Starting phenix.real_space_refine on Fri Sep 19 00:21:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dkh_46958/09_2025/9dkh_46958.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dkh_46958/09_2025/9dkh_46958.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/9dkh_46958/09_2025/9dkh_46958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dkh_46958/09_2025/9dkh_46958.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dkh_46958/09_2025/9dkh_46958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dkh_46958/09_2025/9dkh_46958.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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 1 5.21 5 S 94 5.16 5 C 13479 2.51 5 N 3538 2.21 5 O 3883 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s 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: 21004 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 18097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2335, 18097 Classifications: {'peptide': 2335} Incomplete info: {'truncation_to_alanine': 215} Link IDs: {'PTRANS': 65, 'TRANS': 2269} Chain breaks: 11 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 779 Unresolved non-hydrogen angles: 956 Unresolved non-hydrogen dihedrals: 634 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 8, 'ASN:plan1': 17, 'TRP:plan': 2, 'GLU:plan': 45, 'PHE:plan': 5, 'ASP:plan': 23, 'TYR:plan': 1, 'ARG:plan': 14, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 467 Chain: "C" Number of atoms: 2794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2794 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 16, 'TRANS': 339} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'TRP:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ARG%COO:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 113 Unusual residues: {' MG': 1, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 4.89, per 1000 atoms: 0.23 Number of scatterers: 21004 At special positions: 0 Unit cell: (111.36, 154.28, 175.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 94 16.00 P 9 15.00 Mg 1 11.99 O 3883 8.00 N 3538 7.00 C 13479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 927.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5330 Ramachandran restraints generated. 2665 Oldfield, 0 Emsley, 2665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5126 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 22 sheets defined 56.5% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 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: 4.102A 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 1562 through 1567 removed outlier: 3.517A pdb=" N PHE A1566 " --> pdb=" O MET A1562 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1632 removed outlier: 3.639A pdb=" N TRP A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1640 removed outlier: 4.206A 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: 4.282A 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 1787 Processing helix chain 'A' and resid 1802 through 1812 Processing helix chain 'A' and resid 1830 through 1842 Processing helix chain 'A' and resid 1849 through 1853 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 Processing helix chain 'A' and resid 1942 through 1959 Processing helix chain 'A' and resid 1969 through 1988 removed outlier: 3.509A pdb=" N LEU A1973 " --> pdb=" O GLY A1969 " (cutoff:3.500A) removed outlier: 4.214A 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: 4.831A pdb=" N GLU A1986 " --> pdb=" O PRO A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1990 through 2003 removed outlier: 3.876A 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 2045 Processing helix chain 'A' and resid 2050 through 2067 removed outlier: 3.955A 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 Processing helix chain 'A' and resid 2144 through 2148 removed outlier: 3.787A pdb=" N SER A2148 " --> pdb=" O PHE A2145 " (cutoff:3.500A) Processing helix chain 'A' and resid 2159 through 2165 Processing helix chain 'A' and resid 2166 through 2171 removed outlier: 4.413A pdb=" N ASP A2171 " --> pdb=" O ASN A2167 " (cutoff:3.500A) 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: 4.088A pdb=" N PHE A2257 " --> pdb=" O ILE A2253 " (cutoff:3.500A) Processing helix chain 'A' and resid 2258 through 2270 removed outlier: 4.398A 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: 3.821A 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 removed outlier: 3.528A pdb=" N ALA A2327 " --> pdb=" O LEU A2323 " (cutoff:3.500A) Processing helix chain 'A' and resid 2331 through 2347 Processing helix chain 'A' and resid 2370 through 2374 removed outlier: 3.698A pdb=" N SER A2373 " --> pdb=" O SER A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2381 through 2385 removed outlier: 3.525A pdb=" N GLU A2384 " --> pdb=" O GLU A2381 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A2385 " --> pdb=" O ALA A2382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2381 through 2385' Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2423 through 2434 removed outlier: 3.634A pdb=" N ASN A2434 " --> pdb=" O ASN A2430 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2460 removed outlier: 4.149A pdb=" N ILE A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) Processing helix chain 'A' and resid 2501 through 2512 Processing helix chain 'A' and resid 2547 through 2552 removed outlier: 3.612A 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: 5.736A pdb=" N SER A2587 " --> pdb=" O GLU A2584 " (cutoff:3.500A) Processing helix chain 'A' and resid 2588 through 2607 removed outlier: 3.611A pdb=" N PHE A2592 " --> pdb=" O TYR A2588 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A2607 " --> pdb=" O CYS A2603 " (cutoff:3.500A) Processing helix chain 'A' and resid 2618 through 2634 removed outlier: 3.919A pdb=" N LEU A2622 " --> pdb=" O SER A2618 " (cutoff:3.500A) Processing helix chain 'A' and resid 2640 through 2656 Processing helix chain 'A' and resid 2662 through 2681 Processing helix chain 'A' and resid 2690 through 2694 removed outlier: 3.595A pdb=" N LEU A2694 " --> pdb=" O SER A2691 " (cutoff:3.500A) Processing helix chain 'A' and resid 2708 through 2727 Processing helix chain 'A' and resid 2735 through 2751 removed outlier: 3.818A 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: 4.035A pdb=" N PHE A2795 " --> pdb=" O ASN A2791 " (cutoff:3.500A) Processing helix chain 'A' and resid 2818 through 2822 removed outlier: 3.524A pdb=" N ILE A2822 " --> pdb=" O GLU A2819 " (cutoff:3.500A) Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 3.956A pdb=" N LEU A2828 " --> pdb=" O GLU A2824 " (cutoff:3.500A) Processing helix chain 'A' and resid 2840 through 2844 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: 3.700A pdb=" N ASN A2910 " --> pdb=" O PRO A2906 " (cutoff:3.500A) Processing helix chain 'A' and resid 2921 through 2934 removed outlier: 3.768A 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 removed outlier: 3.777A pdb=" N ALA A2964 " --> pdb=" O THR A2960 " (cutoff:3.500A) Processing helix chain 'A' and resid 2989 through 3039 Processing helix chain 'A' and resid 3285 through 3318 removed outlier: 3.808A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3333 removed outlier: 3.667A pdb=" N THR A3332 " --> pdb=" O SER A3328 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A3333 " --> pdb=" O ILE A3329 " (cutoff:3.500A) Processing helix chain 'A' and resid 3334 through 3337 removed outlier: 4.030A 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: 3.722A pdb=" N GLY A3383 " --> pdb=" O TRP A3379 " (cutoff:3.500A) Processing helix chain 'A' and resid 3387 through 3399 Processing helix chain 'A' and resid 3413 through 3423 removed outlier: 4.015A 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 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 removed outlier: 3.603A pdb=" N ASN A3538 " --> pdb=" O LEU A3534 " (cutoff:3.500A) Processing helix chain 'A' and resid 3538 through 3569 removed outlier: 3.859A pdb=" N GLN A3542 " --> pdb=" O ASN A3538 " (cutoff:3.500A) Processing helix chain 'A' and resid 3580 through 3606 removed outlier: 4.021A pdb=" N GLU A3606 " --> pdb=" O SER A3602 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3618 removed outlier: 3.547A pdb=" N PHE A3611 " --> pdb=" O PHE A3607 " (cutoff:3.500A) Processing