Starting phenix.real_space_refine on Fri May 23 08:12:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dh5_46856/05_2025/9dh5_46856.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dh5_46856/05_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_46856/05_2025/9dh5_46856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dh5_46856/05_2025/9dh5_46856.map" model { file = "/net/cci-nas-00/data/ceres_data/9dh5_46856/05_2025/9dh5_46856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dh5_46856/05_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 14.60, 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: 6.46 Conformation dependent library (CDL) restraints added in 3.1 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: 3.97 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: 15.81 Time building geometry restraints manager: 7.46 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: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.970 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 62.510 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.090 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:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.050 ------------------------------------------------------------------------------- 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 : 2.528 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: 1.6731 time to fit residues: 1067.2396 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 : 2.643 ------------------------------------------------------------------------------- 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: 0.9990 chunk 139 optimal weight: 0.0270 chunk 170 optimal weight: 0.9990 chunk 266 optimal weight: 5.9990 overall best weight: 0.7844 ------------------------------------------------------------------------------- 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 A4397 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.156007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.115559 restraints weight = 25176.978| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.65 r_work: 0.3150 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24195 Z= 0.153 Angle : 0.573 9.487 32815 Z= 0.292 Chirality : 0.042 0.157 3690 Planarity : 0.005 0.075 4203 Dihedral : 7.761 170.682 3264 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.27 % Allowed : 10.22 % 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: 1.92 (0.15), residues: 2927 helix: 1.87 (0.12), residues: 1721 sheet: -0.04 (0.34), residues: 236 loop : 0.71 (0.21), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2234 HIS 0.013 0.001 HIS A1810 PHE 0.021 0.002 PHE A2912 TYR 0.021 0.002 TYR A2748 ARG 0.005 0.001 ARG A2091 Details of bonding type rmsd hydrogen bonds : bond 0.05162 ( 1414) hydrogen bonds : angle 4.48920 ( 4095) covalent geometry : bond 0.00333 (24195) covalent geometry : angle 0.57333 (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 427 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 368 time to evaluate : 2.528 Fit side-chains REVERT: A 1471 ASN cc_start: 0.7678 (m-40) cc_final: 0.7432 (m110) REVERT: A 1473 TYR cc_start: 0.7453 (t80) cc_final: 0.7193 (t80) REVERT: A 1892 MET cc_start: 0.8874 (mmp) cc_final: 0.8647 (mmp) REVERT: A 2012 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8286 (tmt) REVERT: A 2060 ARG cc_start: 0.7881 (mtm110) cc_final: 0.7271 (ptt90) REVERT: A 2106 GLU cc_start: 0.7536 (pt0) cc_final: 0.7301 (mt-10) REVERT: A 2113 ARG cc_start: 0.6599 (mtm-85) cc_final: 0.6283 (mtm110) REVERT: A 2175 MET cc_start: 0.7614 (mtp) cc_final: 0.7336 (mtt) REVERT: A 2188 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7780 (pt0) REVERT: A 2221 MET cc_start: 0.9202 (mtt) cc_final: 0.8983 (mtt) REVERT: A 2442 GLN cc_start: 0.7833 (mm110) cc_final: 0.7619 (mp10) REVERT: A 2801 ARG cc_start: 0.8233 (mtt90) cc_final: 0.8002 (ttp-170) REVERT: A 2844 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7318 (ttm-80) REVERT: A 2898 LYS cc_start: 0.8531 (tttt) cc_final: 0.8105 (tttm) REVERT: A 2970 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7334 (pt0) REVERT: A 3006 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.6970 (tm-30) REVERT: A 3068 MET cc_start: 0.9175 (ptm) cc_final: 0.8896 (ptp) REVERT: A 3073 GLU cc_start: 0.7139 (pm20) cc_final: 0.6937 (tp30) REVERT: A 3132 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8514 (mppt) REVERT: A 3487 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6753 (pt0) REVERT: A 3551 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7659 (mm-30) REVERT: A 3747 LYS cc_start: 0.7041 (mtpp) cc_final: 0.6601 (tttt) REVERT: A 3985 GLN cc_start: 0.7767 (tt0) cc_final: 0.7481 (tt0) REVERT: A 4081 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.8042 (t0) REVERT: A 4276 ARG cc_start: 0.7189 (mmp80) cc_final: 0.6941 (mtm-85) REVERT: A 4343 MET cc_start: 0.8639 (mtp) cc_final: 0.8359 (mtp) REVERT: A 4377 MET cc_start: 0.6520 (mtp) cc_final: 0.6227 (mtp) REVERT: A 4419 MET cc_start: 0.6892 (ptp) cc_final: 0.6404 (pmm) REVERT: A 4453 ASN cc_start: 0.7144 (m110) cc_final: 0.6807 (t0) REVERT: A 4481 ASP cc_start: 0.7733 (t0) cc_final: 0.7224 (t70) REVERT: A 4574 LYS cc_start: 0.7082 (OUTLIER) cc_final: 0.6730 (ttmm) REVERT: A 4583 THR cc_start: 0.8095 (m) cc_final: 0.7678 (p) REVERT: A 4589 GLN cc_start: 0.7715 (mt0) cc_final: 0.7368 (mt0) REVERT: A 4591 ARG cc_start: 0.6999 (ttt90) cc_final: 0.6367 (ttt180) outliers start: 59 outliers final: 18 residues processed: 401 average time/residue: 1.6215 time to fit residues: 737.1561 Evaluate side-chains 332 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 306 time to evaluate : 2.872 ------------------------------------------------------------------------------- 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 2012 MET 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 3132 LYS Chi-restraints excluded: chain A residue 3192 SER Chi-restraints excluded: chain A residue 3487 GLU 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: 1.9990 chunk 245 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 198 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 200 optimal weight: 0.0980 chunk 281 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1931 ASN A1985 HIS A2187 GLN A2476 HIS A2485 GLN A3063 HIS A3523 GLN A3735 GLN A3799 GLN A3800 GLN A3837 HIS A4063 ASN A4108 GLN A4335 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.151639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.110592 restraints weight = 24933.419| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.70 r_work: 0.3060 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24195 Z= 0.181 Angle : 0.563 7.529 32815 Z= 0.285 Chirality : 0.042 0.180 3690 Planarity : 0.005 0.074 4203 Dihedral : 7.779 169.072 3262 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.61 % Allowed : 11.83 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.00 (0.16), residues: 2927 helix: 1.98 (0.12), residues: 1720 sheet: -0.05 (0.34), residues: 214 loop : 0.64 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A4222 HIS 0.013 0.001 HIS A1810 PHE 0.022 0.002 PHE A2912 TYR 0.023 0.002 TYR A2748 ARG 0.008 0.001 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.05299 ( 1414) hydrogen bonds : angle 4.34473 ( 4095) covalent geometry : bond 0.00424 (24195) covalent geometry : angle 0.56266 (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 411 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 343 time to evaluate : 2.678 Fit side-chains REVERT: A 1471 ASN cc_start: 0.7716 (m-40) cc_final: 0.7442 (m110) REVERT: A 1613 LYS cc_start: 0.8352 (mmtm) cc_final: 0.8055 (mmpt) REVERT: A 2012 MET cc_start: 0.8845 (ppp) cc_final: 0.8319 (tmt) REVERT: A 2060 ARG cc_start: 0.7987 (mtm110) cc_final: 0.7335 (ptt90) REVERT: A 2074 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8029 (mtmt) REVERT: A 2106 GLU cc_start: 0.7473 (pt0) cc_final: 0.7085 (mt-10) REVERT: A 2113 ARG cc_start: 0.6687 (mtm-85) cc_final: 0.6264 (mtm-85) REVERT: A 2175 MET cc_start: 0.7906 (mtp) cc_final: 0.7608 (mtt) REVERT: A 2188 GLU cc_start: 0.8551 (mt-10) cc_final: 0.7999 (pt0) REVERT: A 2442 GLN cc_start: 0.8057 (mm110) cc_final: 0.7841 (mp10) REVERT: A 2801 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8139 (ttp-170) REVERT: A 2844 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7207 (ttm-80) REVERT: A 2863 ARG cc_start: 0.7639 (mtp85) cc_final: 0.7313 (tmt90) REVERT: A 2867 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7826 (mtp) REVERT: A 2898 LYS cc_start: 0.8637 (tttt) cc_final: 0.8123 (tttm) REVERT: A 3006 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8267 (mm-30) REVERT: A 3016 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7903 (pt0) REVERT: A 3022 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8031 (mp0) REVERT: A 3073 GLU cc_start: 0.7200 (pm20) cc_final: 0.6998 (tp30) REVERT: A 3113 MET cc_start: 0.9055 (mtp) cc_final: 0.8829 (mtp) REVERT: A 3206 ARG cc_start: 0.7733 (ptt-90) cc_final: 0.7484 (ttp80) REVERT: A 3464 ASP cc_start: 0.5877 (t0) cc_final: 0.5595 (m-30) REVERT: A 3551 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7674 (mm-30) REVERT: A 3747 LYS cc_start: 0.7316 (mtpp) cc_final: 0.6890 (tppt) REVERT: A 3795 GLU cc_start: 0.6853 (tp30) cc_final: 0.6649 (mm-30) REVERT: A 3985 GLN cc_start: 0.7715 (tt0) cc_final: 0.7378 (tt0) REVERT: A 4012 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8142 (m110) REVERT: A 4329 ARG cc_start: 0.7365 (ttm110) cc_final: 0.6509 (mtm-85) REVERT: A 4343 MET cc_start: 0.8681 (mtp) cc_final: 0.8462 (mtp) REVERT: A 4419 MET cc_start: 0.7218 (ptp) cc_final: 0.6538 (pmm) REVERT: A 4424 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7435 (tp) REVERT: A 4453 ASN cc_start: 0.7122 (m110) cc_final: 0.6807 (t0) REVERT: A 4481 ASP cc_start: 0.7899 (t0) cc_final: 0.7376 (t70) REVERT: A 4574 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6768 (ttmm) REVERT: A 4583 THR cc_start: 