Starting phenix.real_space_refine on Fri Jun 20 17:16:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dh5_46856/06_2025/9dh5_46856.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dh5_46856/06_2025/9dh5_46856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dh5_46856/06_2025/9dh5_46856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dh5_46856/06_2025/9dh5_46856.map" model { file = "/net/cci-nas-00/data/ceres_data/9dh5_46856/06_2025/9dh5_46856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dh5_46856/06_2025/9dh5_46856.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.068 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 2 5.21 5 S 117 5.16 5 C 15057 2.51 5 N 4087 2.21 5 O 4417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23689 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 23575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2935, 23575 Classifications: {'peptide': 2935} Link IDs: {'PTRANS': 131, 'TRANS': 2803} Chain breaks: 3 Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 114 Unusual residues: {' MG': 2, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 14.61, per 1000 atoms: 0.62 Number of scatterers: 23689 At special positions: 0 Unit cell: (141.191, 121.516, 208.314, 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 117 16.00 P 9 15.00 Mg 2 11.99 O 4417 8.00 N 4087 7.00 C 15057 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: 5.89 Conformation dependent library (CDL) restraints added in 2.9 seconds 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5584 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 20 sheets defined 64.5% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.92 Creating SS restraints... Processing helix chain 'A' and resid 1457 through 1471 Processing helix chain 'A' and resid 1489 through 1509 removed outlier: 3.545A pdb=" N LYS A1508 " --> pdb=" O VAL A1504 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A1509 " --> pdb=" O SER A1505 " (cutoff:3.500A) Processing helix chain 'A' and resid 1510 through 1514 removed outlier: 4.151A pdb=" N LYS A1514 " --> pdb=" O PRO A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1554 removed outlier: 3.914A pdb=" N VAL A1536 " --> pdb=" O ALA A1532 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A1546 " --> pdb=" O ARG A1542 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A1554 " --> pdb=" O ILE A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1561 removed outlier: 4.068A pdb=" N HIS A1559 " --> pdb=" O ALA A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1585 Processing helix chain 'A' and resid 1587 through 1593 Processing helix chain 'A' and resid 1596 through 1614 Processing helix chain 'A' and resid 1615 through 1626 removed outlier: 3.953A pdb=" N SER A1624 " --> pdb=" O GLU A1620 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER A1625 " --> pdb=" O ARG A1621 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A1626 " --> pdb=" O GLU A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1632 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1646 through 1652 removed outlier: 3.585A pdb=" N GLN A1651 " --> pdb=" O ALA A1648 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1658 removed outlier: 3.641A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1728 removed outlier: 3.592A pdb=" N TRP A1701 " --> pdb=" O LYS A1697 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A1727 " --> pdb=" O GLU A1723 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 removed outlier: 3.515A pdb=" N TYR A1745 " --> pdb=" O TRP A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1769 Processing helix chain 'A' and resid 1770 through 1772 No H-bonds generated for 'chain 'A' and resid 1770 through 1772' Processing helix chain 'A' and resid 1777 through 1797 Processing helix chain 'A' and resid 1801 through 1828 Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1852 through 1855 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 Processing helix chain 'A' and resid 1937 through 1952 Processing helix chain 'A' and resid 1960 through 1963 Processing helix chain 'A' and resid 1964 through 1987 removed outlier: 3.894A pdb=" N GLN A1973 " --> pdb=" O SER A1969 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN A1974 " --> pdb=" O ALA A1970 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS A1985 " --> pdb=" O ALA A1981 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A1986 " --> pdb=" O LEU A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2034 Processing helix chain 'A' and resid 2045 through 2058 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix removed outlier: 3.506A pdb=" N GLU A2078 " --> pdb=" O LYS A2074 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2117 removed outlier: 3.680A pdb=" N GLU A2117 " --> pdb=" O ARG A2113 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2130 Processing helix chain 'A' and resid 2132 through 2146 Processing helix chain 'A' and resid 2147 through 2149 No H-bonds generated for 'chain 'A' and resid 2147 through 2149' Processing helix chain 'A' and resid 2150 through 2152 No H-bonds generated for 'chain 'A' and resid 2150 through 2152' Processing helix chain 'A' and resid 2153 through 2165 Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2215 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2255 through 2259 removed outlier: 3.875A pdb=" N ILE A2259 " --> pdb=" O PRO A2256 " (cutoff:3.500A) Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2293 through 2297 removed outlier: 3.521A pdb=" N GLN A2296 " --> pdb=" O GLY A2293 " (cutoff:3.500A) Processing helix chain 'A' and resid 2308 through 2313 Processing helix chain 'A' and resid 2315 through 2320 Processing helix chain 'A' and resid 2352 through 2358 removed outlier: 3.630A pdb=" N ARG A2358 " --> pdb=" O ALA A2354 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2385 Processing helix chain 'A' and resid 2411 through 2424 Processing helix chain 'A' and resid 2425 through 2428 removed outlier: 3.669A pdb=" N THR A2428 " --> pdb=" O PRO A2425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2425 through 2428' Processing helix chain 'A' and resid 2431 through 2443 removed outlier: 3.782A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A2443 " --> pdb=" O HIS A2439 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 Processing helix chain 'A' and resid 2482 through 2504 removed outlier: 3.998A pdb=" N ARG A2492 " --> pdb=" O ARG A2488 " (cutoff:3.500A) Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2549 through 2552 Processing helix chain 'A' and resid 2558 through 2562 removed outlier: 3.950A pdb=" N VAL A2562 " --> pdb=" O THR A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2587 Processing helix chain 'A' and resid 2600 through 2611 removed outlier: 3.811A pdb=" N ALA A2611 " --> pdb=" O SER A2607 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.209A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2689 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2740 through 2756 Processing helix chain 'A' and resid 2757 through 2758 No H-bonds generated for 'chain 'A' and resid 2757 through 2758' Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 5.062A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2784 Processing helix chain 'A' and resid 2795 through 2809 removed outlier: 3.779A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 Processing helix chain 'A' and resid 2839 through 2858 removed outlier: 3.738A pdb=" N ASP A2851 " --> pdb=" O ASP A2847 " (cutoff:3.500A) Processing helix chain 'A' and resid 2862 through 2868 Processing helix chain 'A' and resid 2885 through 2904 removed outlier: 3.574A pdb=" N VAL A2899 " --> pdb=" O ALA A2895 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A2902 " --> pdb=" O LYS A2898 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2927 removed outlier: 3.503A pdb=" N ILE A2925 " --> pdb=" O ARG A2921 " (cutoff:3.500A) Processing helix chain 'A' and resid 2942 through 2954 Processing helix chain 'A' and resid 2968 through 2985 Processing helix chain 'A' and resid 2997 through 2999 No H-bonds generated for 'chain 'A' and resid 2997 through 2999' Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 4.299A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A3006 " --> pdb=" O SER A3002 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A3007 " --> pdb=" O GLY A3003 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A3010 " --> pdb=" O GLU A3006 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A3013 " --> pdb=" O ASN A3009 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3040 removed outlier: 3.537A pdb=" N GLU A3040 " --> pdb=" O GLY A3036 " (cutoff:3.500A) Processing helix chain 'A' and resid 3046 through 3061 Processing helix chain 'A' and resid 3071 through 3082 removed outlier: 4.228A pdb=" N ALA A3080 " --> pdb=" O LYS A3076 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A3081 " --> pdb=" O ASP A3077 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3088 Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3164 removed outlier: 3.561A pdb=" N LEU A3154 " --> pdb=" O VAL A3150 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS A3155 " --> pdb=" O HIS A3151 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 3241 removed outlier: 3.622A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3450 through 3482 Processing helix chain 'A' and resid 3482 through 3495 Processing helix chain 'A' and resid 3495 through 3517 removed outlier: 4.939A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLY A3505 " --> pdb=" O SER A3501 " (cutoff:3.500A) Processing helix chain 'A' and resid 3518 through 3520 No H-bonds generated for 'chain 'A' and resid 3518 through 3520' Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3583 Processing helix chain 'A' and resid 3594 through 3604 Processing helix chain 'A' and resid 3618 through 3630 Processing helix chain 'A' and resid 3637 through 3641 Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3650 