helix chain 'A' and resid 3619 through 3639 removed outlier: 3.545A pdb=" N HIS A3639 " --> pdb=" O PHE A3635 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3659 removed outlier: 3.556A pdb=" N VAL A3656 " --> pdb=" O CYS A3652 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) Processing helix chain 'A' and resid 3669 through 3687 removed outlier: 3.808A 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 3728 Processing helix chain 'A' and resid 3742 through 3753 Processing helix chain 'A' and resid 3755 through 3767 removed outlier: 4.558A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.864A 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: 4.152A pdb=" N ILE A3834 " --> pdb=" O SER A3830 " (cutoff:3.500A) Processing helix chain 'A' and resid 3847 through 3859 removed outlier: 4.891A pdb=" N HIS A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LYS A3857 " --> pdb=" O THR A3853 " (cutoff:3.500A) Processing helix chain 'A' and resid 3885 through 3891 Processing helix chain 'A' and resid 3903 through 3913 Processing helix chain 'A' and resid 3922 through 3945 removed outlier: 3.781A pdb=" N ARG A3944 " --> pdb=" O THR A3940 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A3945 " --> pdb=" O ALA A3941 " (cutoff:3.500A) Processing helix chain 'A' and resid 3945 through 3950 removed outlier: 3.610A pdb=" N PHE A3950 " --> pdb=" O VAL A3946 " (cutoff:3.500A) Processing helix chain 'A' and resid 3957 through 3974 removed outlier: 3.898A 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 removed outlier: 3.624A pdb=" N THR A4052 " --> pdb=" O ILE A4048 " (cutoff:3.500A) Processing helix chain 'A' and resid 4057 through 4062 Processing helix chain 'A' and resid 4066 through 4091 removed outlier: 3.739A pdb=" N ILE A4070 " --> pdb=" O PRO A4066 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A4091 " --> pdb=" O GLN A4087 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 369 Processing sheet with id=AA1, first strand: chain 'A' and resid 1569 through 1574 removed outlier: 3.677A 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: 3.593A pdb=" N SER A1750 " --> pdb=" O LYS A1733 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1818 through 1819 removed outlier: 6.138A pdb=" N VAL A1818 " --> pdb=" O CYS A1846 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLY A1845 " --> pdb=" O PHE A1895 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N THR A1897 " --> pdb=" O GLY A1845 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A1792 " --> pdb=" O VAL A1894 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLY A1791 " --> pdb=" O ARG A1917 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N PHE A1919 " --> pdb=" O GLY A1791 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N CYS A1793 " --> pdb=" O PHE A1919 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1878 through 1881 Processing sheet with id=AA5, first strand: chain 'A' and resid 2099 through 2104 removed outlier: 3.546A pdb=" N VAL A2100 " --> pdb=" O ARG A2149 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP A2151 " --> pdb=" O VAL A2100 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE A2150 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N LEU A2193 " --> pdb=" O ILE A2150 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL A2152 " --> pdb=" O LEU A2193 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N GLU A2195 " --> pdb=" O VAL A2152 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE A2154 " --> pdb=" O GLU A2195 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU A2070 " --> pdb=" O PHE A2194 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N THR A2196 " --> pdb=" O LEU A2070 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU A2072 " --> pdb=" O THR A2196 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE A2071 " --> pdb=" O LEU A2213 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N PHE A2215 " --> pdb=" O ILE A2071 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL A2073 " --> pdb=" O PHE A2215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2116 through 2119 removed outlier: 3.528A pdb=" N LEU A2119 " --> pdb=" O GLU A2124 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A2124 " --> pdb=" O LEU A2119 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2438 through 2441 removed outlier: 5.943A pdb=" N ASP A2439 " --> pdb=" O VAL A2483 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY A2413 " --> pdb=" O ALA A2555 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU A2557 " --> pdb=" O GLY A2413 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A2415 " --> pdb=" O LEU A2557 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2462 through 2464 Processing sheet with id=AA9, first strand: chain 'A' and resid 2696 through 2697 removed outlier: 3.570A pdb=" N LYS A2705 " --> pdb=" O SER A2697 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2781 through 2782 removed outlier: 6.696A pdb=" N VAL A2782 " --> pdb=" O ILE A2816 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR A2813 " --> pdb=" O HIS A2886 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL A2888 " --> pdb=" O THR A2813 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A2815 " --> pdb=" O VAL A2888 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N THR A2890 " --> pdb=" O LEU A2815 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE A2817 " --> pdb=" O THR A2890 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A2756 " --> pdb=" O VAL A2887 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N MET A2757 " --> pdb=" O ASN A2915 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N MET A2917 " --> pdb=" O MET A2757 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ILE A2759 " --> pdb=" O MET A2917 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 3427 through 3430 removed outlier: 6.516A pdb=" N VAL A3450 " --> pdb=" O PHE A3495 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N HIS A3497 " --> pdb=" O VAL A3450 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE A3452 " --> pdb=" O HIS A3497 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A3496 " --> pdb=" O PRO A3405 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3471 through 3473 removed outlier: 3.566A pdb=" N ARG A3476 " --> pdb=" O ALA A3473 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A3481 " --> pdb=" O HIS A3484 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3811 through 3815 removed outlier: 6.365A pdb=" N LYS A3812 " --> pdb=" O LEU A3840 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLN A3842 " --> pdb=" O LYS A3812 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE A3814 " --> pdb=" O GLN A3842 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 4020 through 4021 Processing sheet with id=AB6, first strand: chain 'C' and resid 150 through 153 removed outlier: 3.571A pdb=" N CYS C 150 " --> pdb=" O VAL C 491 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 491 " --> pdb=" O CYS C 150 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS C 488 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL C 481 " --> pdb=" O LEU C 464 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU C 464 " --> pdb=" O VAL C 481 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLY C 483 " --> pdb=" O ASN C 462 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 161 through 163 removed outlier: 3.781A pdb=" N PHE C 171 " --> pdb=" O LYS C 162 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 178 through 179 Processing sheet with id=AB9, first strand: chain 'C' and resid 201 through 208 removed outlier: 6.995A pdb=" N ALA C 225 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N MET C 204 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL C 223 " --> pdb=" O MET C 204 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL C 206 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL C 221 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU C 220 " --> pdb=" O TRP C 236 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE C 231 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N SER C 248 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 7.004A 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: 3.621A pdb=" N ALA C 258 " --> pdb=" O CYS C 273 