0.8135 (m) cc_final: 0.7500 (p) REVERT: A 4589 GLN cc_start: 0.7801 (mt0) cc_final: 0.7436 (mt0) REVERT: A 4591 ARG cc_start: 0.6859 (ttt90) cc_final: 0.6356 (ttt90) REVERT: A 4625 GLU cc_start: 0.7716 (mp0) cc_final: 0.7500 (mm-30) outliers start: 68 outliers final: 27 residues processed: 381 average time/residue: 1.6265 time to fit residues: 699.8676 Evaluate side-chains 343 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 307 time to evaluate : 2.715 ------------------------------------------------------------------------------- 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 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 2267 THR Chi-restraints excluded: chain A residue 2272 THR Chi-restraints excluded: chain A residue 2460 SER Chi-restraints excluded: chain A residue 2535 ILE 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 3038 GLN Chi-restraints excluded: chain A residue 3043 MET Chi-restraints excluded: chain A residue 3121 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 4127 THR 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 4300 ILE 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: 0.7980 chunk 209 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 248 optimal weight: 0.0470 chunk 88 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1784 ASN A2187 GLN A2476 HIS A3087 ASN A3523 GLN A3799 GLN A3800 GLN A4063 ASN A4108 GLN A4572 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.153111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.112520 restraints weight = 25119.455| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.68 r_work: 0.3087 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24195 Z= 0.126 Angle : 0.501 9.636 32815 Z= 0.252 Chirality : 0.040 0.151 3690 Planarity : 0.004 0.076 4203 Dihedral : 6.903 140.079 3259 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.27 % Allowed : 13.41 % Favored : 84.33 % 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: 2.16 (0.16), residues: 2927 helix: 2.13 (0.12), residues: 1726 sheet: 0.11 (0.36), residues: 203 loop : 0.61 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2234 HIS 0.008 0.001 HIS A1810 PHE 0.018 0.001 PHE A2912 TYR 0.020 0.001 TYR A2748 ARG 0.007 0.000 ARG A2467 Details of bonding type rmsd hydrogen bonds : bond 0.04394 ( 1414) hydrogen bonds : angle 4.13955 ( 4095) covalent geometry : bond 0.00279 (24195) covalent geometry : angle 0.50148 (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 391 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 332 time to evaluate : 2.877 Fit side-chains REVERT: A 1471 ASN cc_start: 0.7799 (m-40) cc_final: 0.7579 (m110) REVERT: A 1573 THR cc_start: 0.8025 (OUTLIER) cc_final: 0.7752 (p) REVERT: A 1613 LYS cc_start: 0.8276 (mmtm) cc_final: 0.7976 (mmpt) REVERT: A 1892 MET cc_start: 0.8856 (mmp) cc_final: 0.8555 (mmp) REVERT: A 2012 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8379 (tmt) REVERT: A 2074 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7993 (mtmt) REVERT: A 2106 GLU cc_start: 0.7477 (pt0) cc_final: 0.7110 (mt-10) REVERT: A 2113 ARG cc_start: 0.6625 (mtm-85) cc_final: 0.6214 (mtm-85) REVERT: A 2175 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7379 (mtt) REVERT: A 2188 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8093 (pt0) REVERT: A 2442 GLN cc_start: 0.8007 (mm110) cc_final: 0.7759 (mp-120) REVERT: A 2554 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7105 (tm-30) REVERT: A 2801 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.8135 (ttp-170) REVERT: A 2867 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7828 (mtp) REVERT: A 2898 LYS cc_start: 0.8614 (tttt) cc_final: 0.8106 (tttm) REVERT: A 3006 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8244 (mm-30) REVERT: A 3016 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7894 (pt0) REVERT: A 3113 MET cc_start: 0.9004 (mtp) cc_final: 0.8778 (mtp) REVERT: A 3464 ASP cc_start: 0.5876 (t0) cc_final: 0.5604 (m-30) REVERT: A 3551 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7708 (mm-30) REVERT: A 3747 LYS cc_start: 0.7228 (mtpp) cc_final: 0.6862 (tppt) REVERT: A 3793 GLU cc_start: 0.6953 (tm-30) cc_final: 0.6593 (tt0) REVERT: A 3795 GLU cc_start: 0.6829 (tp30) cc_final: 0.6626 (mm-30) REVERT: A 3985 GLN cc_start: 0.7651 (tt0) cc_final: 0.7218 (tt0) REVERT: A 4012 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.8048 (m110) REVERT: A 4020 ILE cc_start: 0.7982 (mm) cc_final: 0.7367 (mp) REVERT: A 4081 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.8025 (t70) REVERT: A 4329 ARG cc_start: 0.7233 (ttm110) cc_final: 0.6511 (mtm-85) REVERT: A 4343 MET cc_start: 0.8661 (mtp) cc_final: 0.8439 (mtp) REVERT: A 4424 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7413 (tp) REVERT: A 4453 ASN cc_start: 0.7012 (m110) cc_final: 0.6723 (t0) REVERT: A 4481 ASP cc_start: 0.7799 (t0) cc_final: 0.7055 (t0) REVERT: A 4574 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6782 (ttmm) REVERT: A 4583 THR cc_start: 