Processing helix chain 'A' and resid 3689 through 3695 removed outlier: 3.609A pdb=" N ARG A3695 " --> pdb=" O ASP A3691 " (cutoff:3.500A) Processing helix chain 'A' and resid 3704 through 3721 Processing helix chain 'A' and resid 3721 through 3756 Processing helix chain 'A' and resid 3763 through 3799 removed outlier: 3.604A pdb=" N ILE A3767 " --> pdb=" O ASP A3763 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A3790 " --> pdb=" O GLU A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3801 through 3817 Processing helix chain 'A' and resid 3818 through 3821 Processing helix chain 'A' and resid 3828 through 3842 removed outlier: 3.612A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3847 removed outlier: 3.654A pdb=" N LYS A3847 " --> pdb=" O PRO A3844 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 removed outlier: 3.591A pdb=" N PHE A3864 " --> pdb=" O THR A3860 " (cutoff:3.500A) Processing helix chain 'A' and resid 3874 through 3875 No H-bonds generated for 'chain 'A' and resid 3874 through 3875' Processing helix chain 'A' and resid 3876 through 3878 No H-bonds generated for 'chain 'A' and resid 3876 through 3878' Processing helix chain 'A' and resid 3879 through 3895 Processing helix chain 'A' and resid 3901 through 3909 Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 Processing helix chain 'A' and resid 3965 through 3969 Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4014 Processing helix chain 'A' and resid 4018 through 4023 Processing helix chain 'A' and resid 4026 through 4034 Processing helix chain 'A' and resid 4051 through 4063 Processing helix chain 'A' and resid 4073 through 4088 Processing helix chain 'A' and resid 4098 through 4101 Processing helix chain 'A' and resid 4102 through 4115 removed outlier: 3.631A pdb=" N GLN A4108 " --> pdb=" O GLY A4104 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A4115 " --> pdb=" O LYS A4111 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4142 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.590A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4175 through 4194 removed outlier: 3.770A pdb=" N LEU A4194 " --> pdb=" O ILE A4190 " (cutoff:3.500A) Processing helix chain 'A' and resid 4196 through 4201 removed outlier: 3.880A pdb=" N TRP A4201 " --> pdb=" O ALA A4197 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4227 Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 removed outlier: 3.522A pdb=" N PHE A4305 " --> pdb=" O ARG A4301 " (cutoff:3.500A) Processing helix chain 'A' and resid 4317 through 4322 Processing helix chain 'A' and resid 4324 through 4327 Processing helix chain 'A' and resid 4328 through 4347 Processing helix chain 'A' and resid 4375 through 4391 Processing helix chain 'A' and resid 4401 through 4406 removed outlier: 4.213A pdb=" N LYS A4406 " --> pdb=" O VAL A4402 " (cutoff:3.500A) Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4474 through 4498 removed outlier: 3.580A pdb=" N SER A4480 " --> pdb=" O ILE A4476 " (cutoff:3.500A) Processing helix chain 'A' and resid 4500 through 4505 removed outlier: 3.524A pdb=" N LYS A4505 " --> pdb=" O LYS A4502 " (cutoff:3.500A) Processing helix chain 'A' and resid 4516 through 4532 removed outlier: 3.567A pdb=" N TYR A4520 " --> pdb=" O VAL A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4535 through 4537 No H-bonds generated for 'chain 'A' and resid 4535 through 4537' Processing helix chain 'A' and resid 4631 through 4638 removed outlier: 3.577A pdb=" N PHE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1477 through 1480 removed outlier: 3.884A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1663 through 1666 removed outlier: 7.566A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.381A pdb=" N PHE A1686 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1842 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 removed outlier: 6.536A pdb=" N GLY A1901 " --> pdb=" O ARG A2037 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU A2039 " --> pdb=" O GLY A1901 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER A1903 " --> pdb=" O LEU A2039 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1931 removed outlier: 6.323A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASP A1958 " --> pdb=" O LEU A1928 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE A1930 " --> pdb=" O ASP A1958 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA7, first strand: chain 'A' and resid 2249 through 2254 Processing sheet with id=AA8, first strand: chain 'A' and resid 2266 through 2268 Processing sheet with id=AA9, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AB1, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 6.142A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2644 removed outlier: 4.044A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2873 through 2874 Processing sheet with id=AB5, first strand: chain 'A' and resid 2957 through 2959 removed outlier: 6.290A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU A2935 " --> pdb=" O MET A3068 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N HIS A2932 " --> pdb=" O VAL A3090 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ASN A3092 " --> pdb=" O HIS A2932 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A2934 " --> pdb=" O ASN A3092 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE A3094 " --> pdb=" O LEU A2934 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ILE A2936 " --> pdb=" O PHE A3094 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3610 through 3613 Processing sheet with id=AB7, first strand: chain 'A' and resid 3653 through 3656 Processing sheet with id=AB8, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.246A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A4042 " --> pdb=" O PHE A4145 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N PHE A4147 " --> pdb=" O LEU A4042 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N CYS A4044 " --> pdb=" O PHE A4147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4283 through 4285 Processing sheet with id=AC1, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.129A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A4587 " --> pdb=" O THR A4546 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4564 through 4571 removed outlier: 7.191A pdb=" N ILE A4581 " --> pdb=" O GLY A4567 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N THR A4569 " --> pdb=" O ASN A4579 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N ASN A4579 " --> pdb=" O THR A4569 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N ASN A4571 " --> pdb=" O LEU A4577 " (cutoff:3.500A) removed outlier: 10.187A pdb=" N LEU A4577 " --> pdb=" O ASN A4571 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL A4609 " --> pdb=" O ILE A4619 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N THR A4621 " --> pdb=" O LEU A4607 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU A4607 " --> pdb=" O THR A4621 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP A4623 " --> pdb=" O VAL A4605 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A4605 " --> pdb=" O ASP A4623 " (cutoff:3.500A) 1414 hydrogen bonds defined for protein. 4095 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: 17.91 Time building geometry restraints manager: 7.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7812 1.34 - 1.46: 4917 1.46 - 1.58: 11256 1.58 - 1.69: 14 1.69 - 1.81: 196 Bond restraints: 24195 Sorted by residual: bond pdb=" C4 ADP A4704 " pdb=" C5 ADP A4704 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C4 ADP A4701 " pdb=" C5 ADP A4701 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP A4703 " pdb=" C5 ADP A4703 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C5 ADP A4703 " pdb=" C6 ADP A4703 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C5 ADP A4704 " pdb=" C6 ADP A4704 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.68e+01 ... (remaining 24190 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 32449 2.45 - 4.90: 321 4.90 - 7.35: 28 7.35 - 9.80: 10 9.80 - 12.25: 7 Bond angle restraints: 32815 Sorted by residual: angle pdb=" PB ATP A4702 " pdb=" O3B ATP A4702 " pdb=" PG ATP A4702 " ideal model delta sigma weight residual 139.87 134.09 5.78 1.00e+00 1.00e+00 3.34e+01 angle pdb=" PA ADP A4704 " pdb=" O3A ADP A4704 " pdb=" PB ADP A4704 " ideal model delta sigma weight residual 120.50 132.75 -12.25 3.00e+00 1.11e-01 1.67e+01 angle pdb=" PA ADP A4703 " pdb=" O3A ADP A4703 " pdb=" PB ADP A4703 " ideal model delta sigma weight residual 120.50 132.71 -12.21 3.00e+00 1.11e-01 1.66e+01 angle pdb=" PA ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PB ADP A4701 " ideal model delta sigma weight residual 120.50 131.51 -11.01 3.00e+00 1.11e-01 1.35e+01 angle pdb=" C1' ADP A4701 " pdb=" C2' ADP A4701 " pdb=" C3' ADP A4701 " ideal model delta sigma weight residual 111.00 100.17 10.83 3.00e+00 1.11e-01 1.30e+01 ... (remaining 32810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.16: 14292 31.16 - 62.33: 317 62.33 - 93.49: 67 93.49 - 124.66: 2 124.66 - 155.82: 2 Dihedral angle restraints: 14680 sinusoidal: 6083 harmonic: 8597 Sorted by residual: dihedral pdb=" O1B ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PB ADP A4701 " pdb=" PA ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 95.82 -155.82 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" C5' ADP A4703 " pdb=" O5' ADP A4703 " pdb=" PA ADP A4703 " pdb=" O2A ADP A4703 " ideal model delta sinusoidal sigma weight residual 300.00 174.35 125.66 1 2.00e+01 2.50e-03 3.80e+01 dihedral pdb=" C5' ADP A4701 " pdb=" O5' ADP A4701 " pdb=" PA ADP A4701 " pdb=" O2A ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 50.61 -110.60 1 2.00e+01 2.50e-03 3.24e+01 ... (remaining 14677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2751 0.042 - 0.083: 712 0.083 - 0.125: 202 0.125 - 0.167: 19 0.167 - 0.208: 6 Chirality restraints: 3690 Sorted by residual: chirality pdb=" CA VAL