE B 171 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LEU B 163 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE B 169 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS B 178 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA B 192 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 201 through 208 removed outlier: 7.117A pdb=" N ALA B 225 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N MET B 204 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B 223 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL B 206 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL B 221 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU B 220 " --> pdb=" O TRP B 236 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TRP B 236 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER B 226 " --> pdb=" O GLN B 230 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLN B 230 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE B 231 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER B 248 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL B 233 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 237 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 242 " --> pdb=" O VAL B 237 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 256 through 263 removed outlier: 6.993A pdb=" N CYS B 273 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL B 259 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA B 271 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ILE B 261 " --> pdb=" O HIS B 269 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N HIS B 269 " --> pdb=" O ILE B 261 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 300 through 304 removed outlier: 6.415A pdb=" N GLY B 313 " --> pdb=" O ARG B 301 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE B 303 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE B 311 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 312 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG B 320 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU B 319 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL B 332 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU B 321 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 343 through 345 removed outlier: 3.679A pdb=" N CYS B 373 " --> pdb=" O TRP B 385 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 383 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 411 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU B 386 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N CYS B 409 " --> pdb=" O GLU B 386 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 420 through 426 removed outlier: 4.687A pdb=" N ASP B 422 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG B 426 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR B 429 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS B 441 " --> pdb=" O HIS B 451 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N HIS B 451 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ASP B 443 " --> pdb=" O CYS B 449 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N CYS B 449 " --> pdb=" O ASP B 443 " (cutoff:3.500A) 1231 hydrogen bonds defined for protein. 3612 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: 7.28 Time building geometry restraints manager: 2.44 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: 7658 1.34 - 1.46: 5752 1.46 - 1.58: 10850 1.58 - 1.70: 12 1.70 - 1.82: 168 Bond restraints: 24440 Sorted by residual: bond pdb=" C THR A2518 " pdb=" N PRO A2519 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.90e+00 bond pdb=" CG LEU A1956 " pdb=" CD2 LEU A1956 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.47e+00 bond pdb=" C4 ADP A4103 " pdb=" C5 ADP A4103 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.22e+00 bond pdb=" C4 ADP A4104 " pdb=" C5 ADP A4104 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.19e+00 bond pdb=" C4 ADP A4102 " pdb=" C5 ADP A4102 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.09e+00 ... (remaining 24435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 32464 1.77 - 3.54: 585 3.54 - 5.31: 102 5.31 - 7.07: 40 7.07 - 8.84: 9 Bond angle restraints: 33200 Sorted by residual: angle pdb=" N VAL A2169 " pdb=" CA VAL A2169 " pdb=" C VAL A2169 " ideal model delta sigma weight residual 113.42 108.47 4.95 1.17e+00 7.31e-01 1.79e+01 angle pdb=" N ILE A3903 " pdb=" CA ILE A3903 " pdb=" C ILE A3903 " ideal model delta sigma weight residual 112.96 108.91 4.05 1.00e+00 1.00e+00 1.64e+01 angle pdb=" C ASP C 316 " pdb=" N THR C 317 " pdb=" CA THR C 317 " ideal model delta sigma weight residual 122.08 126.61 -4.53 1.47e+00 4.63e-01 9.49e+00 angle pdb=" CB MET A2386 " pdb=" CG MET A2386 " pdb=" SD MET A2386 " ideal model delta sigma weight residual 112.70 121.54 -8.84 3.00e+00 1.11e-01 8.69e+00 angle pdb=" CB MET A2831 " pdb=" CG MET A2831 " pdb=" SD MET A2831 " ideal model delta sigma weight residual 112.70 121.31 -8.61 3.00e+00 1.11e-01 8.23e+00 ... (remaining 33195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.34: 13937 28.34 - 56.68: 560 56.68 - 85.02: 29 85.02 - 113.36: 6 113.36 - 141.70: 2 Dihedral angle restraints: 14534 sinusoidal: 5606 harmonic: 8928 Sorted by residual: 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 -126.75 -141.70 1 2.00e+01 2.50e-03 4.28e+01 dihedral pdb=" O2A ADP A4104 " pdb=" O3A ADP A4104 " pdb=" PA ADP A4104 " pdb=" PB ADP A4104 " ideal model delta sinusoidal sigma weight residual -60.00 63.59 -123.59 1 2.00e+01 2.50e-03 3.73e+01 dihedral pdb=" CA CYS B 449 " pdb=" C CYS B 449 " pdb=" N LEU B 450 " pdb=" CA LEU B 450 " ideal model delta harmonic sigma weight residual 180.00 158.95 21.05 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 14531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2912 0.049 - 0.097: 708 0.097 - 0.146: 196 0.146 - 0.195: 7 0.195 - 0.243: 2 Chirality restraints: 3825 Sorted by residual: chirality pdb=" CB ILE C 387 " pdb=" CA ILE C 387 " pdb=" CG1 ILE C 387 " pdb=" CG2 ILE C 387 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB VAL A2935 " pdb=" CA VAL A2935 " pdb=" CG1 VAL A2935 " pdb=" CG2 VAL A2935 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB ILE A3529 " pdb=" CA ILE A3529 " pdb=" CG1 ILE A3529 " pdb=" CG2 ILE A3529 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.15e-01 ... (remaining 3822 not shown) Planarity restraints: 4169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A3313 " -0.017 2.00e-02 2.50e+03 2.09e-02 7.66e+00 pdb=" CG PHE A3313 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A3313 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A3313 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE A3313 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A3313 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A3313 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1772 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO A1773 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A1773 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1773 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 294 " 0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO C 295 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 295 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 295 " 0.029 5.00e-02 4.00e+02 ... (remaining 4166 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 228 2.60 - 3.17: 19395 3.17 - 3.75: 38756 3.75 - 4.32: 49486 4.32 - 4.90: 82505 Nonbonded interactions: 190370 Sorted by model distance: nonbonded pdb=" O3B ADP A4104 " pdb="MG MG A4105 " model vdw 2.020 2.170 nonbonded pdb=" OH TYR C 365 " pdb=" OE2 GLU C 386 " model vdw 2.207 3.040 nonbonded pdb=" OD1 ASN A2409 " pdb=" OH TYR A2438 " model vdw 2.231 3.040 nonbonded pdb=" OG SER C 377 " pdb=" OD1 ASP C 379 " model vdw 2.238 3.040 nonbonded pdb=" O ALA A2761 " pdb=" OG1 THR A2764 " model vdw 2.263 3.040 ... (remaining 190365 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 139 through 213 or (resid 214 and (name N or name CA or na \ me C or name O or name CB )) or resid 215 through 238 or (resid 239 through 240 \ and (name N or name CA or name C or name O or name CB )) or resid 241 through 24 \ 3 or (resid 244 and (name N or name CA or name C or name O or name CB )) or resi \ d 245 through 263 or (resid 264 through 265 and (name N or name CA or name C or \ name O or name CB )) or resid 266 or (resid 267 and (name N or name CA or name C \ or name O or name CB )) or resid 268 through 307 or (resid 308 and (name N or n \ ame CA or name C or name O or name CB )) or resid 309 through 327 or (resid 328 \ and (name N or name CA or name C or name O or name CB )) or resid 329 through 36 \ 2 or (resid 363 and (name N or name CA or name C or name O or name CB )) or resi \ d 364 through 390 or (resid 391 and (name N or name CA or name C or name O or na \ me CB )) or resid 392 or (resid 393 through 397 and (name N or name CA or name C \ or name O or name CB )) or resid 398 through 403 or (resid 404 and (name N or n \ ame CA or name C or name O or name CB )) or resid 405 through 493 or (resid 494 \ and (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 139 through 298 or (resid 299 and (name N or name CA or na \ me C or name O or name CB )) or resid 300 through 353 or (resid 354 and (name N \ or name CA or name C or name O or name CB )) or resid 355 or (resid 356 and (nam \ e N or name CA or name C or name O or name CB )) or resid 357 through 365 or (re \ sid 366 and (name N or name CA or name C or name O or name CB )) or resid 367 th \ rough 454 or (resid 455 and (name N or name CA or name C or name O or name CB )) \ or resid 456 through 493 or (resid 494 and (name N or name CA or name C or name \ O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.940 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 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 0.040 24440 Z= 0.129 Angle : 0.616 8.843 33200 Z= 0.308 Chirality : 0.044 0.243 3825 Planarity : 0.004 0.054 4169 Dihedral : 14.440 141.701 8728 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.04 % Allowed : 1.10 % Favored : 98.87 % 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: -0.13 (0.15), residues: 3019 helix: 1.00 (0.13), residues: 1398 sheet: -0.07 (0.27), residues: 436 loop : -1.40 (0.16), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2412 TYR 0.022 0.001 TYR A2324 PHE 0.048 0.001 PHE A3313 TRP 0.029 0.001 TRP B 442 HIS 0.005 0.001 HIS B 416 Details of bonding type rmsd covalent geometry : bond 0.00277 (24440) covalent geometry : angle 0.61639 (33200) hydrogen bonds : bond 0.15063 ( 1231) hydrogen bonds : angle 6.33787 ( 3612) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 252 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1624 ARG cc_start: 0.8999 (ttt-90) cc_final: 0.8672 (ttm-80) REVERT: A 1704 GLU cc_start: 0.8782 (mp0) cc_final: 0.8374 (mp0) REVERT: A 1705 TYR cc_start: 0.8768 (m-10) cc_final: 0.8424 (m-80) REVERT: A 1955 LEU cc_start: 0.8495 (mt) cc_final: 0.8211 (pp) REVERT: A 2091 MET cc_start: 0.7816 (ttp) cc_final: 0.7571 (ttp) REVERT: A 2102 TYR cc_start: 0.7174 (m-10) cc_final: 0.6916 (m-80) REVERT: A 2190 PHE cc_start: 0.7128 (t80) cc_final: 0.6927 (t80) REVERT: A 2285 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6461 (tm-30) REVERT: A 2552 ARG cc_start: 0.8829 (tmm160) cc_final: 0.8496 (ttp80) REVERT: A 2797 MET cc_start: 0.8979 (ptp) cc_final: 0.8517 (ptt) REVERT: A 2914 ILE cc_start: 0.8939 (mm) cc_final: 0.8104 (mm) REVERT: A 2938 MET cc_start: 0.8943 (tpp) cc_final: 0.8628 (tpp) REVERT: A 3463 SER cc_start: 0.9001 (p) cc_final: 0.8650 (t) REVERT: A 3998 ILE cc_start: 0.9461 (mt) cc_final: 0.9196 (tp) REVERT: A 4080 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8746 (mm-30) REVERT: C 294 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8114 (tm-30) REVERT: C 371 GLN cc_start: 0.7370 (tp40) cc_final: 0.7005 (tp-100) REVERT: C 480 MET cc_start: 0.8786 (ttp) cc_final: 0.8210 (tmm) REVERT: B 253 GLU cc_start: 0.8376 (mp0) cc_final: 0.8165 (mp0) REVERT: B 444 LEU cc_start: 0.8467 (tt) cc_final: 0.7878 (mt) outliers start: 1 outliers final: 0 residues processed: 253 average time/residue: 0.1429 time to fit residues: 61.8292 Evaluate side-chains 174 residues out of total 2786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 294 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1745 ASN A1757 GLN A1864 ASN ** A1873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2059 GLN A2293 HIS ** A2490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2536 ASN ** A2821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3765 ASN A3845 GLN C 286 ASN ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.089505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.068007 restraints weight = 87236.