0.8161 (m) cc_final: 0.7538 (p) REVERT: A 4589 GLN cc_start: 0.7820 (mt0) cc_final: 0.7620 (mt0) outliers start: 59 outliers final: 23 residues processed: 363 average time/residue: 1.6217 time to fit residues: 669.7285 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 : 2.510 ------------------------------------------------------------------------------- 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 2004 LYS Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2074 LYS Chi-restraints excluded: chain A residue 2084 SER Chi-restraints excluded: chain A residue 2175 MET 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 2615 MET Chi-restraints excluded: chain A residue 2616 GLU 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 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 3750 LEU Chi-restraints excluded: chain A residue 4012 ASN 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 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 4465 SER 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: 6.9990 chunk 206 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 263 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 200 optimal weight: 0.0970 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ** 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 = 0.3760 r_free = 0.3760 target = 0.152128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.111659 restraints weight = 24911.056| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.69 r_work: 0.3063 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3251 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= 0.146 Angle : 0.518 11.999 32815 Z= 0.260 Chirality : 0.040 0.160 3690 Planarity : 0.004 0.081 4203 Dihedral : 6.928 137.889 3259 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.65 % Allowed : 13.98 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.18 (0.16), residues: 2927 helix: 2.17 (0.12), residues: 1727 sheet: -0.10 (0.34), residues: 223 loop : 0.65 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.009 0.001 HIS A1810 PHE 0.018 0.002 PHE A2912 TYR 0.022 0.001 TYR A2748 ARG 0.008 0.000 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 1414) hydrogen bonds : angle 4.11949 ( 4095) covalent geometry : bond 0.00336 (24195) covalent geometry : angle 0.51804 (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 390 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 321 time to evaluate : 2.544 Fit side-chains REVERT: A 1471 ASN cc_start: 0.7812 (m-40) cc_final: 0.7579 (m110) REVERT: A 1573 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7777 (p) REVERT: A 1580 LYS cc_start: 0.7771 (mmmt) cc_final: 0.7257 (mttt) REVERT: A 1613 LYS cc_start: 0.8296 (mmtm) cc_final: 0.8066 (mmtm) REVERT: A 1892 MET cc_start: 0.8862 (mmp) cc_final: 0.8557 (mmp) REVERT: A 2000 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: A 2012 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8371 (tmt) REVERT: A 2060 ARG cc_start: 0.7970 (mtm110) cc_final: 0.7391 (ptt90) REVERT: A 2074 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8028 (mtmt) REVERT: A 2106 GLU cc_start: 0.7470 (pt0) cc_final: 0.7076 (mt-10) REVERT: A 2113 ARG cc_start: 0.6681 (mtm-85) cc_final: 0.6255 (mtm-85) REVERT: A 2175 MET cc_start: 0.7867 (mtp) cc_final: 0.7552 (mtt) REVERT: A 2188 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8073 (pt0) REVERT: A 2554 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: A 2617 VAL cc_start: 0.9340 (OUTLIER) cc_final: 0.9086 (p) REVERT: A 2801 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8202 (ttp-170) REVERT: A 2863 ARG cc_start: 0.7283 (ttt-90) cc_final: 0.7055 (tmt90) REVERT: A 2865 LYS cc_start: 0.8117 (mtpp) cc_final: 0.7496 (mttp) REVERT: A 2867 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7814 (mtp) REVERT: A 2898 LYS cc_start: 0.8651 (tttt) cc_final: 0.8169 (tttm) REVERT: A 2968 THR cc_start: 0.8866 (p) cc_final: 0.8483 (t) REVERT: A 3006 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8254 (mm-30) REVERT: A 3016 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7872 (pt0) REVERT: A 3022 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8191 (mp0) REVERT: A 3113 MET cc_start: 0.9082 (mtp) cc_final: 0.8850 (mtp) REVERT: A 3464 ASP cc_start: 0.5917 (t0) cc_final: 0.5610 (m-30) REVERT: A 3524 MET cc_start: 0.8840 (tpt) cc_final: 0.8402 (mmm) REVERT: A 3551 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7747 (mm-30) REVERT: A 3747 LYS cc_start: 0.7243 (mtpp) cc_final: 0.6886 (tppt) REVERT: A 3793 GLU cc_start: 0.6903 (tm-30) cc_final: 0.6624 (tt0) REVERT: A 3902 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7525 (m-30) REVERT: A 3985 GLN cc_start: 0.7747 (tt0) cc_final: 0.7433 (tt0) REVERT: A 4012 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.8059 (m110) REVERT: A 4020 ILE cc_start: 0.8000 (mm) cc_final: 0.7402 (mp) REVERT: A 4081 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.8051 (t70) REVERT: A 4171 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7244 (mmmt) REVERT: A 4329 ARG cc_start: 0.7271 (ttm110) cc_final: 0.6564 (mtm-85) REVERT: A 4343 MET cc_start: 0.8689 (mtp) cc_final: 0.8450 (mtp) REVERT: A 4424 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7614 (tp) REVERT: A 4453 ASN cc_start: 0.7048 (m110) cc_final: 0.6788 (t0) REVERT: A 4481 ASP cc_start: 0.7857 (t0) cc_final: 0.7148 (t0) REVERT: A 4574 LYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6652 (ttmm) REVERT: A 4589 GLN cc_start: 0.7944 (mt0) cc_final: 0.7662 (mt0) outliers start: 69 outliers final: 29 residues processed: 360 average time/residue: 1.6125 time to fit residues: 656.9730 Evaluate side-chains 356 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 310 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1851 THR Chi-restraints excluded: chain A residue 1973 GLN 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 2272 THR 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 2617 VAL 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 4012 ASN 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 4202 SER 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 4516 VAL Chi-restraints excluded: chain A residue 4574 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 283 optimal weight: 6.9990 chunk 224 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 284 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 245 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 276 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.151134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110173 restraints weight = 24929.118| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.68 r_work: 0.3031 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24195 Z= 0.171 Angle : 0.540 14.829 32815 Z= 0.270 Chirality : 0.042 0.168 3690 Planarity : 0.004 0.083 4203 Dihedral : 7.015 135.676 3259 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.19 % Allowed : 14.10 % Favored : 82.71 % 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: 2.12 (0.16), residues: 2927 helix: 2.14 (0.12), residues: 1723 sheet: -0.25 (0.34), residues: 225 loop : 0.62 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A4222 HIS 0.012 0.001 HIS A1810 PHE 0.019 0.002 PHE A1568 TYR 0.024 0.002 TYR A2748 ARG 0.005 0.001 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.04704 ( 1414) hydrogen bonds : angle 4.16640 ( 4095) covalent geometry : bond 0.00402 (24195) covalent geometry : angle 0.54022 (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 400 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 317 time to evaluate : 2.627 Fit side-chains REVERT: A 1471 ASN cc_start: 0.7864 (m-40) cc_final: 0.7604 (m110) REVERT: A 1573 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7799 (p) REVERT: A 1580 LYS cc_start: 0.7782 (mmmt) cc_final: 0.7269 (mttt) REVERT: A 1602 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7948 (mt-10) REVERT: A 1613 LYS cc_start: 0.8344 (mmtm) cc_final: 0.8126 (mmtm) REVERT: A 1635 GLU cc_start: 0.8254 (tp30) cc_final: 0.7774 (tm-30) REVERT: A 1892 MET cc_start: 0.8857 (mmp) cc_final: 0.8601 (mmp) REVERT: A 2012 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8359 (tmt) REVERT: A 2060 ARG cc_start: 0.7993 (mtm110) cc_final: 0.7430 (ptt90) REVERT: A 2074 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8089 (mtmt) REVERT: A 2106 GLU cc_start: 0.7524 (pt0) cc_final: 0.7142 (mt-10) REVERT: A 2113 ARG cc_start: 0.6781 (mtm-85) cc_final: 0.6357 (mtm-85) REVERT: A 2175 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7664 (mtt) REVERT: A 2188 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8119 (pt0) REVERT: A 2554 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7335 (tm-30) REVERT: A 2617 VAL cc_start: 0.9360 (OUTLIER) cc_final: 0.9107 (p) REVERT: A 2801 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8399 (ttp-170) REVERT: A 2844 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7140 (mtt90) REVERT: A 2855 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7612 (mm) REVERT: A 2867 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7783 (mtp) REVERT: A 2898 LYS cc_start: 0.8701 (tttt) cc_final: 0.8213 (tttm) REVERT: A 3016 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7909 (pt0) REVERT: A 3113 MET cc_start: 0.9135 (mtp) cc_final: 0.8927 (mtp) REVERT: A 3464 ASP cc_start: 0.6111 (t0) cc_final: 0.5752 (m-30) REVERT: A 3551 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7768 (mm-30) REVERT: A 3747 LYS cc_start: 0.7343 (mtpp) cc_final: 0.6931 (tppt) REVERT: A 3782 ARG cc_start: 0.7271 (ttp-110) cc_final: 0.7059 (tmm160) REVERT: A 3793 GLU cc_start: 0.7003 (tm-30) cc_final: 0.6716 (tt0) REVERT: A 3902 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7562 (m-30) REVERT: A 3985 GLN cc_start: 0.7762 (tt0) cc_final: 0.7438 (tt0) REVERT: A 3990 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6652 (tp) REVERT: A 4012 ASN cc_start: 0.8401 (OUTLIER) cc_final: 0.8052 (m110) REVERT: A 4020 ILE