A2345 " pdb=" N VAL A2345 " pdb=" C VAL A2345 " pdb=" CB VAL A2345 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA LEU A2668 " pdb=" N LEU A2668 " pdb=" C LEU A2668 " pdb=" CB LEU A2668 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA ILE A2016 " pdb=" N ILE A2016 " pdb=" C ILE A2016 " pdb=" CB ILE A2016 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.81e-01 ... (remaining 3687 not shown) Planarity restraints: 4203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A4195 " -0.448 9.50e-02 1.11e+02 2.01e-01 2.47e+01 pdb=" NE ARG A4195 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A4195 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A4195 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A4195 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1537 " -0.012 2.00e-02 2.50e+03 1.36e-02 4.63e+00 pdb=" CG TRP A1537 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A1537 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A1537 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1537 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A1537 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1537 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1537 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1537 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A1537 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A2858 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.48e+00 pdb=" N PRO A2859 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A2859 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A2859 " -0.026 5.00e-02 4.00e+02 ... (remaining 4200 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 31 2.38 - 3.01: 12559 3.01 - 3.64: 37771 3.64 - 4.27: 58393 4.27 - 4.90: 93663 Nonbonded interactions: 202417 Sorted by model distance: nonbonded pdb=" OE2 GLU A2344 " pdb="MG MG A4706 " model vdw 1.745 2.170 nonbonded pdb=" OG SER A2231 " pdb="MG MG A4706 " model vdw 1.959 2.170 nonbonded pdb=" O2G ATP A4702 " pdb="MG MG A4706 " model vdw 2.072 2.170 nonbonded pdb=" OG1 THR A1913 " pdb="MG MG A4705 " model vdw 2.096 2.170 nonbonded pdb=" O3B ADP A4701 " pdb="MG MG A4705 " model vdw 2.103 2.170 ... (remaining 202412 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 65.630 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.110 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:15.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 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 : 0.004 0.110 24195 Z= 0.211 Angle : 0.621 12.255 32815 Z= 0.328 Chirality : 0.041 0.208 3690 Planarity : 0.005 0.201 4203 Dihedral : 14.205 155.821 9096 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.54 % Favored : 98.39 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.15), residues: 2927 helix: 1.48 (0.12), residues: 1703 sheet: 0.08 (0.34), residues: 235 loop : 0.77 (0.21), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1537 HIS 0.015 0.001 HIS A1810 PHE 0.017 0.002 PHE A1960 TYR 0.018 0.002 TYR A2472 ARG 0.009 0.001 ARG A2492 Details of bonding type rmsd hydrogen bonds : bond 0.20814 ( 1414) hydrogen bonds : angle 6.46867 ( 4095) covalent geometry : bond 0.00386 (24195) covalent geometry : angle 0.62070 (32815) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 569 time to evaluate : 2.743 Fit side-chains REVERT: A 2189 MET cc_start: 0.8500 (mtp) cc_final: 0.8263 (mtp) REVERT: A 2232 MET cc_start: 0.8641 (mmt) cc_final: 0.8380 (mmm) REVERT: A 3068 MET cc_start: 0.8450 (ptm) cc_final: 0.8174 (ptp) outliers start: 0 outliers final: 2 residues processed: 569 average time/residue: 1.7477 time to fit residues: 1115.0100 Evaluate side-chains 333 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 331 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 2970 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 247 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 229 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 139 optimal weight: 0.0270 chunk 170 optimal weight: 0.9990 chunk 266 optimal weight: 5.9990 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1471 ASN A1670 ASN A1736 ASN A1855 GLN A1881 GLN A1931 ASN A1973 GLN A2047 GLN A2051 GLN A2187 GLN A2476 HIS A2485 GLN A2491 GLN A2713 ASN A2849 ASN A3087 ASN A3092 ASN A3584 ASN A3650 ASN ** A3754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3800 GLN A4012 ASN A4063 ASN A4108 GLN A4307 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.156508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.116511 restraints weight = 25122.855| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.68 r_work: 0.3129 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24195 Z= 0.144 Angle : 0.564 9.361 32815 Z= 0.287 Chirality : 0.041 0.148 3690 Planarity : 0.005 0.074 4203 Dihedral : 7.790 169.821 3264 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.92 % Allowed : 10.56 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.16), residues: 2927 helix: 1.92 (0.12), residues: 1726 sheet: -0.04 (0.34), residues: 236 loop : 0.72 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2234 HIS 0.013 0.001 HIS A1810 PHE 0.022 0.002 PHE A2912 TYR 0.020 0.002 TYR A2748 ARG 0.007 0.001 ARG A2729 Details of bonding type rmsd hydrogen bonds : bond 0.05425 ( 1414) hydrogen bonds : angle 4.53236 ( 4095) covalent geometry : bond 0.00313 (24195) covalent geometry : angle 0.56415 (32815) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 362 time to evaluate : 2.816 Fit side-chains REVERT: A 1471 ASN cc_start: 0.7634 (m-40) cc_final: 0.7385 (m110) REVERT: A 1473 TYR cc_start: 0.7365 (t80) cc_final: 0.7115 (t80) REVERT: A 1892 MET cc_start: 0.8901 (mmp) cc_final: 0.8678 (mmp) REVERT: A 2060 ARG cc_start: 0.7894 (mtm110) cc_final: 0.7277 (ptt90) REVERT: A 2113 ARG cc_start: 0.6646 (mtm-85) cc_final: 0.6247 (mtm-85) REVERT: A 2175 MET cc_start: 0.7629 (mtp) cc_final: 0.7348 (mtt) REVERT: A 2188 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7863 (pt0) REVERT: A 2232 MET cc_start: 0.9147 (mmt) cc_final: 0.8943 (mmm) REVERT: A 2438 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7510 (mm-30) REVERT: A 2801 ARG cc_start: 0.8288 (mtt90) cc_final: 0.8061 (ttp-170) REVERT: A 2844 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7367 (ttm-80) REVERT: A 2898 LYS cc_start: 0.8573 (tttt) cc_final: 0.8144 (tttm) REVERT: A 2970 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7371 (pt0) REVERT: A 3006 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7018 (tm-30) REVERT: A 3068 MET cc_start: 0.9158 (ptm) cc_final: 0.8874 (ptp) REVERT: A 3164 ARG cc_start: 0.7376 (mtp180) cc_final: 0.7134 (ttp-110) REVERT: A 3551 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7683 (mm-30) REVERT: A 3747 LYS cc_start: 0.7154 (mtpp) cc_final: 0.6722 (tttt) REVERT: A 3902 ASP cc_start: 0.7731 (m-30) cc_final: 0.7476 (m-30) REVERT: A 3985 GLN cc_start: 0.7795 (tt0) cc_final: 0.7494 (tt0) REVERT: A 4081 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.8058 (t0) REVERT: A 4276 ARG cc_start: 0.7216 (mmp80) cc_final: 0.6964 (mtm-85) REVERT: A 4343 MET cc_start: 0.8677 (mtp) cc_final: 0.8422 (mtp) REVERT: A 4377 MET cc_start: 0.6693 (mtp) cc_final: 0.6388 (mtp) REVERT: A 4419 MET cc_start: 0.6942 (ptp) cc_final: 0.6454 (pmm) REVERT: A 4453 ASN cc_start: 0.7195 (m110) cc_final: 0.6851 (t0) REVERT: A 4481 ASP cc_start: 0.7800 (t0) cc_final: 0.7220 (t0) REVERT: A 4574 LYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6835 (ttmm) REVERT: A 4583 THR cc_start: 0.8109 (m) cc_final: 0.7658 (p) REVERT: A 4589 GLN cc_start: 0.7720 (mt0) cc_final: 0.7343 (mt0) outliers start: 50 outliers final: 18 residues processed: 392 average time/residue: 1.6785 time to fit residues: 745.1721 Evaluate side-chains 328 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 305 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1465 GLN Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 2004 LYS Chi-restraints excluded: chain A residue 2074 LYS Chi-restraints excluded: chain A residue 2970 GLU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3082 SER Chi-restraints excluded: chain A residue 3192 SER Chi-restraints excluded: chain A residue 3545 THR Chi-restraints excluded: chain A residue 3551 GLU Chi-restraints excluded: chain A residue 3670 ASP Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3707 SER Chi-restraints excluded: chain A residue 4015 GLU Chi-restraints excluded: chain A residue 4081 ASP Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4137 ASN Chi-restraints excluded: chain A residue 4259 GLU Chi-restraints excluded: chain A residue 4424 LEU Chi-restraints excluded: chain A residue 4431 LEU Chi-restraints excluded: chain A residue 4456 VAL Chi-restraints excluded: chain A residue 4574 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 117 optimal weight: 0.9990 chunk 245 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 240 optimal weight: 1.9990 chunk 198 optimal weight: 0.0370 chunk 5 optimal weight: 4.9990 chunk 200 optimal weight: 0.0170 chunk 281 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1784 ASN A1931 ASN A1985 HIS A2187 GLN A2476 HIS A2485 GLN A2491 GLN A3063 HIS A3087 ASN A3523 GLN A3735 GLN A3799 GLN A3800 GLN A3826 GLN A3837 HIS A4063 ASN A4108 GLN A4335 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.156561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.116242 restraints weight = 25049.206| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.79 r_work: 0.3156 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24195 Z= 0.113 Angle : 0.490 6.571 32815 Z= 0.248 Chirality : 0.039 0.144 3690 Planarity : 0.004 0.074 4203 Dihedral : 7.525 171.029 3262 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.23 % Allowed : 11.76 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.16), residues: 2927 helix: 2.16 (0.12), residues: 1728 sheet: 0.17 (0.34), residues: 230 loop : 0.71 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.009 0.001 HIS A1810 PHE 