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE C 293 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 281 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS C 291 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASP C 283 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER C 289 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 300 through 306 removed outlier: 4.035A pdb=" N SER C 302 " --> pdb=" O GLY C 313 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER C 312 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 320 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER C 314 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N THR C 318 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER C 331 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS C 323 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 6.448A 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: 7.031A pdb=" N ALA C 376 " --> pdb=" O GLU C 341 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL C 343 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL C 374 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N PHE C 345 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N TYR C 372 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER C 377 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 411 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLU C 386 " --> pdb=" O CYS C 409 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N CYS C 409 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 420 through 426 removed outlier: 4.296A pdb=" N ASP C 422 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS C 451 " --> pdb=" O CYS C 441 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASP C 443 " --> pdb=" O CYS C 449 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS C 449 " --> pdb=" O ASP C 443 " (cutoff:3.500A) 1152 hydrogen bonds defined for protein. 3369 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.07 Time building geometry restraints manager: 2.48 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: 6714 1.34 - 1.46: 4422 1.46 - 1.58: 10159 1.58 - 1.70: 11 1.70 - 1.82: 144 Bond restraints: 21450 Sorted by residual: bond pdb=" CA PRO A2187 " pdb=" C PRO A2187 " ideal model delta sigma weight residual 1.517 1.507 0.010 6.70e-03 2.23e+04 2.01e+00 bond pdb=" CA THR A2518 " pdb=" C THR A2518 " ideal model delta sigma weight residual 1.521 1.536 -0.015 1.14e-02 7.69e+03 1.84e+00 bond pdb=" CB ARG A3745 " pdb=" CG ARG A3745 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" CG1 ILE A2655 " pdb=" CD1 ILE A2655 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.46e+00 bond pdb=" CG GLU A3766 " pdb=" CD GLU A3766 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.36e+00 ... (remaining 21445 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 28470 1.85 - 3.69: 547 3.69 - 5.54: 89 5.54 - 7.38: 25 7.38 - 9.23: 5 Bond angle restraints: 29136 Sorted by residual: angle pdb=" C LEU A3945 " pdb=" N VAL A3946 " pdb=" CA VAL A3946 " ideal model delta sigma weight residual 120.33 123.51 -3.18 8.00e-01 1.56e+00 1.58e+01 angle pdb=" C ARG A3792 " pdb=" N ASP A3793 " pdb=" CA ASP A3793 " ideal model delta sigma weight residual 122.08 127.10 -5.02 1.47e+00 4.63e-01 1.17e+01 angle pdb=" C ASP C 316 " pdb=" N THR C 317 " pdb=" CA THR C 317 " ideal model delta sigma weight residual 122.61 127.41 -4.80 1.56e+00 4.11e-01 9.48e+00 angle pdb=" CB LYS A2981 " pdb=" CG LYS A2981 " pdb=" CD LYS A2981 " ideal model delta sigma weight residual 111.30 118.14 -6.84 2.30e+00 1.89e-01 8.86e+00 angle pdb=" CA GLN A3637 " pdb=" CB GLN A3637 " pdb=" CG GLN A3637 " ideal model delta sigma weight residual 114.10 119.54 -5.44 2.00e+00 2.50e-01 7.40e+00 ... (remaining 29131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.81: 12298 29.81 - 59.62: 433 59.62 - 89.43: 36 89.43 - 119.24: 0 119.24 - 149.06: 2 Dihedral angle restraints: 12769 sinusoidal: 4884 harmonic: 7885 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 -119.40 -149.06 1 2.00e+01 2.50e-03 4.46e+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 64.01 -124.01 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" CA PRO A2957 " pdb=" C PRO A2957 " pdb=" N ILE A2958 " pdb=" CA ILE A2958 " ideal model delta harmonic sigma weight residual -180.00 -159.06 -20.94 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 12766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2202 0.037 - 0.074: 839 0.074 - 0.111: 268 0.111 - 0.148: 59 0.148 - 0.185: 7 Chirality restraints: 3375 Sorted by residual: chirality pdb=" CB ILE A3621 " pdb=" CA ILE A3621 " pdb=" CG1 ILE A3621 " pdb=" CG2 ILE A3621 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CB ILE C 281 " pdb=" CA ILE C 281 " pdb=" CG1 ILE C 281 " pdb=" CG2 ILE C 281 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CA THR A2518 " pdb=" N THR A2518 " pdb=" C THR A2518 " pdb=" CB THR A2518 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.30e-01 ... (remaining 3372 not shown) Planarity restraints: 3658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A3313 " -0.015 2.00e-02 2.50e+03 2.07e-02 7.52e+00 pdb=" CG PHE A3313 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE A3313 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A3313 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A3313 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A3313 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A3313 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1772 " -0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO A1773 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A1773 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1773 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1708 " -0.002 2.00e-02 2.50e+03 1.57e-02 4.29e+00 pdb=" CG PHE A1708 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A1708 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A1708 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A1708 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A1708 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A1708 " 0.001 2.00e-02 2.50e+03 ... (remaining 3655 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 166 2.57 - 3.15: 16549 3.15 - 3.74: 34097 3.74 - 4.32: 43356 4.32 - 4.90: 71900 Nonbonded interactions: 166068 Sorted by model distance: nonbonded pdb=" O3B ADP A4104 " pdb="MG MG A4105 " model vdw 1.991 2.170 nonbonded pdb=" NZ LYS A2424 " pdb="MG MG A4105 " model vdw 2.162 2.250 nonbonded pdb=" OG1 THR A2081 " pdb=" OE2 GLU A2195 " model vdw 2.207 3.040 nonbonded pdb=" NE2 GLN A3680 " pdb=" O PHE A3767 " model vdw 2.241 3.120 nonbonded pdb=" OG SER C 226 " pdb=" OD1 ASP C 228 " model vdw 2.259 3.040 ... (remaining 166063 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.620 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 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 0.047 21450 Z= 0.149 Angle : 0.648 9.231 29136 Z= 0.331 Chirality : 0.044 0.185 3375 Planarity : 0.004 0.057 3658 Dihedral : 14.616 149.056 7643 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: -0.12 (0.16), residues: 2665 helix: 0.80 (0.13), residues: 1381 sheet: -0.20 (0.28), residues: 349 loop : -1.30 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1815 TYR 0.023 0.001 TYR A2571 PHE 0.047 0.002 PHE A3313 TRP 0.022 0.001 TRP A1656 HIS 0.008 0.001 HIS A2598 Details of bonding type rmsd covalent geometry : bond 0.00321 (21450) covalent geometry : angle 0.64760 (29136) hydrogen bonds : bond 0.13610 ( 1152) hydrogen bonds : angle 5.67992 ( 3369) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5330 Ramachandran restraints generated. 2665 Oldfield, 0 Emsley, 2665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5330 Ramachandran restraints generated. 