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.070008 restraints weight = 46341.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.071314 restraints weight = 30704.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.072207 restraints weight = 23451.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.072772 restraints weight = 19558.332| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 24440 Z= 0.338 Angle : 0.733 8.337 33200 Z= 0.382 Chirality : 0.047 0.180 3825 Planarity : 0.005 0.051 4169 Dihedral : 6.581 140.069 3309 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.33 % Allowed : 9.35 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.15), residues: 3019 helix: 1.37 (0.14), residues: 1398 sheet: -0.28 (0.25), residues: 459 loop : -1.48 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 426 TYR 0.020 0.002 TYR A3330 PHE 0.032 0.002 PHE B 345 TRP 0.040 0.003 TRP B 442 HIS 0.007 0.002 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00759 (24440) covalent geometry : angle 0.73287 (33200) hydrogen bonds : bond 0.04483 ( 1231) hydrogen bonds : angle 5.14935 ( 3612) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.7966 (ppp) cc_final: 0.7582 (ppp) REVERT: A 1624 ARG cc_start: 0.9009 (ttt-90) cc_final: 0.8701 (ttm-80) REVERT: A 1704 GLU cc_start: 0.8744 (mp0) cc_final: 0.8132 (mp0) REVERT: A 1705 TYR cc_start: 0.8691 (m-10) cc_final: 0.8389 (m-80) REVERT: A 2036 GLN cc_start: 0.8604 (tp-100) cc_final: 0.8310 (tp-100) REVERT: A 2091 MET cc_start: 0.7826 (ttp) cc_final: 0.7387 (ttp) REVERT: A 2552 ARG cc_start: 0.9076 (tmm160) cc_final: 0.8429 (ttp80) REVERT: A 2797 MET cc_start: 0.8784 (ptp) cc_final: 0.8301 (ptt) REVERT: A 3313 PHE cc_start: 0.7223 (OUTLIER) cc_final: 0.6745 (t80) REVERT: A 3330 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.6301 (t80) REVERT: A 3345 MET cc_start: 0.8770 (mmt) cc_final: 0.8547 (tpp) REVERT: A 3463 SER cc_start: 0.9140 (p) cc_final: 0.8786 (t) REVERT: A 3700 MET cc_start: 0.8614 (tmm) cc_final: 0.8333 (tmm) REVERT: A 3850 TRP cc_start: 0.7753 (t60) cc_final: 0.7467 (t60) REVERT: A 3998 ILE cc_start: 0.9477 (mt) cc_final: 0.9272 (tp) REVERT: C 294 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8289 (tm-30) REVERT: B 303 ILE cc_start: 0.8722 (mm) cc_final: 0.8443 (mm) REVERT: B 444 LEU cc_start: 0.8234 (tt) cc_final: 0.7561 (mt) REVERT: B 463 CYS cc_start: 0.8439 (p) cc_final: 0.8131 (p) outliers start: 34 outliers final: 24 residues processed: 198 average time/residue: 0.1466 time to fit residues: 49.3142 Evaluate side-chains 178 residues out of total 2786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1782 LEU Chi-restraints excluded: chain A residue 1822 CYS Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1892 THR Chi-restraints excluded: chain A residue 2087 VAL Chi-restraints excluded: chain A residue 2105 ASP Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2286 THR Chi-restraints excluded: chain A residue 2403 ILE Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2958 ILE Chi-restraints excluded: chain A residue 3031 VAL Chi-restraints excluded: chain A residue 3032 ASN Chi-restraints excluded: chain A residue 3313 PHE Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3525 ILE Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain B residue 207 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 72 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 289 optimal weight: 0.0570 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 295 optimal weight: 0.0170 chunk 161 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2228 HIS ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.093117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.071585 restraints weight = 85473.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.073760 restraints weight = 44345.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.075165 restraints weight = 28714.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.076061 restraints weight = 21569.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.076727 restraints weight = 17901.167| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24440 Z= 0.107 Angle : 0.534 8.112 33200 Z= 0.271 Chirality : 0.042 0.142 3825 Planarity : 0.004 0.049 4169 Dihedral : 6.267 140.372 3309 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.53 % Allowed : 11.65 % Favored : 86.82 % 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: 0.51 (0.15), residues: 3019 helix: 1.85 (0.14), residues: 1396 sheet: -0.27 (0.25), residues: 444 loop : -1.30 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1536 TYR 0.012 0.001 TYR C 372 PHE 0.021 0.001 PHE A2972 TRP 0.032 0.001 TRP A2516 HIS 0.004 0.001 HIS A2741 Details of bonding type rmsd covalent geometry : bond 0.00233 (24440) covalent geometry : angle 0.53435 (33200) hydrogen bonds : bond 0.03533 ( 1231) hydrogen bonds : angle 4.65597 ( 3612) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.8172 (ppp) cc_final: 0.6410 (ppp) REVERT: A 1566 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8292 (m-10) REVERT: A 1624 ARG cc_start: 0.8990 (ttt-90) cc_final: 0.8677 (ttm-80) REVERT: A 1704 GLU cc_start: 0.8802 (mp0) cc_final: 0.8220 (mp0) REVERT: A 1705 TYR cc_start: 0.8717 (m-10) cc_final: 0.8404 (m-80) REVERT: A 2036 GLN cc_start: 0.8488 (tp-100) cc_final: 0.8213 (tp-100) REVERT: A 2091 MET cc_start: 0.7802 (ttp) cc_final: 0.7341 (ttp) REVERT: A 2552 ARG cc_start: 0.8853 (tmm160) cc_final: 0.8455 (ttp80) REVERT: A 2797 MET cc_start: 0.8812 (ptp) cc_final: 0.8452 (ptt) REVERT: A 3313 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.6945 (t80) REVERT: A 3330 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.6079 (t80) REVERT: A 3463 SER cc_start: 0.9100 (p) cc_final: 0.8732 (t) REVERT: A 3850 TRP cc_start: 0.7768 (t60) cc_final: 0.7497 (t60) REVERT: A 3998 ILE cc_start: 0.9447 (mt) cc_final: 0.9214 (tp) REVERT: B 393 MET cc_start: 0.8186 (ptp) cc_final: 0.7793 (mpp) REVERT: B 444 LEU cc_start: 0.8050 (tt) cc_final: 0.7316 (mt) REVERT: B 463 CYS cc_start: 0.8367 (p) cc_final: 0.8025 (p) outliers start: 39 outliers final: 23 residues processed: 216 average time/residue: 