0.018 0.001 PHE A2912 TYR 0.018 0.001 TYR A2748 ARG 0.008 0.000 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.04481 ( 1414) hydrogen bonds : angle 4.14944 ( 4095) covalent geometry : bond 0.00237 (24195) covalent geometry : angle 0.48994 (32815) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 341 time to evaluate : 2.700 Fit side-chains REVERT: A 1471 ASN cc_start: 0.7613 (m-40) cc_final: 0.7345 (m110) REVERT: A 1613 LYS cc_start: 0.8232 (mmtm) cc_final: 0.7914 (mmpt) REVERT: A 1892 MET cc_start: 0.8851 (mmp) cc_final: 0.8568 (mmp) REVERT: A 2012 MET cc_start: 0.8807 (ppp) cc_final: 0.8274 (tmt) REVERT: A 2074 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7923 (mtmt) REVERT: A 2106 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7047 (mt-10) REVERT: A 2188 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7904 (pt0) REVERT: A 2232 MET cc_start: 0.9175 (mmt) cc_final: 0.8836 (mmm) REVERT: A 2438 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7488 (mm-30) REVERT: A 2801 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.8041 (ttp-170) REVERT: A 2844 ARG cc_start: 0.8016 (ttp80) cc_final: 0.7178 (mtt90) REVERT: A 2863 ARG cc_start: 0.7629 (mtp85) cc_final: 0.7262 (tmt90) REVERT: A 2867 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7834 (mtp) REVERT: A 2898 LYS cc_start: 0.8534 (tttt) cc_final: 0.8085 (tttm) REVERT: A 3008 MET cc_start: 0.9043 (mmm) cc_final: 0.8787 (mmp) REVERT: A 3016 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7868 (pt0) REVERT: A 3022 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8227 (mp0) REVERT: A 3068 MET cc_start: 0.9221 (ptm) cc_final: 0.8984 (ptp) REVERT: A 3464 ASP cc_start: 0.5506 (t0) cc_final: 0.5297 (m-30) REVERT: A 3524 MET cc_start: 0.8800 (tpt) cc_final: 0.8568 (tpt) REVERT: A 3551 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7620 (mm-30) REVERT: A 3747 LYS cc_start: 0.6947 (mtpp) cc_final: 0.6591 (tppt) REVERT: A 3775 ARG cc_start: 0.7876 (ttm-80) cc_final: 0.7604 (ttp-110) REVERT: A 3893 LYS cc_start: 0.7551 (mtpt) cc_final: 0.7298 (mttp) REVERT: A 3985 GLN cc_start: 0.7705 (tt0) cc_final: 0.7334 (tt0) REVERT: A 3989 ARG cc_start: 0.7538 (mpt-90) cc_final: 0.7305 (mpt-90) REVERT: A 4331 LEU cc_start: 0.7676 (tp) cc_final: 0.7248 (mm) REVERT: A 4377 MET cc_start: 0.6836 (mtp) cc_final: 0.6522 (mtp) REVERT: A 4419 MET cc_start: 0.7252 (ptp) cc_final: 0.6560 (pmm) REVERT: A 4424 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7228 (tp) REVERT: A 4446 ASN cc_start: 0.8551 (m-40) cc_final: 0.8306 (m110) REVERT: A 4453 ASN cc_start: 0.7094 (m110) cc_final: 0.6776 (t0) REVERT: A 4481 ASP cc_start: 0.7746 (t0) cc_final: 0.7078 (t0) REVERT: A 4574 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6630 (ttmm) REVERT: A 4583 THR cc_start: 0.8200 (m) cc_final: 0.7738 (p) REVERT: A 4589 GLN cc_start: 0.7742 (mt0) cc_final: 0.7396 (mt0) outliers start: 58 outliers final: 17 residues processed: 373 average time/residue: 1.6439 time to fit residues: 696.5390 Evaluate side-chains 327 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 302 time to evaluate : 3.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1552 THR Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 2074 LYS Chi-restraints excluded: chain A residue 2084 SER Chi-restraints excluded: chain A residue 2106 GLU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2616 GLU Chi-restraints excluded: chain A residue 2801 ARG Chi-restraints excluded: chain A residue 2867 MET Chi-restraints excluded: chain A residue 3016 GLU Chi-restraints excluded: chain A residue 3082 SER Chi-restraints excluded: chain A residue 3121 ILE Chi-restraints excluded: chain A residue 3551 GLU Chi-restraints excluded: chain A residue 3670 ASP Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3750 LEU Chi-restraints excluded: chain A residue 4015 GLU Chi-restraints excluded: chain A residue 4137 ASN Chi-restraints excluded: chain A residue 4199 LEU Chi-restraints excluded: chain A residue 4259 GLU Chi-restraints excluded: chain A residue 4424 LEU Chi-restraints excluded: chain A residue 4431 LEU Chi-restraints excluded: chain A residue 4574 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 284 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 275 optimal weight: 0.8980 chunk 209 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2187 GLN A2476 HIS A2485 GLN ** A3181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3523 GLN ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3800 GLN A4063 ASN A4108 GLN A4397 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.151735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.111086 restraints weight = 25156.815| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.74 r_work: 0.3049 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24195 Z= 0.188 Angle : 0.560 10.294 32815 Z= 0.282 Chirality : 0.042 0.240 3690 Planarity : 0.005 0.075 4203 Dihedral : 7.062 141.780 3259 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.46 % Allowed : 12.87 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.16), residues: 2927 helix: 2.08 (0.12), residues: 1718 sheet: -0.10 (0.36), residues: 198 loop : 0.64 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A4222 HIS 0.012 0.001 HIS A1810 PHE 0.021 0.002 PHE A2912 TYR 0.025 0.002 TYR A2748 ARG 0.006 0.001 ARG A1543 Details of bonding type rmsd hydrogen bonds : bond 0.04952 ( 1414) hydrogen bonds : angle 4.23304 ( 4095) covalent geometry : bond 0.00448 (24195) covalent geometry : angle 0.56033 (32815) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 332 time to evaluate : 2.807 Fit side-chains REVERT: A 1471 ASN cc_start: 0.7761 (m-40) cc_final: 0.7534 (m110) REVERT: A 1613 LYS cc_start: 0.8329 (mmtm) cc_final: 0.8032 (mmpt) REVERT: A 2004 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7816 (mppt) REVERT: A 2012 MET cc_start: 0.8831 (ppp) cc_final: 0.8347 (tmt) REVERT: A 2074 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8054 (mtmt) REVERT: A 2106 GLU cc_start: 0.7493 (pt0) cc_final: 0.7106 (mt-10) REVERT: A 2113 ARG cc_start: 0.6699 (mtm-85) cc_final: 0.6294 (mtm-85) REVERT: A 2188 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7811 (pt0) REVERT: A 2232 MET cc_start: 0.9265 (mmt) cc_final: 0.9039 (mmm) REVERT: A 2438 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7566 (mm-30) REVERT: A 2485 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: A 2554 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7033 (tm-30) REVERT: A 2801 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8183 (ttp-170) REVERT: A 2863 ARG cc_start: 0.7643 (mtp85) cc_final: 0.7373 (mmm160) REVERT: A 2865 LYS cc_start: 0.8094 (mtpp) cc_final: 0.7464 (mttp) REVERT: A 2867 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7863 (mtp) REVERT: A 2898 LYS cc_start: 0.8648 (tttt) cc_final: 0.8158 (tttm) REVERT: A 3006 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8240 (mm-30) REVERT: A 3016 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7909 (pt0) REVERT: A 3464 ASP cc_start: 0.5907 (t0) cc_final: 0.5629 (m-30) REVERT: A 3551 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7723 (mm-30) REVERT: A 3747 LYS cc_start: 0.7289 (mtpp) cc_final: 0.6921 (tppt) REVERT: A 3775 ARG cc_start: 0.7969 (ttm-80) cc_final: 0.7709 (ttp-110) REVERT: A 3793 GLU cc_start: 0.6930 (tm-30) cc_final: 0.6594 (tt0) REVERT: A 3893 LYS cc_start: 0.7754 (mtpt) cc_final: 0.7194 (mttp) REVERT: A 3985 GLN cc_start: 0.7701 (tt0) cc_final: 0.7300 (tt0) REVERT: A 4012 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.8093 (m110) REVERT: A 4020 ILE cc_start: 0.8023 (mm) cc_final: 0.7409 (mp) REVERT: A 4081 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.8042 (t70) REVERT: A 4329 ARG cc_start: 0.7325 (ttm110) cc_final: 0.6547 (mtm-85) REVERT: A 4343 MET cc_start: 0.8809 (mtp) cc_final: 0.8592 (mtp) REVERT: A 4424 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7468 (tp) REVERT: A 4453 ASN cc_start: 0.7088 (m110) cc_final: 0.6745 (t0) REVERT: A 4481 ASP cc_start: 0.7906 (t0) cc_final: 0.7215 (t0) REVERT: A 4574 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6821 (ttmm) REVERT: A 4589 GLN cc_start: 0.7858 (mt0) cc_final: 0.7655 (mt0) outliers start: 64 outliers final: 25 residues processed: 368 average time/residue: 1.6704 time to fit residues: 693.9299 Evaluate side-chains 345 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 307 time to evaluate : 3.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1465 GLN Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1580 LYS Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 2004 LYS Chi-restraints excluded: chain A residue 2074 LYS Chi-restraints excluded: chain A residue 2084 SER Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2272 THR Chi-restraints excluded: chain A residue 2332 ARG Chi-restraints excluded: chain A residue 2460 SER Chi-restraints excluded: chain A residue 2485 GLN Chi-restraints excluded: chain A residue 2535 ILE Chi-restraints excluded: chain A residue 2554 GLN Chi-restraints excluded: chain A residue 2801 ARG Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2867 MET Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3016 GLU Chi-restraints excluded: chain A residue 3121 ILE Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3545 THR Chi-restraints excluded: chain A residue 3551 GLU Chi-restraints excluded: chain A residue 3670 ASP Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3750 LEU Chi-restraints excluded: chain A residue 4012 ASN Chi-restraints excluded: chain A residue 4015 GLU Chi-restraints excluded: chain A residue 4081 ASP Chi-restraints excluded: chain A residue 4137 ASN Chi-restraints excluded: chain A residue 4171 LYS Chi-restraints excluded: chain A residue 4259 GLU Chi-restraints excluded: chain A residue 4347 GLN Chi-restraints excluded: chain A residue 4424 LEU Chi-restraints excluded: chain A residue 4431 LEU Chi-restraints excluded: chain A residue 4574 