2665 Oldfield, 0 Emsley, 2665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1448 VAL cc_start: 0.6603 (t) cc_final: 0.6335 (p) REVERT: A 1565 MET cc_start: 0.6768 (ppp) cc_final: 0.5610 (ppp) REVERT: A 1781 THR cc_start: 0.8341 (m) cc_final: 0.8116 (m) REVERT: A 2572 GLU cc_start: 0.8352 (tp30) cc_final: 0.7942 (tp30) REVERT: A 2692 THR cc_start: 0.8465 (p) cc_final: 0.8252 (p) REVERT: A 2805 ASP cc_start: 0.8915 (m-30) cc_final: 0.8398 (t0) REVERT: A 2980 MET cc_start: 0.6981 (mmp) cc_final: 0.6678 (ttp) REVERT: A 3345 MET cc_start: 0.8421 (tpp) cc_final: 0.8059 (mpp) REVERT: A 3398 MET cc_start: 0.8561 (mmm) cc_final: 0.8336 (mmm) REVERT: A 3483 ASP cc_start: 0.8030 (p0) cc_final: 0.7312 (t0) REVERT: A 3631 MET cc_start: 0.8520 (tmm) cc_final: 0.8269 (tmm) REVERT: A 3785 TYR cc_start: 0.6812 (m-10) cc_final: 0.6338 (m-10) REVERT: A 3873 MET cc_start: 0.6792 (ptt) cc_final: 0.6116 (ptt) REVERT: C 210 ASN cc_start: 0.8035 (t0) cc_final: 0.7430 (t0) REVERT: C 230 GLN cc_start: 0.6852 (tp40) cc_final: 0.6422 (tp40) REVERT: C 316 ASP cc_start: 0.7429 (p0) cc_final: 0.7083 (p0) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1400 time to fit residues: 61.8255 Evaluate side-chains 203 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.0170 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1812 ASN A2787 HIS ** A2832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 GLN ** C 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.110790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.090189 restraints weight = 67895.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.093395 restraints weight = 40831.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.094729 restraints weight = 24782.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.094937 restraints weight = 21352.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.094928 restraints weight = 18293.755| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21450 Z= 0.189 Angle : 0.605 8.702 29136 Z= 0.308 Chirality : 0.042 0.224 3375 Planarity : 0.004 0.049 3658 Dihedral : 6.408 146.207 2927 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.26 % Allowed : 10.23 % Favored : 88.50 % 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 (0.16), residues: 2665 helix: 1.51 (0.14), residues: 1384 sheet: -0.27 (0.28), residues: 354 loop : -1.18 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 247 TYR 0.023 0.001 TYR C 372 PHE 0.022 0.002 PHE A3313 TRP 0.022 0.001 TRP A1656 HIS 0.006 0.001 HIS A2741 Details of bonding type rmsd covalent geometry : bond 0.00430 (21450) covalent geometry : angle 0.60502 (29136) hydrogen bonds : bond 0.03901 ( 1152) hydrogen bonds : angle 4.51127 ( 3369) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5330 Ramachandran restraints generated. 2665 Oldfield, 0 Emsley, 2665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5330 Ramachandran restraints generated. 2665 Oldfield, 0 Emsley, 2665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1448 VAL cc_start: 0.6708 (t) cc_final: 0.6485 (p) REVERT: A 1565 MET cc_start: 0.7078 (ppp) cc_final: 0.5767 (ppp) REVERT: A 2198 ASN cc_start: 0.8357 (t0) cc_final: 0.8064 (t0) REVERT: A 2401 GLU cc_start: 0.6762 (mt-10) cc_final: 0.6526 (mt-10) REVERT: A 2523 TRP cc_start: 0.7453 (t-100) cc_final: 0.7053 (t-100) REVERT: A 2572 GLU cc_start: 0.8317 (tp30) cc_final: 0.8008 (mt-10) REVERT: A 2797 MET cc_start: 0.8763 (mpp) cc_final: 0.8446 (mpp) REVERT: A 2980 MET cc_start: 0.7060 (mmp) cc_final: 0.6517 (ttt) REVERT: A 3398 MET cc_start: 0.8525 (mmm) cc_final: 0.8283 (mmm) REVERT: A 3483 ASP cc_start: 0.7930 (p0) cc_final: 0.7255 (t0) REVERT: A 3631 MET cc_start: 0.8485 (tmm) cc_final: 0.8200 (tmm) REVERT: A 3873 MET cc_start: 0.6687 (ptt) cc_final: 0.6297 (ptm) REVERT: C 169 ILE cc_start: 0.8305 (mp) cc_final: 0.8024 (mm) REVERT: C 210 ASN cc_start: 0.7957 (t0) cc_final: 0.7624 (t0) outliers start: 28 outliers final: 23 residues processed: 230 average time/residue: 0.1408 time to fit residues: 54.2818 Evaluate side-chains 215 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1749 ILE Chi-restraints excluded: chain A residue 1963 MET Chi-restraints excluded: chain A residue 2010 ASP Chi-restraints excluded: chain A residue 2070 LEU Chi-restraints excluded: chain A residue 2091 MET Chi-restraints excluded: chain A residue 2292 VAL Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2623 THR Chi-restraints excluded: chain A residue 2674 TYR Chi-restraints excluded: chain A residue 2944 ILE Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3380 LEU Chi-restraints excluded: chain A residue 3465 LEU Chi-restraints excluded: chain A residue 3765 ASN Chi-restraints excluded: chain A residue 4004 LEU Chi-restraints excluded: chain A residue 4049 LEU Chi-restraints excluded: chain A residue 4076 LEU Chi-restraints excluded: chain A residue 4088 LEU Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 385 TRP Chi-restraints excluded: chain C residue 387 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 22 optimal weight: 2.9990 chunk 229 optimal weight: 6.9990 chunk 125 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 221 optimal weight: 0.7980 chunk 240 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1812 ASN A1891 HIS A2787 HIS A2789 HIS ** A2832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3936 HIS C 457 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.111359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.090548 restraints weight = 68009.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.093599 restraints weight = 40073.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.094603 restraints weight = 24150.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.094913 restraints weight = 21413.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.095039 restraints weight = 18753.245| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21450 Z= 0.111 Angle : 0.534 10.083 29136 Z= 0.267 Chirality : 0.040 0.151 3375 Planarity : 0.003 0.046 3658 Dihedral : 6.271 146.813 2927 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.49 % Allowed : 12.62 % Favored : 85.89 % 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: 0.78 (0.16), residues: 2665 helix: 1.75 (0.14), residues: 1393 sheet: -0.15 (0.28), residues: 350 loop : -1.14 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 247 TYR 0.020 0.001 TYR C 372 PHE 0.014 0.001 PHE A3313 TRP 0.018 0.001 TRP C 324 HIS 0.006 0.001 HIS A2598 Details of bonding type rmsd covalent geometry : bond 0.00243 (21450) covalent geometry : angle 0.53407 (29136) hydrogen bonds : bond 0.03417 ( 1152) hydrogen bonds : angle 4.22808 ( 3369) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5330 Ramachandran restraints generated. 2665 Oldfield, 0 Emsley, 2665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5330 Ramachandran restraints generated. 2665 Oldfield, 0 Emsley, 2665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 216 time to evaluate : 0.923 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 1448 VAL cc_start: 0.6690 (t) cc_final: 0.6479 (p) REVERT: A 1565 MET cc_start: 0.6912 (ppp) cc_final: 0.5728 (ppp) REVERT: A 1583 ARG cc_start: 0.8623 (mmt90) cc_final: 0.8405 (mtp85) REVERT: A 2198 ASN cc_start: 0.8402 (t0) cc_final: 0.7964 (t0) REVERT: A 2331 THR cc_start: 0.5933 (OUTLIER) cc_final: 0.5648 (p) REVERT: A 2401 GLU cc_start: 0.6846 (mt-10) cc_final: 0.6583 (mt-10) REVERT: A 2523 TRP cc_start: 0.7404 (t-100) cc_final: 0.7039 (t-100) REVERT: A 2572 GLU cc_start: 0.8335 (tp30) cc_final: 0.8111 (mt-10) REVERT: A 2797 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8370 (mpp) REVERT: A 2980 MET cc_start: 0.7039 (mmp) cc_final: 0.6697 (ttp) REVERT: A 3483 ASP cc_start: 0.7900 (p0) cc_final: 0.7317 (t0) REVERT: A 3631 MET cc_start: 0.8568 (tmm) cc_final: 0.8304 (tmm) REVERT: A 4049 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8779 (tt) REVERT: C 169 ILE cc_start: 0.8340 (mp) cc_final: 0.8132 (mm) REVERT: C 210 ASN cc_start: 0.7906 (t0) cc_final: 0.7540 (t0) outliers start: 33 outliers final: 17 residues processed: 233 average time/residue: 0.1364 time to fit residues: 53.2287 Evaluate side-chains 218 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1590 LEU Chi-restraints excluded: chain A residue 1749 ILE Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 1962 SER Chi-restraints excluded: chain A residue 1963 MET Chi-restraints excluded: chain A residue 2091 MET Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2674 TYR Chi-restraints excluded: chain A residue 2797 MET Chi-restraints excluded: chain A residue 2944 ILE Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3380 LEU Chi-restraints excluded: chain A residue 3465 LEU Chi-restraints excluded: chain A residue 3765 ASN Chi-restraints excluded: chain A residue 4049 LEU Chi-restraints excluded: chain A residue 4076 LEU Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 387 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 245 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 262 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 207 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 chunk 87 optimal weight: 0.0370 chunk 79 optimal weight: 1.