0.1358 time to fit residues: 50.1583 Evaluate side-chains 191 residues out of total 2786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1566 PHE Chi-restraints excluded: chain A residue 1782 LEU Chi-restraints excluded: chain A residue 1822 CYS Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2275 ILE Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2743 LEU Chi-restraints excluded: chain A residue 2912 CYS Chi-restraints excluded: chain A residue 2958 ILE Chi-restraints excluded: chain A residue 3032 ASN Chi-restraints excluded: chain A residue 3313 PHE Chi-restraints excluded: chain A residue 3316 THR Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3760 LEU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 3945 LEU Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 373 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 128 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 208 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 216 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 250 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2463 ASN ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.092934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.071278 restraints weight = 85895.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.073398 restraints weight = 44952.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.074820 restraints weight = 29412.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.075784 restraints weight = 22141.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.076401 restraints weight = 18285.828| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24440 Z= 0.121 Angle : 0.520 7.007 33200 Z= 0.263 Chirality : 0.042 0.152 3825 Planarity : 0.003 0.048 4169 Dihedral : 5.983 141.179 3306 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.60 % Allowed : 13.61 % Favored : 84.79 % 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: 0.65 (0.15), residues: 3019 helix: 2.00 (0.14), residues: 1398 sheet: -0.28 (0.25), residues: 444 loop : -1.25 (0.17), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2387 TYR 0.010 0.001 TYR A2102 PHE 0.017 0.001 PHE A2972 TRP 0.034 0.001 TRP B 442 HIS 0.004 0.001 HIS A2741 Details of bonding type rmsd covalent geometry : bond 0.00273 (24440) covalent geometry : angle 0.51998 (33200) hydrogen bonds : bond 0.03316 ( 1231) hydrogen bonds : angle 4.47903 ( 3612) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.8212 (ppp) cc_final: 0.6462 (ppp) REVERT: A 1566 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8134 (m-10) REVERT: A 1624 ARG cc_start: 0.8987 (ttt-90) cc_final: 0.8677 (ttm-80) REVERT: A 1704 GLU cc_start: 0.8801 (mp0) cc_final: 0.8240 (mp0) REVERT: A 1705 TYR cc_start: 0.8678 (m-10) cc_final: 0.8364 (m-80) REVERT: A 2036 GLN cc_start: 0.8484 (tp-100) cc_final: 0.8206 (tp-100) REVERT: A 2091 MET cc_start: 0.7805 (ttp) cc_final: 0.7332 (ttp) REVERT: A 2797 MET cc_start: 0.8790 (ptp) cc_final: 0.8408 (ptt) REVERT: A 2917 MET cc_start: 0.9204 (mmm) cc_final: 0.8881 (mmt) REVERT: A 2938 MET cc_start: 0.9009 (tpp) cc_final: 0.8777 (tpp) REVERT: A 3313 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6975 (t80) REVERT: A 3330 TYR cc_start: 0.7059 (OUTLIER) cc_final: 0.5950 (t80) REVERT: A 3463 SER cc_start: 0.9107 (p) cc_final: 0.8743 (t) REVERT: A 3700 MET cc_start: 0.8610 (tmm) cc_final: 0.8317 (tmm) REVERT: A 3850 TRP cc_start: 0.7810 (t60) cc_final: 0.7516 (t60) REVERT: A 3998 ILE cc_start: 0.9471 (mt) cc_final: 0.9228 (tp) REVERT: C 167 LEU cc_start: 0.8701 (tt) cc_final: 0.8106 (mp) REVERT: B 393 MET cc_start: 0.8155 (ptp) cc_final: 0.7842 (mpp) REVERT: B 444 LEU cc_start: 0.8065 (tt) cc_final: 0.7445 (mt) REVERT: B 463 CYS cc_start: 0.8356 (p) cc_final: 0.8022 (p) outliers start: 41 outliers final: 28 residues processed: 208 average time/residue: 0.1459 time to fit residues: 51.8096 Evaluate side-chains 199 residues out of total 2786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1566 PHE Chi-restraints excluded: chain A residue 1782 LEU Chi-restraints excluded: chain A residue 1822 CYS Chi-restraints excluded: chain A residue 1960 CYS Chi-restraints excluded: chain A residue 2105 ASP Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2275 ILE Chi-restraints excluded: chain A residue 2286 THR Chi-restraints excluded: chain A residue 2404 PHE Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2743 LEU Chi-restraints excluded: chain A residue 2912 CYS Chi-restraints excluded: chain A residue 2936 VAL Chi-restraints excluded: chain A residue 3032 ASN Chi-restraints excluded: chain A residue 3313 PHE Chi-restraints excluded: chain A residue 3316 THR Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3760 LEU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 3945 LEU Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 288 TRP Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 373 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 84 optimal weight: 0.4980 chunk 6 optimal weight: 4.9990 chunk 255 optimal weight: 6.9990 chunk 202 optimal weight: 0.9980 chunk 218 optimal weight: 0.9990 chunk 258 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 293 optimal weight: 20.0000 chunk 284 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3856 HIS ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.091811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.070213 restraints weight = 86104.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.072285 restraints weight = 45155.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.073657 restraints weight = 29695.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.074592 restraints weight = 22459.