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 166 optimal weight: 0.6980 chunk 206 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 171 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 177 optimal weight: 0.9990 chunk 263 optimal weight: 0.3980 chunk 127 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2187 GLN A2476 HIS A2485 GLN A3087 ASN ** A3181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3523 GLN ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3800 GLN A4063 ASN A4108 GLN A4488 GLN A4572 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.153451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.112930 restraints weight = 25008.997| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.71 r_work: 0.3097 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24195 Z= 0.121 Angle : 0.498 13.929 32815 Z= 0.250 Chirality : 0.039 0.152 3690 Planarity : 0.004 0.079 4203 Dihedral : 6.863 139.122 3259 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.31 % Allowed : 13.71 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.16), residues: 2927 helix: 2.19 (0.12), residues: 1730 sheet: 0.02 (0.33), residues: 230 loop : 0.68 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.007 0.001 HIS A1810 PHE 0.017 0.001 PHE A2912 TYR 0.020 0.001 TYR A2748 ARG 0.007 0.000 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 1414) hydrogen bonds : angle 4.07663 ( 4095) covalent geometry : bond 0.00264 (24195) covalent geometry : angle 0.49817 (32815) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 321 time to evaluate : 2.873 Fit side-chains REVERT: A 1471 ASN cc_start: 0.7778 (m-40) cc_final: 0.7549 (m110) REVERT: A 1573 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7707 (p) REVERT: A 1613 LYS cc_start: 0.8264 (mmtm) cc_final: 0.8017 (mmtm) REVERT: A 1892 MET cc_start: 0.8843 (mmp) cc_final: 0.8546 (mmp) REVERT: A 2000 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: A 2012 MET cc_start: 0.8880 (ppp) cc_final: 0.8435 (tmt) REVERT: A 2074 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7960 (mtmt) REVERT: A 2106 GLU cc_start: 0.7460 (pt0) cc_final: 0.7038 (mt-10) REVERT: A 2113 ARG cc_start: 0.6615 (mtm-85) cc_final: 0.6199 (mtm-85) REVERT: A 2188 GLU cc_start: 0.8456 (mt-10) cc_final: 0.7870 (pt0) REVERT: A 2232 MET cc_start: 0.9227 (mmt) cc_final: 0.9022 (mmm) REVERT: A 2438 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7395 (mm-30) REVERT: A 2476 HIS cc_start: 0.7207 (m-70) cc_final: 0.7005 (m170) REVERT: A 2554 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7108 (tm-30) REVERT: A 2615 MET cc_start: 0.8385 (mtt) cc_final: 0.8114 (mmm) REVERT: A 2801 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.8126 (ttp-170) REVERT: A 2844 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7161 (mtt90) REVERT: A 2867 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7829 (mtp) REVERT: A 2898 LYS cc_start: 0.8608 (tttt) cc_final: 0.8100 (tttm) REVERT: A 3006 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8244 (mm-30) REVERT: A 3016 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7881 (pt0) REVERT: A 3022 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8027 (mp0) REVERT: A 3068 MET cc_start: 0.9211 (ptm) cc_final: 0.8997 (ptp) REVERT: A 3464 ASP cc_start: 0.5811 (t0) cc_final: 0.5546 (m-30) REVERT: A 3551 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7649 (mm-30) REVERT: A 3747 LYS cc_start: 0.6960 (mtpp) cc_final: 0.6609 (tppt) REVERT: A 3793 GLU cc_start: 0.6880 (tm-30) cc_final: 0.6560 (tt0) REVERT: A 3902 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7514 (m-30) REVERT: A 3985 GLN cc_start: 0.7636 (tt0) cc_final: 0.7284 (tt0) REVERT: A 4020 ILE cc_start: 0.7947 (mm) cc_final: 0.7343 (mp) REVERT: A 4081 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.8008 (t70) REVERT: A 4329 ARG cc_start: 0.7214 (ttm110) cc_final: 0.6486 (mtm-85) REVERT: A 4343 MET cc_start: 0.8773 (mtp) cc_final: 0.8526 (mtp) REVERT: A 4424 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7387 (tp) REVERT: A 4453 ASN cc_start: 0.6997 (m110) cc_final: 0.6730 (t0) REVERT: A 4481 ASP cc_start: 0.7828 (t0) cc_final: 0.7123 (t0) REVERT: A 4574 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6775 (ttmm) REVERT: A 4583 THR cc_start: 0.8140 (m) cc_final: 0.7493 (p) REVERT: A 4589 GLN cc_start: 0.7840 (mt0) cc_final: 0.7624 (mt0) REVERT: A 4625 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7319 (mm-30) outliers start: 60 outliers final: 24 residues processed: 353 average time/residue: 1.8763 time to fit residues: 752.3439 Evaluate side-chains 346 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 308 time to evaluate : 2.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 2000 GLU Chi-restraints excluded: chain A residue 2074 LYS Chi-restraints excluded: chain A residue 2084 SER Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2332 ARG Chi-restraints excluded: chain A residue 2535 ILE Chi-restraints excluded: chain A residue 2554 GLN Chi-restraints excluded: chain A residue 2801 ARG Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2867 MET Chi-restraints excluded: chain A residue 2877 LEU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3016 GLU Chi-restraints excluded: chain A residue 3121 ILE Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3551 GLU Chi-restraints excluded: chain A residue 3597 THR Chi-restraints excluded: chain A residue 3670 ASP Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3707 SER Chi-restraints excluded: chain A residue 3750 LEU Chi-restraints excluded: chain A residue 3902 ASP Chi-restraints excluded: chain A residue 4015 GLU Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4081 ASP Chi-restraints excluded: chain A residue 4137 ASN Chi-restraints excluded: chain A residue 4199 LEU Chi-restraints excluded: chain A residue 4259 GLU Chi-restraints excluded: chain A residue 4424 LEU Chi-restraints excluded: chain A residue 4431 LEU Chi-restraints excluded: chain A residue 4465 SER Chi-restraints excluded: chain A residue 4574 LYS Chi-restraints excluded: chain A residue 4625 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 283 optimal weight: 5.9990 chunk 224 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 284 optimal weight: 10.0000 chunk 178 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 245 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 276 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2187 GLN A2485 GLN A3087 ASN ** A3181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3800 GLN A4063 ASN A4108 GLN A4488 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.152915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.112728 restraints weight = 24934.602| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.75 r_work: 0.3075 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24195 Z= 0.138 Angle : 0.512 15.902 32815 Z= 0.255 Chirality : 0.040 0.162 3690 Planarity : 0.004 0.083 4203 Dihedral : 6.838 135.776 3259 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.19 % Allowed : 14.71 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.16), residues: 2927 helix: 2.21 (0.12), residues: 1729 sheet: -0.11 (0.34), residues: 223 loop : 0.67 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.008 0.001 HIS A1810 PHE 0.018 0.002 PHE A1568 TYR 0.022 0.001 TYR A2748 ARG 0.006 0.000 ARG A2467 Details of bonding type rmsd hydrogen bonds : bond 0.04354 ( 1414) hydrogen bonds : angle 4.05765 ( 4095) covalent geometry : bond 0.00316 (24195) covalent geometry : angle 0.51170 (32815) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 324 time to evaluate : 5.107 Fit side-chains REVERT: A 1471 ASN cc_start: 0.7772 (m-40) cc_final: 0.7524 (m110) REVERT: A 1573 THR cc_start: 0.8026 (OUTLIER) cc_final: 0.7751 (p) REVERT: A 1613 LYS cc_start: 0.8288 (mmtm) cc_final: 0.8046 (mmtm) REVERT: A 1649 LYS cc_start: 0.8842 (mttp) cc_final: 0.8640 (mtpp) REVERT: A 1892 MET cc_start: 0.8847 (mmp) cc_final: 0.8547 (mmp) REVERT: A 2000 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: A 2012 MET cc_start: 0.8887 (ppp) cc_final: 0.8418 (tmt) REVERT: A 2060 ARG cc_start: 0.7978 (mtm110) cc_final: 0.7378 (ptt90) REVERT: A 2074 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8197 (mmmt) REVERT: A 2106 GLU cc_start: 0.7437 (pt0) cc_final: 0.7018 (mt-10) REVERT: A 2113 ARG cc_start: 0.6655 (mtm-85) cc_final: 0.6239 (mtm-85) REVERT: A 2188 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8031 (pt0) REVERT: A 2232 MET cc_start: 0.9237 (mmt) cc_final: 0.9010 (mmm) REVERT: A 2438 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7416 (mm-30) REVERT: A 2554 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7184 (tm-30) REVERT: A 2615 MET cc_start: 0.8467 (mtt) cc_final: 0.8153 (mtt) REVERT: A 2801 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.8179 (ttp-170) REVERT: A 2867 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7824 (mtp) REVERT: A 2898 LYS cc_start: 0.8640 (tttt) cc_final: 0.8139 (tttm) REVERT: A 2968 THR cc_start: 0.8848 (p) cc_final: 0.8471 (t) REVERT: A 3006 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8269 (mm-30) REVERT: A 3016 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7903 (pt0) REVERT: A 3068 MET cc_start: 0.9213 (ptm) cc_final: 0.9009 (ptp) REVERT: A 3464 ASP cc_start: 0.5909 (t0) cc_final: 0.5623 (m-30) REVERT: A 3524 MET cc_start: 0.8819 (tpt) cc_final: 0.8386 (mmm) REVERT: A 3551 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7732 (mm-30) REVERT: A 3746 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6847 (tp30) REVERT: A 3747 LYS cc_start: 0.6932 (mtpp) cc_final: 0.6608 (tppt) REVERT: A 3775 ARG cc_start: 0.7863 (ttm-80) cc_final: 0.7635 (ttp-110) REVERT: A 3793 GLU cc_start: 0.6904 (tm-30) cc_final: 0.6599 (tt0) REVERT: A 3902 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7517 (m-30) REVERT: A 3985 GLN cc_start: 0.7617 (tt0) cc_final: 0.7209 (tt0) REVERT: A 3990 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6512 (tp) REVERT: A 4020 ILE cc_start: 0.7958 (mm) cc_final: 0.7360 (mp) REVERT: A 4081 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7997 (t70) REVERT: A 4171 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.7169 (mmmt) REVERT: A 4329 ARG cc_start: 0.7222 (ttm110) cc_final: 0.6505 (mtm-85) REVERT: A 4343 MET cc_start: 0.8779 (mtp) cc_final: 0.8512 (mtp) REVERT: A 4424 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7579 (tp) REVERT: A 4453 ASN cc_start: 0.7021 (m110) cc_final: 0.6731 (t0) REVERT: A 4481 ASP cc_start: 0.7859 (t0) cc_final: 0.7159 (t0) REVERT: A 4574 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6652 (ttmm) REVERT: A 4589 GLN cc_start: 0.7910 (mt0) cc_final: 0.7672 (mt0) outliers start: 57 outliers final: 27 residues processed: 358 average time/residue: 2.0890 time to fit residues: 863.9610 Evaluate side-chains 352 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 310 time to evaluate : 8.