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2832 ASN ** A3387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3978 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.110521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.090178 restraints weight = 68496.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.092125 restraints weight = 43167.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.094643 restraints weight = 27656.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.094544 restraints weight = 22305.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.094550 restraints weight = 19323.613| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21450 Z= 0.123 Angle : 0.539 8.848 29136 Z= 0.268 Chirality : 0.040 0.229 3375 Planarity : 0.003 0.044 3658 Dihedral : 6.230 146.701 2927 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.49 % Allowed : 14.52 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.16), residues: 2665 helix: 1.84 (0.14), residues: 1395 sheet: -0.14 (0.28), residues: 350 loop : -1.08 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 247 TYR 0.016 0.001 TYR A2571 PHE 0.024 0.001 PHE A2505 TRP 0.026 0.001 TRP A3762 HIS 0.006 0.001 HIS A2598 Details of bonding type rmsd covalent geometry : bond 0.00275 (21450) covalent geometry : angle 0.53914 (29136) hydrogen bonds : bond 0.03300 ( 1152) hydrogen bonds : angle 4.11266 ( 3369) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5330 Ramachandran restraints generated. 2665 Oldfield, 0 Emsley, 2665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5330 Ramachandran restraints generated. 2665 Oldfield, 0 Emsley, 2665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1448 VAL cc_start: 0.6651 (t) cc_final: 0.6446 (p) REVERT: A 1565 MET cc_start: 0.6888 (ppp) cc_final: 0.5918 (ppp) REVERT: A 1704 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6463 (mp0) REVERT: A 2198 ASN cc_start: 0.8483 (t0) cc_final: 0.8039 (t0) REVERT: A 2331 THR cc_start: 0.6017 (OUTLIER) cc_final: 0.5739 (p) REVERT: A 2401 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6610 (mt-10) REVERT: A 2523 TRP cc_start: 0.7381 (t-100) cc_final: 0.6938 (t-100) REVERT: A 2572 GLU cc_start: 0.8345 (tp30) cc_final: 0.8108 (mt-10) REVERT: A 2797 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8368 (mpp) REVERT: A 2818 ASP cc_start: 0.7201 (t70) cc_final: 0.6903 (t70) REVERT: A 2890 THR cc_start: 0.8575 (m) cc_final: 0.8225 (p) REVERT: A 2980 MET cc_start: 0.7058 (mmp) cc_final: 0.6632 (ttp) REVERT: A 3483 ASP cc_start: 0.7782 (p0) cc_final: 0.7205 (t0) REVERT: A 3631 MET cc_start: 0.8544 (tmm) cc_final: 0.8241 (tmm) REVERT: A 3785 TYR cc_start: 0.6813 (m-10) cc_final: 0.5851 (m-10) REVERT: A 3873 MET cc_start: 0.6735 (ptt) cc_final: 0.6117 (ptt) REVERT: A 4049 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8797 (tt) REVERT: C 210 ASN cc_start: 0.8083 (t0) cc_final: 0.7656 (t0) outliers start: 33 outliers final: 19 residues processed: 231 average time/residue: 0.1352 time to fit residues: 52.4456 Evaluate side-chains 216 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1590 LEU Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1704 GLU Chi-restraints excluded: chain A residue 1749 ILE Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 1963 MET Chi-restraints excluded: chain A residue 2010 ASP Chi-restraints excluded: chain A residue 2091 MET Chi-restraints excluded: chain A residue 2292 VAL Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2602 GLU Chi-restraints excluded: chain A residue 2797 MET Chi-restraints excluded: chain A residue 2944 ILE Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3380 LEU Chi-restraints excluded: chain A residue 3465 LEU Chi-restraints excluded: chain A residue 4049 LEU Chi-restraints excluded: chain A residue 4076 LEU Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 449 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 73 optimal weight: 4.9990 chunk 174 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 267 optimal weight: 0.9980 chunk 235 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.109771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.089023 restraints weight = 68189.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.091542 restraints weight = 41268.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.092892 restraints weight = 25754.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.093293 restraints weight = 20986.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.093360 restraints weight = 19043.834| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21450 Z= 0.131 Angle : 0.546 9.549 29136 Z= 0.270 Chirality : 0.040 0.166 3375 Planarity : 0.003 0.045 3658 Dihedral : 6.235 146.672 2927 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.62 % Allowed : 15.96 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.95 (0.17), residues: 2665 helix: 1.91 (0.14), residues: 1391 sheet: -0.22 (0.28), residues: 359 loop : -1.01 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1583 TYR 0.023 0.001 TYR C 372 PHE 0.025 0.001 PHE A1708 TRP 0.027 0.001 TRP A2151 HIS 0.006 0.001 HIS A2598 Details of bonding type rmsd covalent geometry : bond 0.00297 (21450) covalent geometry : angle 0.54639 (29136) hydrogen bonds : bond 0.03269 ( 1152) hydrogen bonds : angle 4.05511 ( 3369) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5330 Ramachandran restraints generated. 2665 Oldfield, 0 Emsley, 2665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5330 Ramachandran restraints generated. 2665 Oldfield, 0 Emsley, 2665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.7005 (ppp) cc_final: 0.6188 (ppp) REVERT: A 1627 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8877 (mm) REVERT: A 1704 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6533 (mp0) REVERT: A 1996 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8265 (tp30) REVERT: A 2198 ASN cc_start: 0.8554 (t0) cc_final: 0.8092 (t0) REVERT: A 2331 THR cc_start: 0.5971 (OUTLIER) cc_final: 0.5710 (p) REVERT: A 2401 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6645 (mt-10) REVERT: A 2523 TRP cc_start: 0.7269 (t-100) cc_final: 0.6856 (t-100) REVERT: A 2572 GLU cc_start: 0.8363 (tp30) cc_final: 0.8124 (mt-10) REVERT: A 2797 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8382 (mpp) REVERT: A 2818 ASP cc_start: 0.7267 (t70) cc_final: 0.6962 (t70) REVERT: A 2890 THR cc_start: 0.8638 (m) cc_final: 0.8262 (p) REVERT: A 2980 MET cc_start: 0.7067 (mmp) cc_final: 0.6612 (ttp) REVERT: A 3483 ASP cc_start: 0.7753 (p0) cc_final: 0.7200 (t0) REVERT: A 3631 MET cc_start: 0.8563 (tmm) cc_final: 0.8273 (tmm) REVERT: A 3873 MET cc_start: 0.6825 (ptt) cc_final: 0.6349 (ptm) REVERT: A 4049 LEU cc_start: 0.9018 (mt) cc_final: 0.8815 (tt) REVERT: C 210 ASN cc_start: 0.8095 (t0) cc_final: 0.7672 (t0) outliers start: 36 outliers final: 23 residues processed: 232 average time/residue: 0.1338 time to fit residues: 52.7960 Evaluate side-chains 222 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1590 LEU Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1704 GLU Chi-restraints excluded: chain A residue 1718 CYS Chi-restraints excluded: chain A residue 1749 ILE Chi-restraints excluded: chain A residue 1781 THR Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 1963 MET Chi-restraints excluded: chain A residue 1996 GLU Chi-restraints excluded: chain A residue 2010 ASP Chi-restraints excluded: chain A residue 2070 LEU Chi-restraints excluded: chain A residue 2091 MET Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2602 GLU Chi-restraints excluded: chain A residue 2623 THR Chi-restraints excluded: chain A residue 2797 MET Chi-restraints excluded: chain A residue 2944 ILE Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3465 LEU Chi-restraints excluded: chain A residue 4004 LEU Chi-restraints excluded: chain A residue 4076 LEU Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 449 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 241 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 43 optimal weight: 0.0870 chunk 199 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1555 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.110779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.090298 restraints weight = 67821.