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.075098 restraints weight = 18647.016| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24440 Z= 0.155 Angle : 0.542 9.566 33200 Z= 0.274 Chirality : 0.042 0.212 3825 Planarity : 0.003 0.047 4169 Dihedral : 5.998 138.328 3306 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.80 % Allowed : 15.02 % Favored : 83.18 % 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: 0.66 (0.15), residues: 3019 helix: 2.05 (0.14), residues: 1396 sheet: -0.35 (0.25), residues: 444 loop : -1.26 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2552 TYR 0.017 0.001 TYR C 372 PHE 0.017 0.001 PHE B 345 TRP 0.044 0.001 TRP B 442 HIS 0.004 0.001 HIS A2741 Details of bonding type rmsd covalent geometry : bond 0.00352 (24440) covalent geometry : angle 0.54238 (33200) hydrogen bonds : bond 0.03349 ( 1231) hydrogen bonds : angle 4.45179 ( 3612) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 166 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.8305 (ppp) cc_final: 0.6813 (ppp) REVERT: A 1566 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8272 (m-10) REVERT: A 1624 ARG cc_start: 0.9000 (ttt-90) cc_final: 0.8684 (ttm-80) REVERT: A 1655 MET cc_start: 0.9086 (mmm) cc_final: 0.8462 (tmm) REVERT: A 1704 GLU cc_start: 0.8796 (mp0) cc_final: 0.8247 (mp0) REVERT: A 1705 TYR cc_start: 0.8689 (m-10) cc_final: 0.8394 (m-80) REVERT: A 2036 GLN cc_start: 0.8560 (tp-100) cc_final: 0.8276 (tp-100) REVERT: A 2091 MET cc_start: 0.7901 (ttp) cc_final: 0.7396 (ttp) REVERT: A 2797 MET cc_start: 0.8818 (ptp) cc_final: 0.8443 (ptt) REVERT: A 2938 MET cc_start: 0.9020 (tpp) cc_final: 0.8705 (tpp) REVERT: A 3313 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.7006 (t80) REVERT: A 3330 TYR cc_start: 0.7010 (OUTLIER) cc_final: 0.5950 (t80) REVERT: A 3463 SER cc_start: 0.9112 (p) cc_final: 0.8759 (t) REVERT: A 3850 TRP cc_start: 0.7915 (t60) cc_final: 0.7634 (t60) REVERT: A 3998 ILE cc_start: 0.9466 (mt) cc_final: 0.9236 (tp) REVERT: B 444 LEU cc_start: 0.7773 (tt) cc_final: 0.7156 (mt) REVERT: B 463 CYS cc_start: 0.8327 (p) cc_final: 0.7997 (p) outliers start: 46 outliers final: 31 residues processed: 202 average time/residue: 0.1406 time to fit residues: 49.0610 Evaluate side-chains 191 residues out of total 2786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1566 PHE Chi-restraints excluded: chain A residue 1782 LEU Chi-restraints excluded: chain A residue 1822 CYS Chi-restraints excluded: chain A residue 1960 CYS Chi-restraints excluded: chain A residue 2105 ASP Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2275 ILE Chi-restraints excluded: chain A residue 2286 THR Chi-restraints excluded: chain A residue 2404 PHE Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2743 LEU Chi-restraints excluded: chain A residue 2786 ILE Chi-restraints excluded: chain A residue 2912 CYS Chi-restraints excluded: chain A residue 2936 VAL Chi-restraints excluded: chain A residue 2958 ILE Chi-restraints excluded: chain A residue 3032 ASN Chi-restraints excluded: chain A residue 3313 PHE Chi-restraints excluded: chain A residue 3316 THR Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3760 LEU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 3945 LEU Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 288 TRP Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 416 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 272 optimal weight: 0.8980 chunk 103 optimal weight: 0.0570 chunk 76 optimal weight: 0.4980 chunk 189 optimal weight: 0.5980 chunk 136 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 282 optimal weight: 1.9990 chunk 233 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 HIS ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.093207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.071618 restraints weight = 86250.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.073742 restraints weight = 45079.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.075141 restraints weight = 29493.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.076105 restraints weight = 22205.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.076704 restraints weight = 18417.006| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24440 Z= 0.103 Angle : 0.514 8.990 33200 Z= 0.257 Chirality : 0.041 0.235 3825 Planarity : 0.003 0.048 4169 Dihedral : 5.905 138.930 3306 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.53 % Allowed : 16.11 % Favored : 82.36 % 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: 0.77 (0.16), residues: 3019 helix: 2.12 (0.14), residues: 1398 sheet: -0.33 (0.25), residues: 444 loop : -1.17 (0.17), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2552 TYR 0.012 0.001 TYR C 372 PHE 0.018 0.001 PHE A2972 TRP 0.036 0.001 TRP B 442 HIS 0.003 0.001 HIS A2741 Details of bonding type rmsd covalent geometry : bond 0.00229 (24440) covalent geometry : angle 0.51446 (33200) hydrogen bonds : bond 0.03144 ( 1231) hydrogen bonds : angle 4.34591 ( 3612) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.8343 (ppp) cc_final: 0.6874 (ppp) REVERT: A 1566 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8318 (m-10) REVERT: A 1624 ARG cc_start: 0.8979 (ttt-90) cc_final: 0.8666 (ttm-80) REVERT: A 1655 MET cc_start: 0.9040 (mmm) cc_final: 0.8700 (mmm) REVERT: A 1704 GLU cc_start: 0.8795 (mp0) cc_final: 0.8252 (mp0) REVERT: A 1705 TYR cc_start: 0.8660 (m-10) cc_final: 0.8383 (m-80) REVERT: A 2036 GLN cc_start: 0.8478 (tp-100) cc_final: 0.8203 (tp-100) REVERT: A 2091 MET cc_start: 0.7836 (ttp) cc_final: 0.7287 (ttp) REVERT: A 2196 THR cc_start: 0.7922 (m) cc_final: 0.7668 (m) REVERT: A 2797 MET cc_start: 0.8773 (ptp) cc_final: 0.8374 (ptt) REVERT: A 2938 MET cc_start: 0.9021 (tpp) cc_final: 0.8713 (tpp) REVERT: A 3330 TYR cc_start: 0.6968 (OUTLIER) cc_final: 0.5946 (t80) REVERT: A 3409 ASP cc_start: 0.7604 (t0) cc_final: 0.7349 (t0) REVERT: A 3463 SER cc_start: 0.9099 (p) cc_final: 0.8744 (t) REVERT: A 3700 MET cc_start: 0.8583 (tmm) cc_final: 0.8295 (tmm) REVERT: A 3850 TRP cc_start: 0.7937 (t60) cc_final: 0.7561 (t60) REVERT: B 444 LEU cc_start: 0.7698 (tt) cc_final: 0.7109 (mt) REVERT: B 463 CYS cc_start: 0.8280 (p) cc_final: 0.7706 (p) outliers start: 39 outliers final: 28 residues processed: 213 average time/residue: 0.1430 time to fit residues: 52.3042 Evaluate side-chains 199 residues out of total 2786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1566 PHE Chi-restraints excluded: chain A residue 1782 LEU Chi-restraints excluded: chain A residue 1822 CYS Chi-restraints excluded: chain A residue 1960 CYS Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2275 ILE Chi-restraints excluded: chain A residue 2404 PHE Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2743 LEU Chi-restraints excluded: chain A residue 2786 ILE Chi-restraints excluded: chain A residue 2912 CYS Chi-restraints excluded: chain A residue 2936 VAL Chi-restraints excluded: chain A residue 2958 ILE Chi-restraints excluded: chain A residue 3032 ASN Chi-restraints excluded: chain A residue 3316 THR Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3760 LEU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 288 TRP Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 416 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 192 optimal weight: 20.0000 chunk 238 optimal weight: 0.5980 chunk 226 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 285 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 149 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 ASN ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.093180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.071618 restraints weight = 85748.