cc_start: 0.7983 (mm) cc_final: 0.7397 (mp) REVERT: A 4081 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.8059 (t70) REVERT: A 4171 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7354 (mmmt) REVERT: A 4329 ARG cc_start: 0.7357 (ttm110) cc_final: 0.6653 (mtm-85) REVERT: A 4343 MET cc_start: 0.8740 (mtp) cc_final: 0.8455 (mtp) REVERT: A 4424 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7802 (tp) REVERT: A 4453 ASN cc_start: 0.6974 (m110) cc_final: 0.6750 (t0) REVERT: A 4466 HIS cc_start: 0.8372 (m170) cc_final: 0.8157 (m-70) REVERT: A 4481 ASP cc_start: 0.7900 (t0) cc_final: 0.7266 (t0) REVERT: A 4574 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6777 (ttmm) REVERT: A 4589 GLN cc_start: 0.7997 (mt0) cc_final: 0.7757 (mt0) outliers start: 83 outliers final: 33 residues processed: 366 average time/residue: 1.5980 time to fit residues: 667.5835 Evaluate side-chains 362 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 311 time to evaluate : 3.863 ------------------------------------------------------------------------------- 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 1750 VAL Chi-restraints excluded: chain A residue 1851 THR 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 2175 MET Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2272 THR 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 2617 VAL 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 3016 GLU Chi-restraints excluded: chain A residue 3043 MET 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 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 3796 THR Chi-restraints excluded: chain A residue 3902 ASP Chi-restraints excluded: chain A residue 3990 LEU Chi-restraints excluded: chain A residue 4012 ASN 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 4202 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 78 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 271 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 275 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2187 GLN A2476 HIS A2654 GLN A3087 ASN ** A3145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3523 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.151863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.110952 restraints weight = 25075.040| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.70 r_work: 0.3062 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3485 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= 0.137 Angle : 0.511 15.857 32815 Z= 0.255 Chirality : 0.040 0.161 3690 Planarity : 0.004 0.087 4203 Dihedral : 6.901 134.538 3259 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.38 % Allowed : 15.41 % 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: 2.19 (0.16), residues: 2927 helix: 2.23 (0.12), residues: 1725 sheet: -0.27 (0.33), residues: 233 loop : 0.60 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2234 HIS 0.007 0.001 HIS A1810 PHE 0.018 0.002 PHE A1568 TYR 0.021 0.001 TYR A2748 ARG 0.006 0.000 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 1414) hydrogen bonds : angle 4.07914 ( 4095) covalent geometry : bond 0.00314 (24195) covalent geometry : angle 0.51113 (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 378 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 316 time to evaluate : 3.052 Fit side-chains REVERT: A 1471 ASN cc_start: 0.7795 (m-40) cc_final: 0.7492 (m110) REVERT: A 1556 ASP cc_start: 0.7524 (p0) cc_final: 0.7035 (p0) REVERT: A 1573 THR cc_start: 0.8024 (OUTLIER) cc_final: 0.7781 (p) REVERT: A 1580 LYS cc_start: 0.7750 (mmmt) cc_final: 0.7230 (mttt) REVERT: A 1602 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7937 (mt-10) REVERT: A 1613 LYS cc_start: 0.8297 (mmtm) cc_final: 0.8080 (mmtm) REVERT: A 1635 GLU cc_start: 0.8215 (tp30) cc_final: 0.7755 (tm-30) REVERT: A 1892 MET cc_start: 0.8836 (mmp) cc_final: 0.8576 (mmp) REVERT: A 2000 GLU cc_start: 0.8471 (tt0) cc_final: 0.8255 (tp30) REVERT: A 2012 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8375 (tmt) REVERT: A 2060 ARG cc_start: 0.7987 (mtm110) cc_final: 0.7411 (ptt90) REVERT: A 2074 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8025 (mtmt) REVERT: A 2106 GLU cc_start: 0.7481 (pt0) cc_final: 0.7089 (mt-10) REVERT: A 2113 ARG cc_start: 0.6776 (mtm-85) cc_final: 0.6359 (mtm-85) REVERT: A 2175 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7542 (mtt) REVERT: A 2188 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8121 (pt0) REVERT: A 2554 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7503 (tm-30) REVERT: A 2617 VAL cc_start: 0.9327 (OUTLIER) cc_final: 0.9084 (p) REVERT: A 2801 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8367 (ttp-170) REVERT: A 2855 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7599 (mm) REVERT: A 2867 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7738 (mtp) REVERT: A 2898 LYS cc_start: 0.8688 (tttt) cc_final: 0.8209 (tttm) REVERT: A 3016 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7870 (pt0) REVERT: A 3217 GLU cc_start: 0.6962 (pp20) cc_final: 0.6177 (tt0) REVERT: A 3464 ASP cc_start: 0.6045 (t0) cc_final: 0.5658 (m-30) REVERT: A 3523 GLN cc_start: 0.8150 (mp10) cc_final: 0.7740 (tp-100) REVERT: A 3524 MET cc_start: 0.8833 (tpt) cc_final: 0.8424 (mmm) REVERT: A 3551 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7793 (mm-30) REVERT: A 3746 GLU cc_start: 0.7380 (mm-30) cc_final: 0.6903 (tp30) REVERT: A 3747 LYS cc_start: 0.7066 (mtpp) cc_final: 0.6716 (tppt) REVERT: A 3756 VAL cc_start: 0.7212 (p) cc_final: 0.6892 (p) REVERT: A 3782 ARG cc_start: 0.7305 (ttp-110) cc_final: 0.7101 (tmm160) REVERT: A 3793 GLU cc_start: 0.6929 (tm-30) cc_final: 0.6639 (tt0) REVERT: A 3902 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7527 (m-30) REVERT: A 3985 GLN cc_start: 0.7734 (tt0) cc_final: 0.7413 (tt0) REVERT: A 3990 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6599 (tp) REVERT: A 4012 ASN cc_start: 0.8362 (OUTLIER) cc_final: 0.7967 (m110) REVERT: A 4020 ILE cc_start: 0.7962 (mm) cc_final: 0.7373 (mp) REVERT: A 4081 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.8045 (t70) REVERT: A 4159 ARG cc_start: 0.7746 (ttm170) cc_final: 0.7431 (ttm170) REVERT: A 4171 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7350 (mmmt) REVERT: A 4329 ARG cc_start: 0.7319 (ttm110) cc_final: 0.6613 (mtm-85) REVERT: A 4343 MET cc_start: 0.8735 (mtp) cc_final: 0.8434 (mtp) REVERT: A 4424 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7771 (tp) REVERT: A 4481 ASP cc_start: 0.7779 (t0) cc_final: 0.7166 (t0) REVERT: A 4574 LYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6647 (ttmm) REVERT: A 4589 GLN cc_start: 0.7975 (mt0) cc_final: 0.7748 (mt0) outliers start: 62 outliers final: 24 residues processed: 348 average time/residue: 1.6469 time to fit residues: 648.7337 Evaluate side-chains 355 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 313 time to evaluate : 2.686 ------------------------------------------------------------------------------- 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 2175 MET Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2535 ILE Chi-restraints excluded: chain A residue 2554 GLN Chi-restraints excluded: chain A residue 2617 VAL 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 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 4012 ASN 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 4202 SER 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 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: 0.7980 chunk 132 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 212 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 241 optimal weight: 0.5980 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: 0.7180 ------------------------------------------------------------------------------- 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 A2654 GLN A3087 ASN ** A3145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3523 GLN ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3800 GLN A4063 ASN A4108 GLN A4466 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.112363 restraints weight = 24996.837| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.66 r_work: 0.3065 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24195 Z= 0.124 Angle : 0.502 15.947 32815 Z= 0.250 Chirality : 0.039 0.158 3690 Planarity : 0.004 0.090 4203 Dihedral : 6.793 131.786 3259 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.42 % Allowed : 15.64 % Favored : 81.94 % 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: 2.26 (0.16), residues: 2927 helix: 2.29 (0.12), residues: 1726 sheet: -0.28 (0.33), residues: 232 loop : 0.62 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2234 HIS 0.006 0.001 HIS A2476 PHE 0.026 0.001 PHE A4008 TYR 0.020 0.001 TYR A2748 ARG 0.006 0.000 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 1414) hydrogen bonds : angle 4.02260 ( 4095) covalent geometry : bond 0.00280 (24195) covalent geometry : angle 0.50247 (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: 63 poor density : 312 time to evaluate : 2.615 Fit side-chains REVERT: A 1471 ASN cc_start: 0.7761 (m-40) cc_final: 0.7444 (m110) REVERT: A 1556 ASP cc_start: 0.7542 (p0) cc_final: 0.7063 (p0) REVERT: A 1573 THR cc_start: 0.8026 (OUTLIER) cc_final: 0.7774 (p) REVERT: A 1580 LYS cc_start: 0.7727 (mmmt) cc_final: 0.7227 (mttt) REVERT: A 1602 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7989 (mt-10) REVERT: A 1613 LYS cc_start: 0.8292 (mmtm) cc_final: 0.8077 (mmtm) REVERT: A 1635 GLU cc_start: 0.8168 (tp30) cc_final: 0.7722 (tm-30) REVERT: A 1892 MET cc_start: 0.8840 (mmp) cc_final: 0.8542 (mmp) REVERT: A 2012 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8366 (tmt) REVERT: A 2060 ARG cc_start: 0.8033 (mtm110) cc_final: 0.7506 (ptt90) REVERT: A 2074 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8236 (mmmt) REVERT: A 2106 GLU cc_start: 0.7505 (pt0) cc_final: 0.7109 (mt-10) REVERT: A 2113 ARG cc_start: 0.6834 (mtm-85) cc_final: 