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.092691 restraints weight = 42976.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.093847 restraints weight = 28530.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.094308 restraints weight = 23005.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.094380 restraints weight = 19732.021| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21450 Z= 0.106 Angle : 0.547 12.982 29136 Z= 0.266 Chirality : 0.040 0.259 3375 Planarity : 0.003 0.046 3658 Dihedral : 6.148 146.738 2927 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.67 % Allowed : 17.18 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.17), residues: 2665 helix: 1.95 (0.14), residues: 1393 sheet: -0.21 (0.28), residues: 361 loop : -0.95 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A3365 TYR 0.022 0.001 TYR C 372 PHE 0.023 0.001 PHE A3446 TRP 0.031 0.001 TRP A2151 HIS 0.007 0.001 HIS A2598 Details of bonding type rmsd covalent geometry : bond 0.00234 (21450) covalent geometry : angle 0.54666 (29136) hydrogen bonds : bond 0.03180 ( 1152) hydrogen bonds : angle 3.94617 ( 3369) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5330 Ramachandran restraints generated. 2665 Oldfield, 0 Emsley, 2665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5330 Ramachandran restraints generated. 2665 Oldfield, 0 Emsley, 2665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.6970 (ppp) cc_final: 0.6045 (ppp) REVERT: A 1627 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8820 (mm) REVERT: A 1704 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6557 (mp0) REVERT: A 1996 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8262 (tp30) REVERT: A 2198 ASN cc_start: 0.8580 (t0) cc_final: 0.8106 (t0) REVERT: A 2331 THR cc_start: 0.6098 (OUTLIER) cc_final: 0.5781 (p) REVERT: A 2401 GLU cc_start: 0.6808 (mt-10) cc_final: 0.6574 (mt-10) REVERT: A 2484 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.7741 (tt) REVERT: A 2523 TRP cc_start: 0.7333 (t-100) cc_final: 0.6948 (t-100) REVERT: A 2559 LEU cc_start: 0.8824 (mm) cc_final: 0.8611 (mt) REVERT: A 2572 GLU cc_start: 0.8345 (tp30) cc_final: 0.8097 (mt-10) REVERT: A 2797 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8385 (mpp) REVERT: A 2818 ASP cc_start: 0.7389 (t70) cc_final: 0.7101 (t70) REVERT: A 2890 THR cc_start: 0.8657 (m) cc_final: 0.8267 (p) REVERT: A 2968 ILE cc_start: 0.9400 (tp) cc_final: 0.9082 (mt) REVERT: A 2980 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6618 (ttp) REVERT: A 3483 ASP cc_start: 0.7780 (p0) cc_final: 0.7157 (t0) REVERT: A 3631 MET cc_start: 0.8539 (tmm) cc_final: 0.8250 (tmm) REVERT: A 3785 TYR cc_start: 0.6792 (m-10) cc_final: 0.5959 (m-10) REVERT: A 3873 MET cc_start: 0.6852 (ptt) cc_final: 0.6310 (ptt) REVERT: C 210 ASN cc_start: 0.8131 (t0) cc_final: 0.7617 (t0) REVERT: C 316 ASP cc_start: 0.7570 (p0) cc_final: 0.7042 (p0) outliers start: 37 outliers final: 19 residues processed: 230 average time/residue: 0.1301 time to fit residues: 50.7717 Evaluate side-chains 220 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1590 LEU Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1704 GLU Chi-restraints excluded: chain A residue 1749 ILE Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 1963 MET Chi-restraints excluded: chain A residue 1996 GLU Chi-restraints excluded: chain A residue 2010 ASP Chi-restraints excluded: chain A residue 2070 LEU Chi-restraints excluded: chain A residue 2091 MET Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2484 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2602 GLU Chi-restraints excluded: chain A residue 2716 ILE Chi-restraints excluded: chain A residue 2797 MET Chi-restraints excluded: chain A residue 2944 ILE Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3436 PHE Chi-restraints excluded: chain A residue 3465 LEU Chi-restraints excluded: chain A residue 4076 LEU Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 464 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 264 optimal weight: 3.9990 chunk 232 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 2 optimal weight: 0.0030 chunk 141 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 267 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2043 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.110779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.089689 restraints weight = 67921.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.092085 restraints weight = 39258.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.093670 restraints weight = 27408.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.094724 restraints weight = 21723.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.095345 restraints weight = 18675.184| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 21450 Z= 0.108 Angle : 0.537 10.924 29136 Z= 0.262 Chirality : 0.040 0.238 3375 Planarity : 0.003 0.047 3658 Dihedral : 6.100 146.584 2927 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.85 % Allowed : 17.94 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.17), residues: 2665 helix: 1.96 (0.14), residues: 1395 sheet: -0.20 (0.28), residues: 363 loop : -0.89 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1583 TYR 0.023 0.001 TYR C 372 PHE 0.025 0.001 PHE A3446 TRP 0.034 0.001 TRP A2151 HIS 0.007 0.001 HIS A2598 Details of bonding type rmsd covalent geometry : bond 0.00243 (21450) covalent geometry : angle 0.53747 (29136) hydrogen bonds : bond 0.03097 ( 1152) hydrogen bonds : angle 3.89538 ( 3369) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5330 Ramachandran restraints generated. 2665 Oldfield, 0 Emsley, 2665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5330 Ramachandran restraints generated. 2665 Oldfield, 0 Emsley, 2665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.6891 (ppp) cc_final: 0.6011 (ppp) REVERT: A 1627 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8742 (mm) REVERT: A 1704 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6519 (mp0) REVERT: A 1996 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8235 (tp30) REVERT: A 2198 ASN cc_start: 0.8490 (t0) cc_final: 0.8061 (t0) REVERT: A 2331 THR cc_start: 0.5822 (OUTLIER) cc_final: 0.5490 (p) REVERT: A 2401 GLU cc_start: 0.6785 (mt-10) cc_final: 0.6578 (mt-10) REVERT: A 2458 LEU cc_start: 0.8709 (mt) cc_final: 0.8358 (pp) REVERT: A 2484 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.7732 (tt) REVERT: A 2523 TRP cc_start: 0.7279 (t-100) cc_final: 0.6862 (t-100) REVERT: A 2559 LEU cc_start: 0.8747 (mm) cc_final: 0.8500 (mt) REVERT: A 2797 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8318 (mpp) REVERT: A 2818 ASP cc_start: 0.7452 (t70) cc_final: 0.7147 (t70) REVERT: A 2890 THR cc_start: 0.8574 (m) cc_final: 0.8235 (p) REVERT: A 2968 ILE cc_start: 0.9436 (tp) cc_final: 0.9133 (mt) REVERT: A 2980 MET cc_start: 0.6897 (OUTLIER) cc_final: 0.6608 (ttp) REVERT: A 3483 ASP cc_start: 0.7547 (p0) cc_final: 0.7006 (t0) REVERT: A 3631 MET cc_start: 0.8479 (tmm) cc_final: 0.8244 (tmm) REVERT: A 3785 TYR cc_start: 0.6657 (m-10) cc_final: 0.5873 (m-10) REVERT: A 3873 MET cc_start: 0.6711 (ptt) cc_final: 0.6165 (ptt) REVERT: C 210 ASN cc_start: 0.7802 (t0) cc_final: 0.7293 (t0) REVERT: C 230 GLN cc_start: 0.6527 (tp-100) cc_final: 0.6234 (mt0) REVERT: C 371 GLN cc_start: 0.5447 (tp40) cc_final: 0.5109 (tp-100) outliers start: 41 outliers final: 25 residues processed: 230 average time/residue: 0.1295 time to fit residues: 50.7678 Evaluate side-chains 226 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1590 LEU Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1704 GLU Chi-restraints excluded: chain A residue 1718 CYS Chi-restraints excluded: chain A residue 1749 ILE Chi-restraints excluded: chain A residue 1781 THR Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 1963 MET Chi-restraints excluded: chain A residue 1996 GLU Chi-restraints excluded: chain A residue 2010 ASP Chi-restraints excluded: chain A residue 2070 LEU Chi-restraints excluded: chain A residue 2091 MET Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2484 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2592 PHE Chi-restraints excluded: chain A residue 2716 ILE Chi-restraints excluded: chain A residue 2797 MET Chi-restraints excluded: chain A residue 2869 THR Chi-restraints excluded: chain A residue 2944 ILE Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3436 PHE Chi-restraints excluded: chain A residue 3907 VAL Chi-restraints excluded: chain A residue 4076 LEU Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 464 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 229 optimal weight: 0.0470 chunk 249 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 55 optimal weight: 0.0370 chunk 56 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 chunk 242 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2967 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.111211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.090165 restraints weight = 67591.