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.073739 restraints weight = 44935.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.075140 restraints weight = 29385.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.076089 restraints weight = 22169.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.076653 restraints weight = 18342.760| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24440 Z= 0.107 Angle : 0.525 9.399 33200 Z= 0.261 Chirality : 0.041 0.250 3825 Planarity : 0.003 0.047 4169 Dihedral : 5.848 139.635 3306 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.72 % Allowed : 16.35 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.80 (0.16), residues: 3019 helix: 2.15 (0.14), residues: 1401 sheet: -0.33 (0.25), residues: 444 loop : -1.15 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2552 TYR 0.011 0.001 TYR C 372 PHE 0.025 0.001 PHE A2704 TRP 0.044 0.001 TRP B 442 HIS 0.006 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00239 (24440) covalent geometry : angle 0.52463 (33200) hydrogen bonds : bond 0.03057 ( 1231) hydrogen bonds : angle 4.29211 ( 3612) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.8357 (ppp) cc_final: 0.6879 (ppp) REVERT: A 1566 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8297 (m-10) REVERT: A 1624 ARG cc_start: 0.8981 (ttt-90) cc_final: 0.8671 (ttm-80) REVERT: A 1655 MET cc_start: 0.8987 (mmm) cc_final: 0.8717 (mmm) REVERT: A 1704 GLU cc_start: 0.8794 (mp0) cc_final: 0.8249 (mp0) REVERT: A 1705 TYR cc_start: 0.8693 (m-10) cc_final: 0.8394 (m-80) REVERT: A 1955 LEU cc_start: 0.8469 (mt) cc_final: 0.8175 (pp) REVERT: A 2016 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8169 (m-30) REVERT: A 2036 GLN cc_start: 0.8470 (tp-100) cc_final: 0.8196 (tp-100) REVERT: A 2091 MET cc_start: 0.7831 (ttp) cc_final: 0.7283 (ttp) REVERT: A 2196 THR cc_start: 0.8059 (m) cc_final: 0.7811 (m) REVERT: A 2797 MET cc_start: 0.8784 (ptp) cc_final: 0.8373 (ptt) REVERT: A 2938 MET cc_start: 0.9009 (tpp) cc_final: 0.8681 (tpp) REVERT: A 3330 TYR cc_start: 0.6930 (OUTLIER) cc_final: 0.5892 (t80) REVERT: A 3409 ASP cc_start: 0.7690 (t0) cc_final: 0.7438 (t0) REVERT: A 3463 SER cc_start: 0.9096 (p) cc_final: 0.8749 (t) REVERT: A 3700 MET cc_start: 0.8625 (tmm) cc_final: 0.8343 (tmm) REVERT: A 3850 TRP cc_start: 0.7960 (t60) cc_final: 0.7553 (t60) REVERT: C 155 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8412 (pm20) REVERT: B 444 LEU cc_start: 0.7329 (tt) cc_final: 0.6731 (mt) REVERT: B 463 CYS cc_start: 0.8118 (p) cc_final: 0.7710 (p) outliers start: 44 outliers final: 28 residues processed: 210 average time/residue: 0.1335 time to fit residues: 47.8543 Evaluate side-chains 198 residues out of total 2786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1566 PHE Chi-restraints excluded: chain A residue 1782 LEU Chi-restraints excluded: chain A residue 1822 CYS Chi-restraints excluded: chain A residue 1960 CYS Chi-restraints excluded: chain A residue 2016 ASP Chi-restraints excluded: chain A residue 2105 ASP Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2275 ILE Chi-restraints excluded: chain A residue 2404 PHE Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2743 LEU Chi-restraints excluded: chain A residue 2786 ILE Chi-restraints excluded: chain A residue 2912 CYS Chi-restraints excluded: chain A residue 2936 VAL Chi-restraints excluded: chain A residue 2958 ILE Chi-restraints excluded: chain A residue 3313 PHE Chi-restraints excluded: chain A residue 3316 THR Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3760 LEU Chi-restraints excluded: chain A residue 3766 GLU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 288 TRP Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 416 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 91 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 230 optimal weight: 0.3980 chunk 40 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 192 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.090573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.069057 restraints weight = 86221.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.071082 restraints weight = 45633.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.072436 restraints weight = 30132.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.073306 restraints weight = 22853.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.073917 restraints weight = 19112.285| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 24440 Z= 0.205 Angle : 0.605 11.075 33200 Z= 0.304 Chirality : 0.044 0.314 3825 Planarity : 0.004 0.046 4169 Dihedral : 6.092 138.762 3306 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.99 % Allowed : 16.66 % Favored : 81.35 % 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: 0.64 (0.16), residues: 3019 helix: 2.04 (0.14), residues: 1396 sheet: -0.46 (0.25), residues: 444 loop : -1.22 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2552 TYR 0.012 0.001 TYR A4073 PHE 0.025 0.002 PHE B 470 TRP 0.049 0.002 TRP B 442 HIS 0.010 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00464 (24440) covalent geometry : angle 0.60481 (33200) hydrogen bonds : bond 0.03500 ( 1231) hydrogen bonds : angle 4.47646 ( 3612) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 163 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.8284 (ppp) cc_final: 0.6780 (ppp) REVERT: A 1566 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8245 (m-10) REVERT: A 1624 ARG cc_start: 0.8958 (ttt-90) cc_final: 0.8692 (ttm-80) REVERT: A 1655 MET cc_start: 0.8933 (mmm) cc_final: 0.8689 (mmm) REVERT: A 1704 GLU