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1973 GLN Chi-restraints excluded: chain A residue 2000 GLU Chi-restraints excluded: chain A residue 2063 GLU Chi-restraints excluded: chain A residue 2074 LYS Chi-restraints excluded: chain A residue 2084 SER Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2272 THR Chi-restraints excluded: chain A residue 2332 ARG Chi-restraints excluded: chain A residue 2535 ILE Chi-restraints excluded: chain A residue 2554 GLN Chi-restraints excluded: chain A residue 2659 LEU Chi-restraints excluded: chain A residue 2801 ARG Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2867 MET Chi-restraints excluded: chain A residue 2877 LEU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3016 GLU Chi-restraints excluded: chain A residue 3121 ILE Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3551 GLU Chi-restraints excluded: chain A residue 3597 THR Chi-restraints excluded: chain A residue 3670 ASP Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3707 SER Chi-restraints excluded: chain A residue 3750 LEU Chi-restraints excluded: chain A residue 3902 ASP Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4015 GLU Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4081 ASP Chi-restraints excluded: chain A residue 4137 ASN Chi-restraints excluded: chain A residue 4171 LYS Chi-restraints excluded: chain A residue 4199 LEU Chi-restraints excluded: chain A residue 4259 GLU Chi-restraints excluded: chain A residue 4424 LEU Chi-restraints excluded: chain A residue 4431 LEU Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4574 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 78 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.0870 chunk 106 optimal weight: 5.9990 chunk 271 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 275 optimal weight: 0.2980 chunk 141 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN A1922 GLN A2047 GLN A2187 GLN A2476 HIS A2485 GLN A3087 ASN ** A3181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3800 GLN A4063 ASN A4108 GLN A4466 HIS A4488 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.153701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113577 restraints weight = 25116.621| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.63 r_work: 0.3109 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24195 Z= 0.113 Angle : 0.489 15.721 32815 Z= 0.243 Chirality : 0.039 0.152 3690 Planarity : 0.004 0.086 4203 Dihedral : 6.683 132.947 3259 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.96 % Allowed : 15.29 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.16), residues: 2927 helix: 2.32 (0.12), residues: 1729 sheet: 0.01 (0.34), residues: 230 loop : 0.66 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2234 HIS 0.006 0.001 HIS A2476 PHE 0.016 0.001 PHE A1568 TYR 0.018 0.001 TYR A2748 ARG 0.007 0.000 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 1414) hydrogen bonds : angle 3.96724 ( 4095) covalent geometry : bond 0.00249 (24195) covalent geometry : angle 0.48920 (32815) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 321 time to evaluate : 2.838 Fit side-chains REVERT: A 1471 ASN cc_start: 0.7810 (m-40) cc_final: 0.7543 (m110) REVERT: A 1573 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7763 (p) REVERT: A 1613 LYS cc_start: 0.8250 (mmtm) cc_final: 0.8041 (mmtm) REVERT: A 1635 GLU cc_start: 0.8097 (tp30) cc_final: 0.7695 (tm-30) REVERT: A 1892 MET cc_start: 0.8824 (mmp) cc_final: 0.8532 (mmp) REVERT: A 2000 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8237 (tp30) REVERT: A 2012 MET cc_start: 0.8869 (ppp) cc_final: 0.8435 (tmt) REVERT: A 2060 ARG cc_start: 0.7928 (mtm110) cc_final: 0.7344 (ptt90) REVERT: A 2074 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8167 (mmmt) REVERT: A 2106 GLU cc_start: 0.7448 (pt0) cc_final: 0.7017 (mt-10) REVERT: A 2113 ARG cc_start: 0.6711 (mtm-85) cc_final: 0.6296 (mtm-85) REVERT: A 2188 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8026 (pt0) REVERT: A 2232 MET cc_start: 0.9214 (mmt) cc_final: 0.8997 (mmm) REVERT: A 2438 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7308 (mm-30) REVERT: A 2554 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7242 (tm-30) REVERT: A 2615 MET cc_start: 0.8361 (mtt) cc_final: 0.8097 (mtt) REVERT: A 2801 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8145 (ttp-170) REVERT: A 2855 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7573 (mm) REVERT: A 2867 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7673 (mtp) REVERT: A 2898 LYS cc_start: 0.8641 (tttt) cc_final: 0.8154 (tttm) REVERT: A 2968 THR cc_start: 0.8823 (p) cc_final: 0.8444 (t) REVERT: A 3006 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8286 (mm-30) REVERT: A 3016 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7875 (pt0) REVERT: A 3022 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8102 (mp0) REVERT: A 3164 ARG cc_start: 0.7103 (ttp-110) cc_final: 0.6679 (ttp80) REVERT: A 3217 GLU cc_start: 0.7119 (pp20) cc_final: 0.6326 (tt0) REVERT: A 3464 ASP cc_start: 0.5905 (t0) cc_final: 0.5590 (m-30) REVERT: A 3524 MET cc_start: 0.8798 (tpt) cc_final: 0.8372 (mmm) REVERT: A 3551 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7706 (mm-30) REVERT: A 3746 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6781 (tp30) REVERT: A 3747 LYS cc_start: 0.7110 (mtpp) cc_final: 0.6783 (tppt) REVERT: A 3775 ARG cc_start: 0.7871 (ttm-80) cc_final: 0.7504 (ttp-110) REVERT: A 3793 GLU cc_start: 0.6769 (tm-30) cc_final: 0.6552 (tt0) REVERT: A 3902 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7530 (m-30) REVERT: A 3985 GLN cc_start: 0.7612 (tt0) cc_final: 0.7294 (tt0) REVERT: A 3990 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6599 (tp) REVERT: A 4020 ILE cc_start: 0.7958 (mm) cc_final: 0.7366 (mp) REVERT: A 4081 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7981 (t70) REVERT: A 4329 ARG cc_start: 0.7262 (ttm110) cc_final: 0.6550 (mtm-85) REVERT: A 4343 MET cc_start: 0.8820 (mtp) cc_final: 0.8559 (mtp) REVERT: A 4424 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7671 (tp) REVERT: A 4481 ASP cc_start: 0.7875 (t0) cc_final: 0.7166 (t0) REVERT: A 4574 LYS cc_start: 0.7158 (OUTLIER) cc_final: 0.6668 (ttmm) REVERT: A 4583 THR cc_start: 0.8206 (m) cc_final: 0.7552 (p) REVERT: A 4589 GLN cc_start: 0.7789 (mt0) cc_final: 0.7582 (mt0) outliers start: 51 outliers final: 22 residues processed: 349 average time/residue: 1.6531 time to fit residues: 652.1907 Evaluate side-chains 344 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 307 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1973 GLN Chi-restraints excluded: chain A residue 2000 GLU Chi-restraints excluded: chain A residue 2063 GLU Chi-restraints excluded: chain A residue 2074 LYS Chi-restraints excluded: chain A residue 2084 SER Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2332 ARG Chi-restraints excluded: chain A residue 2535 ILE Chi-restraints excluded: chain A residue 2554 GLN Chi-restraints excluded: chain A residue 2659 LEU Chi-restraints excluded: chain A residue 2801 ARG Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2867 MET Chi-restraints excluded: chain A residue 2877 LEU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3016 GLU Chi-restraints excluded: chain A residue 3121 ILE Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3551 GLU Chi-restraints excluded: chain A residue 3597 THR Chi-restraints excluded: chain A residue 3670 ASP Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3707 SER Chi-restraints excluded: chain A residue 3902 ASP Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4081 ASP Chi-restraints excluded: chain A residue 4137 ASN Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4259 GLU Chi-restraints excluded: chain A residue 4424 LEU Chi-restraints excluded: chain A residue 4431 LEU Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4574 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 4 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 212 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 241 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2187 GLN A2476 HIS A3087 ASN A3181 ASN A3584 ASN A3800 GLN A4063 ASN A4108 GLN A4466 HIS A4488 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.152552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.112143 restraints weight = 25075.535| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.66 r_work: 0.3076 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24195 Z= 0.137 Angle : 0.508 15.864 32815 Z= 0.253 Chirality : 0.040 0.161 3690 Planarity : 0.004 0.091 4203 Dihedral : 6.715 127.719 3259 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.54 % Allowed : 15.14 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.16), residues: 2927 helix: 2.30 (0.12), residues: 1726 sheet: -0.02 (0.33), residues: 229 loop : 0.61 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.008 0.001 HIS A1810 PHE 0.018 0.002 PHE A1568 TYR 0.022 0.001 TYR A2748 ARG 