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.092665 restraints weight = 38099.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.094306 restraints weight = 26128.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.095340 restraints weight = 20467.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.096077 restraints weight = 17540.171| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 21450 Z= 0.101 Angle : 0.543 11.810 29136 Z= 0.264 Chirality : 0.040 0.336 3375 Planarity : 0.003 0.048 3658 Dihedral : 6.031 146.537 2927 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.67 % Allowed : 18.26 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.17), residues: 2665 helix: 2.01 (0.14), residues: 1395 sheet: -0.16 (0.28), residues: 358 loop : -0.88 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1583 TYR 0.020 0.001 TYR C 372 PHE 0.038 0.001 PHE A1708 TRP 0.043 0.001 TRP A1656 HIS 0.012 0.001 HIS A2598 Details of bonding type rmsd covalent geometry : bond 0.00226 (21450) covalent geometry : angle 0.54293 (29136) hydrogen bonds : bond 0.03078 ( 1152) hydrogen bonds : angle 3.85304 ( 3369) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5330 Ramachandran restraints generated. 2665 Oldfield, 0 Emsley, 2665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5330 Ramachandran restraints generated. 2665 Oldfield, 0 Emsley, 2665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.6943 (ppp) cc_final: 0.6142 (ppp) REVERT: A 1627 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8721 (mm) REVERT: A 1704 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6736 (mp0) REVERT: A 1996 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8323 (tp30) REVERT: A 2198 ASN cc_start: 0.8573 (t0) cc_final: 0.8125 (t0) REVERT: A 2401 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6597 (mt-10) REVERT: A 2458 LEU cc_start: 0.8835 (mt) cc_final: 0.8436 (pp) REVERT: A 2523 TRP cc_start: 0.7258 (t-100) cc_final: 0.6847 (t-100) REVERT: A 2559 LEU cc_start: 0.8823 (mm) cc_final: 0.8570 (mt) REVERT: A 2797 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8359 (mpp) REVERT: A 2818 ASP cc_start: 0.7565 (t70) cc_final: 0.7239 (t70) REVERT: A 2890 THR cc_start: 0.8713 (m) cc_final: 0.8344 (p) REVERT: A 2968 ILE cc_start: 0.9441 (tp) cc_final: 0.9157 (mt) REVERT: A 2980 MET cc_start: 0.6981 (mmp) cc_final: 0.6602 (ttp) REVERT: A 3466 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.9130 (tp) REVERT: A 3483 ASP cc_start: 0.7636 (p0) cc_final: 0.7097 (t0) REVERT: A 3485 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8287 (tm-30) REVERT: A 3631 MET cc_start: 0.8541 (tmm) cc_final: 0.8241 (tmm) REVERT: A 3785 TYR cc_start: 0.6759 (m-10) cc_final: 0.6056 (m-10) REVERT: A 3873 MET cc_start: 0.6634 (ptt) cc_final: 0.6038 (ptt) REVERT: C 210 ASN cc_start: 0.7916 (t0) cc_final: 0.7416 (t0) REVERT: C 230 GLN cc_start: 0.6607 (tp-100) cc_final: 0.6222 (mt0) REVERT: C 316 ASP cc_start: 0.7606 (p0) cc_final: 0.7073 (p0) outliers start: 37 outliers final: 24 residues processed: 232 average time/residue: 0.1292 time to fit residues: 50.2984 Evaluate side-chains 227 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1704 GLU Chi-restraints excluded: chain A residue 1718 CYS Chi-restraints excluded: chain A residue 1749 ILE Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 1963 MET Chi-restraints excluded: chain A residue 1996 GLU Chi-restraints excluded: chain A residue 2010 ASP Chi-restraints excluded: chain A residue 2070 LEU Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2091 MET Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2592 PHE Chi-restraints excluded: chain A residue 2716 ILE Chi-restraints excluded: chain A residue 2739 VAL Chi-restraints excluded: chain A residue 2797 MET Chi-restraints excluded: chain A residue 2869 THR Chi-restraints excluded: chain A residue 2944 ILE Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3436 PHE Chi-restraints excluded: chain A residue 3466 ILE Chi-restraints excluded: chain A residue 3485 GLU Chi-restraints excluded: chain A residue 4076 LEU Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 464 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 173 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 243 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 230 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 253 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 191 optimal weight: 0.8980 chunk 24 optimal weight: 0.1980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3624 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.110698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.090285 restraints weight = 67719.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.092881 restraints weight = 40816.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.094539 restraints weight = 24436.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.094777 restraints weight = 20206.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.094735 restraints weight = 18010.649| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21450 Z= 0.112 Angle : 0.551 10.143 29136 Z= 0.268 Chirality : 0.041 0.321 3375 Planarity : 0.003 0.048 3658 Dihedral : 6.021 146.374 2927 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.71 % Allowed : 18.62 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.17), residues: 2665 helix: 1.98 (0.14), residues: 1396 sheet: -0.17 (0.28), residues: 358 loop : -0.84 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1833 TYR 0.028 0.001 TYR C 372 PHE 0.031 0.001 PHE A1708 TRP 0.040 0.001 TRP A1656 HIS 0.011 0.001 HIS A2598 Details of bonding type rmsd covalent geometry : bond 0.00256 (21450) covalent geometry : angle 0.55062 (29136) hydrogen bonds : bond 0.03135 ( 1152) hydrogen bonds : angle 3.87362 ( 3369) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5330 Ramachandran restraints generated. 2665 Oldfield, 0 Emsley, 2665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5330 Ramachandran restraints generated. 2665 Oldfield, 0 Emsley, 2665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.7008 (ppp) cc_final: 0.6196 (ppp) REVERT: A 1627 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8785 (mm) REVERT: A 1704 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6593 (mp0) REVERT: A 1996 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8369 (tp30) REVERT: A 2198 ASN cc_start: 0.8591 (t0) cc_final: 0.8142 (t0) REVERT: A 2401 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6597 (mt-10) REVERT: A 2458 LEU cc_start: 0.8869 (mt) cc_final: 0.8476 (pp) REVERT: A 2484 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.7746 (tt) REVERT: A 2523 TRP cc_start: 0.7218 (t-100) cc_final: 0.6793 (t-100) REVERT: A 2559 LEU cc_start: 0.8810 (mm) cc_final: 0.8552 (mt) REVERT: A 2797 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8363 (mpp) REVERT: A 2818 ASP cc_start: 0.7595 (t70) cc_final: 0.7261 (t70) REVERT: A 2890 THR cc_start: 0.8721 (m) cc_final: 0.8336 (p) REVERT: A 2968 ILE cc_start: 0.9522 (OUTLIER) cc_final: 0.9262 (mt) REVERT: A 2980 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6580 (ttp) REVERT: A 3466 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9178 (tp) REVERT: A 3483 ASP cc_start: 0.7755 (p0) cc_final: 