cc_start: 0.8740 (mp0) cc_final: 0.8231 (mp0) REVERT: A 1705 TYR cc_start: 0.8667 (m-10) cc_final: 0.8352 (m-80) REVERT: A 2016 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8150 (m-30) REVERT: A 2036 GLN cc_start: 0.8536 (tp-100) cc_final: 0.8259 (tp-100) REVERT: A 2091 MET cc_start: 0.7829 (ttp) cc_final: 0.7292 (ttp) REVERT: A 3330 TYR cc_start: 0.7059 (OUTLIER) cc_final: 0.5995 (t80) REVERT: A 3463 SER cc_start: 0.9139 (p) cc_final: 0.8782 (t) REVERT: A 3850 TRP cc_start: 0.8013 (t60) cc_final: 0.7664 (t60) REVERT: A 4085 THR cc_start: 0.7766 (m) cc_final: 0.7503 (m) REVERT: C 155 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8586 (pm20) REVERT: C 288 TRP cc_start: 0.6827 (OUTLIER) cc_final: 0.6621 (m-90) REVERT: B 444 LEU cc_start: 0.7458 (tt) cc_final: 0.6682 (mt) REVERT: B 463 CYS cc_start: 0.8134 (p) cc_final: 0.7837 (p) outliers start: 51 outliers final: 34 residues processed: 204 average time/residue: 0.1489 time to fit residues: 52.3119 Evaluate side-chains 198 residues out of total 2786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1566 PHE Chi-restraints excluded: chain A residue 1782 LEU Chi-restraints excluded: chain A residue 1822 CYS Chi-restraints excluded: chain A residue 1960 CYS Chi-restraints excluded: chain A residue 2016 ASP Chi-restraints excluded: chain A residue 2105 ASP Chi-restraints excluded: chain A residue 2222 ILE Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2275 ILE Chi-restraints excluded: chain A residue 2286 THR Chi-restraints excluded: chain A residue 2404 PHE Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2743 LEU Chi-restraints excluded: chain A residue 2786 ILE Chi-restraints excluded: chain A residue 2912 CYS Chi-restraints excluded: chain A residue 2936 VAL Chi-restraints excluded: chain A residue 2958 ILE Chi-restraints excluded: chain A residue 3316 THR Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3525 ILE Chi-restraints excluded: chain A residue 3760 LEU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 3945 LEU Chi-restraints excluded: chain A residue 4003 ASP Chi-restraints excluded: chain A residue 4010 LEU Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 288 TRP Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 416 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 238 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 192 optimal weight: 30.0000 chunk 286 optimal weight: 0.0570 chunk 135 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 293 optimal weight: 7.9990 chunk 223 optimal weight: 4.9990 overall best weight: 2.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1840 GLN ** A1866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.089637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.068062 restraints weight = 87276.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.070075 restraints weight = 45994.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.071351 restraints weight = 30295.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.072295 restraints weight = 23177.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.072886 restraints weight = 19244.723| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 24440 Z= 0.223 Angle : 0.631 13.578 33200 Z= 0.318 Chirality : 0.044 0.272 3825 Planarity : 0.004 0.045 4169 Dihedral : 6.261 137.161 3306 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.92 % Allowed : 17.25 % Favored : 80.84 % 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: 0.43 (0.15), residues: 3019 helix: 1.84 (0.14), residues: 1400 sheet: -0.57 (0.25), residues: 442 loop : -1.29 (0.17), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2552 TYR 0.030 0.002 TYR C 372 PHE 0.024 0.002 PHE B 470 TRP 0.030 0.002 TRP B 442 HIS 0.009 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00505 (24440) covalent geometry : angle 0.63123 (33200) hydrogen bonds : bond 0.03646 ( 1231) hydrogen bonds : angle 4.56656 ( 3612) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 158 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.8255 (ppp) cc_final: 0.7763 (ppp) REVERT: A 1624 ARG cc_start: 0.8998 (ttt-90) cc_final: 0.8718 (ttm-80) REVERT: A 1655 MET cc_start: 0.8937 (mmm) cc_final: 0.8674 (mmm) REVERT: A 1704 GLU cc_start: 0.8795 (mp0) cc_final: 0.8310 (mp0) REVERT: A 1705 TYR cc_start: 0.8707 (m-10) cc_final: 0.8405 (m-80) REVERT: A 2016 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.8160 (m-30) REVERT: A 2036 GLN cc_start: 0.8571 (tp-100) cc_final: 0.8326 (tp-100) REVERT: A 2091 MET cc_start: 0.7825 (ttp) cc_final: 0.7275 (ttp) REVERT: A 2526 ILE cc_start: 0.4909 (OUTLIER) cc_final: 0.4672 (pt) REVERT: A 2670 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8451 (pp20) REVERT: A 3330 TYR cc_start: 0.7186 (OUTLIER) cc_final: 0.6170 (t80) REVERT: A 3364 TYR cc_start: 0.8334 (t80) cc_final: 0.8072 (t80) REVERT: A 3463 SER cc_start: 0.9147 (p) cc_final: 0.8768 (t) REVERT: A 3700 MET cc_start: 0.8561 (tmm) cc_final: 0.8336 (tmm) REVERT: A 3850 TRP cc_start: 0.8008 (t60) cc_final: 0.7597 (t60) REVERT: C 155 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8610 (pm20) REVERT: C 370 MET cc_start: 0.8247 (mmt) cc_final: 0.7970 (mmm) REVERT: B 444 LEU cc_start: 0.7515 (tt) cc_final: 0.6830 (mt) outliers start: 49 outliers final: 38 residues processed: 197 average time/residue: 0.1381 time to fit residues: 46.7256 Evaluate side-chains 194 residues out of total 2786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 151 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1782 LEU Chi-restraints excluded: chain A residue 1822 CYS Chi-restraints excluded: chain A residue 1960 CYS Chi-restraints excluded: chain A residue 2016 ASP Chi-restraints excluded: chain A residue 2105 ASP Chi-restraints excluded: chain A residue 2153 VAL Chi-restraints excluded: chain A residue 2222 ILE Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2275 ILE Chi-restraints excluded: chain A residue 2286 THR Chi-restraints excluded: chain A residue 2404 PHE Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2526 ILE Chi-restraints excluded: chain A residue 2670 GLU Chi-restraints excluded: chain A residue 2743 LEU Chi-restraints excluded: chain A residue 2786 ILE Chi-restraints excluded: chain A residue 2912 CYS Chi-restraints excluded: chain A residue 2936 VAL Chi-restraints excluded: chain A residue 2958 ILE Chi-restraints excluded: chain A residue 3032 ASN Chi-restraints excluded: chain A residue 3316 THR Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3525 ILE Chi-restraints excluded: chain A residue 3760 LEU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 3945 LEU Chi-restraints excluded: chain A residue 4010 LEU Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 288 TRP Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 416 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 27 optimal weight: 0.9990 chunk 224 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 292 optimal weight: 4.9990 chunk 265 optimal weight: 0.9980 chunk 272 optimal weight: 0.8980 chunk 192 optimal weight: 0.0170 chunk 174 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.091842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.070452 restraints weight = 86245.