0.006 0.000 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.04251 ( 1414) hydrogen bonds : angle 4.00857 ( 4095) covalent geometry : bond 0.00314 (24195) covalent geometry : angle 0.50831 (32815) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 309 time to evaluate : 2.822 Fit side-chains REVERT: A 1471 ASN cc_start: 0.7834 (m-40) cc_final: 0.7590 (m110) REVERT: A 1573 THR cc_start: 0.8007 (OUTLIER) cc_final: 0.7736 (p) REVERT: A 1635 GLU cc_start: 0.8228 (tp30) cc_final: 0.7719 (tm-30) REVERT: A 1646 ASN cc_start: 0.7590 (m110) cc_final: 0.6515 (t0) REVERT: A 1892 MET cc_start: 0.8832 (mmp) cc_final: 0.8526 (mmp) REVERT: A 2000 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8268 (tp30) REVERT: A 2004 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7793 (mppt) REVERT: A 2012 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8453 (tmt) REVERT: A 2060 ARG cc_start: 0.8017 (mtm110) cc_final: 0.7478 (ptt90) REVERT: A 2074 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8223 (mmmt) REVERT: A 2106 GLU cc_start: 0.7494 (pt0) cc_final: 0.7082 (mt-10) REVERT: A 2113 ARG cc_start: 0.6766 (mtm-85) cc_final: 0.6359 (mtm-85) REVERT: A 2188 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7894 (pt0) REVERT: A 2232 MET cc_start: 0.9241 (mmt) cc_final: 0.9018 (mmm) REVERT: A 2438 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7376 (mm-30) REVERT: A 2554 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: A 2615 MET cc_start: 0.8522 (mtt) cc_final: 0.8299 (mtt) REVERT: A 2801 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8300 (ttp-170) REVERT: A 2855 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7578 (mm) REVERT: A 2867 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7684 (mtp) REVERT: A 2898 LYS cc_start: 0.8669 (tttt) cc_final: 0.8182 (tttm) REVERT: A 2968 THR cc_start: 0.8849 (p) cc_final: 0.8477 (t) REVERT: A 3006 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8282 (mm-30) REVERT: A 3016 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7900 (pt0) REVERT: A 3022 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8158 (mp0) REVERT: A 3164 ARG cc_start: 0.7168 (ttp-110) cc_final: 0.6725 (ttp80) REVERT: A 3464 ASP cc_start: 0.5942 (t0) cc_final: 0.5624 (m-30) REVERT: A 3524 MET cc_start: 0.8826 (tpt) cc_final: 0.8397 (mmm) REVERT: A 3551 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7780 (mm-30) REVERT: A 3746 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6814 (tp30) REVERT: A 3747 LYS cc_start: 0.7204 (mtpp) cc_final: 0.6845 (tppt) REVERT: A 3775 ARG cc_start: 0.7870 (ttm-80) cc_final: 0.7424 (ttp-110) REVERT: A 3782 ARG cc_start: 0.7289 (ttp-110) cc_final: 0.7077 (tmm160) REVERT: A 3893 LYS cc_start: 0.7759 (mtpt) cc_final: 0.7023 (ttpp) REVERT: A 3902 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7554 (m-30) REVERT: A 3985 GLN cc_start: 0.7614 (tt0) cc_final: 0.7296 (tt0) REVERT: A 3990 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6594 (tp) REVERT: A 4020 ILE cc_start: 0.7963 (mm) cc_final: 0.7373 (mp) REVERT: A 4081 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.8015 (t70) REVERT: A 4329 ARG cc_start: 0.7286 (ttm110) cc_final: 0.6578 (mtm-85) REVERT: A 4343 MET cc_start: 0.8818 (mtp) cc_final: 0.8555 (mtp) REVERT: A 4424 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7741 (tp) REVERT: A 4481 ASP cc_start: 0.7915 (t0) cc_final: 0.7195 (t0) REVERT: A 4574 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6663 (mttm) REVERT: A 4589 GLN cc_start: 0.7780 (mt0) cc_final: 0.7563 (mt0) outliers start: 66 outliers final: 28 residues processed: 347 average time/residue: 1.8901 time to fit residues: 757.3070 Evaluate side-chains 351 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 306 time to evaluate : 4.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1465 GLN Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 2000 GLU Chi-restraints excluded: chain A residue 2004 LYS Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2063 GLU Chi-restraints excluded: chain A residue 2074 LYS Chi-restraints excluded: chain A residue 2084 SER Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2332 ARG Chi-restraints excluded: chain A residue 2460 SER Chi-restraints excluded: chain A residue 2535 ILE Chi-restraints excluded: chain A residue 2554 GLN Chi-restraints excluded: chain A residue 2659 LEU Chi-restraints excluded: chain A residue 2801 ARG Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2867 MET Chi-restraints excluded: chain A residue 2877 LEU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3016 GLU Chi-restraints excluded: chain A residue 3121 ILE Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3551 GLU Chi-restraints excluded: chain A residue 3597 THR Chi-restraints excluded: chain A residue 3670 ASP Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3707 SER Chi-restraints excluded: chain A residue 3750 LEU Chi-restraints excluded: chain A residue 3902 ASP Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4015 GLU Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4081 ASP Chi-restraints excluded: chain A residue 4137 ASN Chi-restraints excluded: chain A residue 4199 LEU Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4259 GLU Chi-restraints excluded: chain A residue 4424 LEU Chi-restraints excluded: chain A residue 4431 LEU Chi-restraints excluded: chain A residue 4462 ARG Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4574 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 244 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 290 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 274 optimal weight: 4.9990 chunk 136 optimal weight: 0.2980 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2187 GLN A2476 HIS A3087 ASN ** A3145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3800 GLN A4063 ASN A4108 GLN A4488 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.152308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.111922 restraints weight = 24942.837| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.57 r_work: 0.3084 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24195 Z= 0.140 Angle : 0.514 15.527 32815 Z= 0.256 Chirality : 0.040 0.162 3690 Planarity : 0.004 0.095 4203 Dihedral : 6.738 125.313 3259 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.11 % Allowed : 15.60 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.16), residues: 2927 helix: 2.29 (0.12), residues: 1726 sheet: -0.03 (0.33), residues: 229 loop : 0.58 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.008 0.001 HIS A1810 PHE 0.017 0.002 PHE A1568 TYR 0.022 0.001 TYR A2748 ARG 0.006 0.000 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 1414) hydrogen bonds : angle 4.01949 ( 4095) covalent geometry : bond 0.00324 (24195) covalent geometry : angle 0.51429 (32815) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 309 time to evaluate : 3.010 Fit side-chains REVERT: A 1471 ASN cc_start: 0.7760 (m-40) cc_final: 0.7449 (m110) REVERT: A 1556 ASP cc_start: 0.7493 (p0) cc_final: 0.7035 (p0) REVERT: A 1573 THR cc_start: 0.8006 (OUTLIER) cc_final: 0.7743 (p) REVERT: A 1635 GLU cc_start: 0.8195 (tp30) cc_final: 0.7786 (tm-30) REVERT: A 1646 ASN cc_start: 0.7601 (m110) cc_final: 0.6775 (t0) REVERT: A 1892 MET cc_start: 0.8840 (mmp) cc_final: 0.8540 (mmp) REVERT: A 2004 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7788 (mppt) REVERT: A 2012 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8444 (tmt) REVERT: A 2060 ARG cc_start: 0.7994 (mtm110) cc_final: 0.7473 (ptt90) REVERT: A 2074 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8210 (mmmt) REVERT: A 2106 GLU cc_start: 0.7459 (pt0) cc_final: 0.7048 (mt-10) REVERT: A 2113 ARG cc_start: 0.6781 (mtm-85) cc_final: 0.6368 (mtm-85) REVERT: A 2188 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7862 (pt0) REVERT: A 2232 MET cc_start: 0.9231 (mmt) cc_final: 0.9004 (mmm) REVERT: A 2438 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7343 (mm-30) REVERT: A 2554 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7500 (tm-30) REVERT: A 2801 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8334 (ttp-170) REVERT: A 2855 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7558 (mm) REVERT: A 2867 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7676 (mtp) REVERT: A 2898 LYS cc_start: 0.8663 (tttt) cc_final: 0.8173 (tttm) REVERT: A 2968 THR cc_start: 0.8847 (p) cc_final: 0.8468 (t) REVERT: A 3006 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8274 (mm-30) REVERT: A 3016 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7884 (pt0) REVERT: A 3022 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8146 (mp0) REVERT: A 3164 ARG cc_start: 0.7291 (ttp-110) cc_final: 0.6816 (ttp80) REVERT: A 3217 GLU cc_start: 0.7081 (pp20) cc_final: 0.6379 (tt0) REVERT: A 3464 ASP cc_start: 0.5930 (t0) cc_final: 0.5583 (m-30) REVERT: A 3524 MET cc_start: 0.8817 (tpt) cc_final: 0.8386 (mmm) REVERT: A 3551 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7764 (mm-30) REVERT: A 3746 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6799 (tp30) REVERT: A 3747 LYS cc_start: 0.7220 (mtpp) cc_final: 0.6886 (tttp) REVERT: A 3775 ARG cc_start: 0.7887 (ttm-80) cc_final: 0.7555 (ttp-110) REVERT: A 3782 ARG cc_start: 0.7287 (ttp-110) cc_final: 0.7078 (tmm160) REVERT: A 3795 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6468 (tm-30) REVERT: A 3893 LYS cc_start: 0.7791 (mtpt) cc_final: 0.7037 (ttpp) REVERT: A 3902 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7550 (m-30) REVERT: A 3985 GLN cc_start: 0.7670 (tt0) cc_final: 0.7282 (tt0) REVERT: A 3990 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6557 (tp) REVERT: A 4020 ILE cc_start: 0.7966 (mm) cc_final: 0.7376 (mp) REVERT: A 4081 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7998 (t70) REVERT: A 4171 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7311 (mmmt) REVERT: A 4329 ARG cc_start: 0.7288 (ttm110) cc_final: 0.6592 (mtm-85) REVERT: A 4343 MET cc_start: 0.8807 (mtp) cc_final: 0.8550 (mtp) REVERT: A 4424 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7756 (tp) REVERT: A 4481 ASP cc_start: 0.7588 (t0) cc_final: 0.7018 (t0) REVERT: A 4574 LYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6675 (mttm) REVERT: A 4589 GLN cc_start: 0.7808 (mt0) cc_final: 0.7592 (mt0) outliers start: 55 outliers final: 26 residues processed: 340 average time/residue: 1.6770 time to fit residues: 643.5786 Evaluate side-chains 348 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 305 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1465 GLN Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 2004 LYS Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2063 GLU Chi-restraints excluded: chain A residue 2074 LYS Chi-restraints excluded: chain A residue 2084 SER Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2332 ARG Chi-restraints excluded: chain A residue 2535 ILE Chi-restraints excluded: chain A residue 2554 GLN Chi-restraints excluded: chain A residue 2659 LEU Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2801 ARG Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2867 MET Chi-restraints excluded: chain A residue 2877 LEU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3016 GLU Chi-restraints excluded: chain A residue 3121 ILE Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3551 GLU Chi-restraints excluded: chain A residue 3597 THR Chi-restraints excluded: chain A residue 3670 ASP Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3707 SER Chi-restraints excluded: chain A residue 3750 LEU Chi-restraints excluded: chain A residue 3902 ASP Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4081 ASP Chi-restraints excluded: chain A residue 4137 ASN Chi-restraints excluded: chain A residue 4171 LYS Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4259 GLU Chi-restraints excluded: chain A residue 4424 LEU Chi-restraints excluded: chain A residue 4431 LEU Chi-restraints excluded: chain A residue 4462 ARG Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4574 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 278 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 241 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 160 optimal weight: 0.0980 chunk 239 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2187 GLN A3087 ASN ** A3181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3800 GLN A4063 ASN A4108 GLN A4488 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.150978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.110068 restraints weight = 25114.891| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.65 r_work: 0.3043 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24195 Z= 0.176 Angle : 0.549 15.027 32815 Z= 0.274 Chirality : 0.042 0.172 3690 Planarity : 0.005 0.098 4203 Dihedral : 6.940 125.965 3259 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.92 % Allowed : 15.87 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.16), residues: 2927 helix: 2.18 (0.12), residues: 1725 sheet: -0.11 (0.34), residues: 223 loop : 0.54 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A4222 HIS 0.010 0.001 HIS A1810 PHE 0.019 0.002 PHE A1568 TYR 0.024 0.002 TYR A2748 ARG 0.011 0.001 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.04672 ( 1414) hydrogen bonds : angle 4.12519 ( 4095) covalent geometry : bond 0.00417 (24195) covalent geometry : angle 0.54878 (32815) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 311 time to evaluate : 2.709 Fit side-chains REVERT: A 1471 ASN cc_start: 0.7732 (m-40) cc_final: 0.7416 (m110) REVERT: A 1556 ASP cc_start: 0.7524 (p0) cc_final: 0.7012 (p0) REVERT: A 1569 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7328 (mm-40) REVERT: A 1573 THR cc_start: 0.8037 (OUTLIER) cc_final: 0.7776 (p) REVERT: A 1635 GLU cc_start: 0.8231 (tp30) cc_final: 0.7757 (tm-30) REVERT: A 1646 ASN cc_start: 0.7667 (m110) cc_final: 0.6853 (t0) REVERT: A 2004 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7828 (mppt) REVERT: A 2012 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8448 (tmt) REVERT: A 2074 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8280 (mmmt) REVERT: A 2106 GLU cc_start: 0.7509 (pt0) cc_final: 0.7139 (mt-10) REVERT: A 2113 ARG cc_start: 0.6874 (mtm-85) cc_final: 0.6429 (mtm-85) REVERT: A 2188 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8049 (pt0) REVERT: A 2232 MET cc_start: 0.9248 (mmt) cc_final: 0.9038 (mmm) REVERT: A 2438 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7381 (mm-30) REVERT: A 2615 MET cc_start: 0.8423 (mtt) cc_final: 0.8183 (mmm) REVERT: A 2801 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8357 (ttp-170) REVERT: A 2855 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7601 (mm) REVERT: A 2867 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7703 (mtp) REVERT: A 2898 LYS cc_start: 0.8702 (tttt) cc_final: 0.8208 (tttm) REVERT: A 3006 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8290 (mm-30) REVERT: A 3016 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7927 (pt0) REVERT: A 3464 ASP cc_start: 0.6094 (t0) cc_final: 0.5697 (m-30) REVERT: A 3551 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7731 (mm-30) REVERT: A 3746 GLU cc_start: 0.7414 (mm-30) cc_final: 0.6933 (tp30) REVERT: A 3747 LYS cc_start: 0.7330 (mtpp) cc_final: 0.6868 (tppt) REVERT: A 3775 ARG cc_start: 0.7929 (ttm-80) cc_final: 0.7597 (ttp-110) REVERT: A 3782 ARG cc_start: 0.7346 (ttp-110) cc_final: 0.7139 (tmm160) REVERT: A 3795 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6564 (tt0) REVERT: A 3902 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7659 (m-30) REVERT: A 3985 GLN cc_start: 0.7757 (tt0) cc_final: 0.7458 (tt0) REVERT: A 3990 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6659 (tp) REVERT: A 4020 ILE cc_start: 0.8004 (mm) cc_final: 0.7414 (mp) REVERT: A 4081 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.8042 (t70) REVERT: A 4159 ARG cc_start: 0.7772 (ttm170) cc_final: 0.7444 (ttm170) REVERT: A 4171 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7238 (mmmt) REVERT: A 4329 ARG cc_start: 0.7348 (ttm110) cc_final: 0.6644 (mtm-85) REVERT: A 4343 MET cc_start: 0.8855 (mtp) cc_final: 0.8563 (mtp) REVERT: A 4424 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7855 (tp) REVERT: A 4431 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7531 (mp) REVERT: A 4481 ASP cc_start: 0.7634 (t0) cc_final: 0.7079 (t0) REVERT: A 4574 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6796 (mttm) REVERT: A 4589 GLN cc_start: 0.7872 (mt0) cc_final: 0.7637 (mt0) outliers start: 50 outliers final: 28 residues processed: 339 average time/residue: 1.7075 time to fit residues: 654.2643 Evaluate side-chains 350 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 305 time to evaluate : 3.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1465 GLN Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 2004 LYS Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2063 GLU Chi-restraints excluded: chain A residue 2074 LYS Chi-restraints excluded: chain A residue 2084 SER Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2272 THR Chi-restraints excluded: chain A residue 2332 ARG Chi-restraints excluded: chain A residue 2460 SER Chi-restraints excluded: chain A residue 2535 ILE Chi-restraints excluded: chain A residue 2554 GLN Chi-restraints excluded: chain A residue 2659 LEU Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2801 ARG Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2867 MET Chi-restraints excluded: chain A residue 2877 LEU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3016 GLU Chi-restraints excluded: chain A residue 3121 ILE Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3551 GLU Chi-restraints excluded: chain A residue 3597 THR Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3707 SER Chi-restraints excluded: chain A residue 3750 LEU Chi-restraints excluded: chain A residue 3902 ASP Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4081 ASP Chi-restraints excluded: chain A residue 4137 ASN Chi-restraints excluded: chain A residue 4171 LYS Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4259 GLU Chi-restraints excluded: chain A residue 4424 LEU Chi-restraints excluded: chain A residue 4431 LEU Chi-restraints excluded: chain A residue 4462 ARG Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4574 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 269 optimal weight: 3.9990 chunk 251 optimal weight: 0.4980 chunk 131 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 279 optimal weight: 6.9990 chunk 281 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 282 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2187 GLN A3087 ASN A3145 ASN ** A3181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3800 GLN A4063 ASN A4108 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.151031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.110278 restraints weight = 24925.795| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.73 r_work: 0.3031 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24195 Z= 0.170 Angle : 0.543 14.970 32815 Z= 0.271 Chirality : 0.041 0.171 3690 Planarity : 0.004 0.097 4203 Dihedral : 6.926 126.827 3259 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.96 % Allowed : 15.94 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.15), residues: 2927 helix: 2.14 (0.12), residues: 1725 sheet: -0.23 (0.33), residues: 231 loop : 0.53 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A2234 HIS 0.010 0.001 HIS A1810 PHE 0.025 0.002 PHE A4008 TYR 0.023 0.002 TYR A2748 ARG 0.010 0.000 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.04593 ( 1414) hydrogen bonds : angle 4.11879 ( 4095) covalent geometry : bond 0.00401 (24195) covalent geometry : angle 0.54323 (32815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25237.91 seconds wall clock time: 442 minutes 5.47 seconds (26525.47 seconds total)