0.7209 (t0) REVERT: A 3485 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8324 (tm-30) REVERT: A 3631 MET cc_start: 0.8542 (tmm) cc_final: 0.8290 (tmm) REVERT: A 3785 TYR cc_start: 0.6743 (m-10) cc_final: 0.6032 (m-10) REVERT: A 3873 MET cc_start: 0.6672 (ptt) cc_final: 0.6046 (ptt) REVERT: C 210 ASN cc_start: 0.8107 (t0) cc_final: 0.7624 (t0) REVERT: C 230 GLN cc_start: 0.6637 (tp-100) cc_final: 0.6309 (mt0) outliers start: 38 outliers final: 26 residues processed: 223 average time/residue: 0.1259 time to fit residues: 47.4566 Evaluate side-chains 231 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1704 GLU Chi-restraints excluded: chain A residue 1718 CYS Chi-restraints excluded: chain A residue 1749 ILE Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 1963 MET Chi-restraints excluded: chain A residue 1996 GLU Chi-restraints excluded: chain A residue 2010 ASP Chi-restraints excluded: chain A residue 2070 LEU Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2091 MET Chi-restraints excluded: chain A residue 2484 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2592 PHE Chi-restraints excluded: chain A residue 2716 ILE Chi-restraints excluded: chain A residue 2739 VAL Chi-restraints excluded: chain A residue 2797 MET Chi-restraints excluded: chain A residue 2869 THR Chi-restraints excluded: chain A residue 2944 ILE Chi-restraints excluded: chain A residue 2968 ILE Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3436 PHE Chi-restraints excluded: chain A residue 3466 ILE Chi-restraints excluded: chain A residue 3485 GLU Chi-restraints excluded: chain A residue 3907 VAL Chi-restraints excluded: chain A residue 4076 LEU Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 464 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 131 optimal weight: 6.9990 chunk 161 optimal weight: 0.9980 chunk 233 optimal weight: 0.0770 chunk 239 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 266 optimal weight: 0.3980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.110125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.090050 restraints weight = 67462.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.092584 restraints weight = 41035.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.094066 restraints weight = 24822.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.094399 restraints weight = 20853.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.094253 restraints weight = 18373.824| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 21450 Z= 0.107 Angle : 0.564 12.419 29136 Z= 0.271 Chirality : 0.041 0.318 3375 Planarity : 0.003 0.048 3658 Dihedral : 6.043 146.215 2927 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.58 % Allowed : 18.58 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.17), residues: 2665 helix: 1.95 (0.14), residues: 1398 sheet: -0.19 (0.28), residues: 357 loop : -0.80 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1833 TYR 0.017 0.001 TYR A2324 PHE 0.029 0.001 PHE A1952 TRP 0.026 0.001 TRP A1656 HIS 0.007 0.001 HIS A2598 Details of bonding type rmsd covalent geometry : bond 0.00243 (21450) covalent geometry : angle 0.56361 (29136) hydrogen bonds : bond 0.03102 ( 1152) hydrogen bonds : angle 3.88302 ( 3369) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5330 Ramachandran restraints generated. 2665 Oldfield, 0 Emsley, 2665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5330 Ramachandran restraints generated. 2665 Oldfield, 0 Emsley, 2665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 MET cc_start: 0.7007 (ppp) cc_final: 0.6199 (ppp) REVERT: A 1627 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8748 (mm) REVERT: A 1704 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6359 (mp0) REVERT: A 1718 CYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7743 (m) REVERT: A 2198 ASN cc_start: 0.8616 (t0) cc_final: 0.8188 (t0) REVERT: A 2401 GLU cc_start: 0.6826 (mt-10) cc_final: 0.6593 (mt-10) REVERT: A 2458 LEU cc_start: 0.8880 (mt) cc_final: 0.8512 (pp) REVERT: A 2484 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.7800 (tt) REVERT: A 2523 TRP cc_start: 0.7303 (t-100) cc_final: 0.6856 (t-100) REVERT: A 2559 LEU cc_start: 0.8833 (mm) cc_final: 0.8570 (mt) REVERT: A 2797 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8351 (mpp) REVERT: A 2818 ASP cc_start: 0.7600 (t70) cc_final: 0.7215 (t70) REVERT: A 2890 THR cc_start: 0.8733 (m) cc_final: 0.8331 (p) REVERT: A 2968 ILE cc_start: 0.9519 (OUTLIER) cc_final: 0.9259 (mt) REVERT: A 2980 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6667 (ttp) REVERT: A 3466 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9164 (tp) REVERT: A 3483 ASP cc_start: 0.7750 (p0) cc_final: 0.7089 (t0) REVERT: A 3485 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8276 (tm-30) REVERT: A 3631 MET cc_start: 0.8557 (tmm) cc_final: 0.8284 (tmm) REVERT: A 3708 PHE cc_start: 0.8024 (t80) cc_final: 0.7789 (t80) REVERT: A 3785 TYR cc_start: 0.6685 (m-10) cc_final: 0.6060 (m-10) REVERT: A 3873 MET cc_start: 0.6665 (ptt) cc_final: 0.6036 (ptt) REVERT: C 210 ASN cc_start: 0.8094 (t0) cc_final: 0.7628 (t0) REVERT: C 230 GLN cc_start: 0.6595 (tp-100) cc_final: 0.6299 (mt0) outliers start: 35 outliers final: 23 residues processed: 222 average time/residue: 0.1214 time to fit residues: 45.7504 Evaluate side-chains 230 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1704 GLU Chi-restraints excluded: chain A residue 1718 CYS Chi-restraints excluded: chain A residue 1749 ILE Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1963 MET Chi-restraints excluded: chain A residue 2010 ASP Chi-restraints excluded: chain A residue 2070 LEU Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2091 MET Chi-restraints excluded: chain A residue 2484 LEU Chi-restraints excluded: chain A residue 2502 VAL Chi-restraints excluded: chain A residue 2518 THR Chi-restraints excluded: chain A residue 2592 PHE Chi-restraints excluded: chain A residue 2716 ILE Chi-restraints excluded: chain A residue 2739 VAL Chi-restraints excluded: chain A residue 2797 MET Chi-restraints excluded: chain A residue 2869 THR Chi-restraints excluded: chain A residue 2944 ILE Chi-restraints excluded: chain A residue 2968 ILE Chi-restraints excluded: chain A residue 2980 MET Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3436 PHE Chi-restraints excluded: chain A residue 3466 ILE Chi-restraints excluded: chain A residue 3485 GLU Chi-restraints excluded: chain A residue 3907 VAL Chi-restraints excluded: chain A residue 4076 LEU Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 464 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 251 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 202 optimal weight: 0.0060 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 0.0470 chunk 206 optimal weight: 4.9990 chunk 213 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 overall best weight: 0.5094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.111312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.090411 restraints weight = 67810.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.092897 restraints weight = 38201.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.094533 restraints weight = 26141.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.095573 restraints weight = 20435.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.096313 restraints weight = 17471.280| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 21450 Z= 0.105 Angle : 0.569 16.447 29136 Z= 0.273 Chirality : 0.040 0.316 3375 Planarity : 0.003 0.048 3658 Dihedral : 5.998 145.836 2927 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.62 % Allowed : 18.71 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.17), residues: 2665 helix: 1.94 (0.14), residues: 1397 sheet: -0.15 (0.28), residues: 358 loop : -0.79 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1583 TYR 0.038 0.001 TYR A2234 PHE 0.035 0.001 PHE A1708 TRP 0.024 0.001 TRP C 324 HIS 0.005 0.001 HIS A2598 Details of bonding type rmsd covalent geometry : bond 0.00238 (21450) covalent geometry : angle 0.56908 (29136) hydrogen bonds : bond 0.03105 ( 1152) hydrogen bonds : angle 3.87512 ( 3369) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3361.32 seconds wall clock time: 59 minutes 13.85 seconds (3553.85 seconds total)