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.072557 restraints weight = 44882.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.073957 restraints weight = 29223.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.074877 restraints weight = 21964.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.075482 restraints weight = 18196.939| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24440 Z= 0.111 Angle : 0.564 10.785 33200 Z= 0.279 Chirality : 0.042 0.281 3825 Planarity : 0.003 0.048 4169 Dihedral : 6.053 137.583 3306 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.41 % Allowed : 17.95 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.65 (0.16), residues: 3019 helix: 2.03 (0.14), residues: 1400 sheet: -0.45 (0.25), residues: 443 loop : -1.21 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1583 TYR 0.022 0.001 TYR C 372 PHE 0.019 0.001 PHE A2972 TRP 0.025 0.001 TRP A2516 HIS 0.009 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00254 (24440) covalent geometry : angle 0.56434 (33200) hydrogen bonds : bond 0.03260 ( 1231) hydrogen bonds : angle 4.37746 ( 3612) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6038 Ramachandran restraints generated. 3019 Oldfield, 0 Emsley, 3019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.8268 (ppp) cc_final: 0.7699 (ppp) REVERT: A 1624 ARG cc_start: 0.8962 (ttt-90) cc_final: 0.8696 (ttm-80) REVERT: A 1655 MET cc_start: 0.8906 (mmm) cc_final: 0.8657 (mmm) REVERT: A 1704 GLU cc_start: 0.8817 (mp0) cc_final: 0.8293 (mp0) REVERT: A 1705 TYR cc_start: 0.8708 (m-10) cc_final: 0.8409 (m-80) REVERT: A 1955 LEU cc_start: 0.8449 (mt) cc_final: 0.8143 (mt) REVERT: A 2016 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8081 (m-30) REVERT: A 2036 GLN cc_start: 0.8552 (tp-100) cc_final: 0.8292 (tp-100) REVERT: A 2058 MET cc_start: 0.6696 (ppp) cc_final: 0.6220 (ppp) REVERT: A 2091 MET cc_start: 0.7889 (ttp) cc_final: 0.7319 (ttp) REVERT: A 2526 ILE cc_start: 0.5045 (OUTLIER) cc_final: 0.4710 (pt) REVERT: A 2670 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8400 (pp20) REVERT: A 3330 TYR cc_start: 0.7117 (OUTLIER) cc_final: 0.6076 (t80) REVERT: A 3364 TYR cc_start: 0.8233 (t80) cc_final: 0.8001 (t80) REVERT: A 3409 ASP cc_start: 0.7945 (t0) cc_final: 0.7527 (t0) REVERT: A 3463 SER cc_start: 0.9111 (p) cc_final: 0.8734 (t) REVERT: A 3700 MET cc_start: 0.8606 (tmm) cc_final: 0.8380 (tmm) REVERT: B 444 LEU cc_start: 0.7398 (tt) cc_final: 0.6716 (mt) outliers start: 36 outliers final: 29 residues processed: 197 average time/residue: 0.1459 time to fit residues: 49.4577 Evaluate side-chains 190 residues out of total 2786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1782 LEU Chi-restraints excluded: chain A residue 1822 CYS Chi-restraints excluded: chain A residue 1960 CYS Chi-restraints excluded: chain A residue 2016 ASP Chi-restraints excluded: chain A residue 2105 ASP Chi-restraints excluded: chain A residue 2153 VAL Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2275 ILE Chi-restraints excluded: chain A residue 2404 PHE Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2526 ILE Chi-restraints excluded: chain A residue 2670 GLU Chi-restraints excluded: chain A residue 2743 LEU Chi-restraints excluded: chain A residue 2786 ILE Chi-restraints excluded: chain A residue 2912 CYS Chi-restraints excluded: chain A residue 2936 VAL Chi-restraints excluded: chain A residue 2958 ILE Chi-restraints excluded: chain A residue 3316 THR Chi-restraints excluded: chain A residue 3329 ILE Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3760 LEU Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain A residue 4010 LEU Chi-restraints excluded: chain A residue 4021 LEU Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 288 TRP Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 416 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 302 optimal weight: 4.9990 chunk 288 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 256 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 169 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.091301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.069941 restraints weight = 85961.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.072000 restraints weight = 45145.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.073383 restraints weight = 29638.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.074288 restraints weight = 22369.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.074867 restraints weight = 18612.074| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24440 Z= 0.136 Angle : 0.572 11.159 33200 Z= 0.283 Chirality : 0.042 0.280 3825 Planarity : 0.003 0.047 4169 Dihedral : 6.006 137.279 3306 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.56 % Allowed : 17.79 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.66 (0.16), residues: 3019 helix: 2.03 (0.14), residues: 1402 sheet: -0.46 (0.25), residues: 443 loop : -1.20 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2552 TYR 0.022 0.001 TYR C 372 PHE 0.028 0.001 PHE A3313 TRP 0.025 0.001 TRP C 288 HIS 0.009 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00313 (24440) covalent geometry : angle 0.57208 (33200) hydrogen bonds : bond 0.03263 ( 1231) hydrogen bonds : angle 4.36770 ( 3612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4173.15 seconds wall clock time: 73 minutes 13.64 seconds (4393.64 seconds total)