0.6407 (mtm-85) REVERT: A 2175 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7583 (mtt) REVERT: A 2188 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8148 (pt0) REVERT: A 2617 VAL cc_start: 0.9322 (OUTLIER) cc_final: 0.9085 (p) REVERT: A 2801 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8381 (ttp-170) REVERT: A 2804 ARG cc_start: 0.8418 (tpt170) cc_final: 0.8197 (tpt170) REVERT: A 2855 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7596 (mm) REVERT: A 2867 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7730 (mtp) REVERT: A 2898 LYS cc_start: 0.8690 (tttt) cc_final: 0.8221 (tttm) REVERT: A 3006 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: A 3016 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7874 (pt0) REVERT: A 3464 ASP cc_start: 0.6058 (t0) cc_final: 0.5671 (m-30) REVERT: A 3523 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7765 (tp-100) REVERT: A 3524 MET cc_start: 0.8823 (tpt) cc_final: 0.8368 (mmm) REVERT: A 3551 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7791 (mm-30) REVERT: A 3746 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6892 (tp30) REVERT: A 3747 LYS cc_start: 0.7209 (mtpp) cc_final: 0.6874 (tppt) REVERT: A 3756 VAL cc_start: 0.7142 (p) cc_final: 0.6718 (p) REVERT: A 3775 ARG cc_start: 0.7885 (ttm-80) cc_final: 0.7577 (ttp-110) REVERT: A 3782 ARG cc_start: 0.7312 (ttp-110) cc_final: 0.7111 (tmm160) REVERT: A 3793 GLU cc_start: 0.6849 (tm-30) cc_final: 0.6623 (tt0) REVERT: A 3902 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7554 (m-30) REVERT: A 3985 GLN cc_start: 0.7756 (tt0) cc_final: 0.7322 (tt0) REVERT: A 3990 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6677 (tp) REVERT: A 4020 ILE cc_start: 0.8002 (mm) cc_final: 0.7412 (mp) REVERT: A 4081 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.8038 (t70) REVERT: A 4159 ARG cc_start: 0.7757 (ttm170) cc_final: 0.7441 (ttm170) REVERT: A 4171 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7342 (mmmt) REVERT: A 4329 ARG cc_start: 0.7330 (ttm110) cc_final: 0.6644 (mtm-85) REVERT: A 4343 MET cc_start: 0.8748 (mtp) cc_final: 0.8444 (mtp) REVERT: A 4424 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7823 (tp) REVERT: A 4481 ASP cc_start: 0.7570 (t0) cc_final: 0.6970 (t0) REVERT: A 4574 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6643 (mttm) REVERT: A 4589 GLN cc_start: 0.7966 (mt0) cc_final: 0.7733 (mt0) outliers start: 63 outliers final: 28 residues processed: 345 average time/residue: 1.6140 time to fit residues: 629.7264 Evaluate side-chains 352 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 306 time to evaluate : 2.532 ------------------------------------------------------------------------------- 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 1973 GLN 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 2175 MET 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 2617 VAL 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 3523 GLN 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 4251 ILE Chi-restraints excluded: chain A residue 4259 GLU Chi-restraints excluded: chain A residue 4424 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 244 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 290 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 0.0980 chunk 239 optimal weight: 2.9990 chunk 237 optimal weight: 0.9990 chunk 274 optimal weight: 3.9990 chunk 136 optimal weight: 0.0270 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2047 GLN A2187 GLN A2476 HIS A2654 GLN A3087 ASN ** A3145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3523 GLN ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3800 GLN A4063 ASN A4108 GLN A4466 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.152470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.111644 restraints weight = 24972.340| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.70 r_work: 0.3065 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24195 Z= 0.131 Angle : 0.510 16.183 32815 Z= 0.253 Chirality : 0.040 0.160 3690 Planarity : 0.004 0.094 4203 Dihedral : 6.783 130.214 3259 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.27 % Allowed : 16.06 % Favored : 81.67 % 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: 2.27 (0.16), residues: 2927 helix: 2.30 (0.12), residues: 1726 sheet: -0.17 (0.32), residues: 240 loop : 0.60 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.007 0.001 HIS A1810 PHE 0.024 0.001 PHE A4008 TYR 0.022 0.001 TYR A2748 ARG 0.010 0.000 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.04217 ( 1414) hydrogen bonds : angle 4.02889 ( 4095) covalent geometry : bond 0.00301 (24195) covalent geometry : angle 0.51012 (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 367 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 308 time to evaluate : 2.523 Fit side-chains REVERT: A 1471 ASN cc_start: 0.7757 (m-40) cc_final: 0.7431 (m110) REVERT: A 1556 ASP cc_start: 0.7550 (p0) cc_final: 0.7061 (p0) REVERT: A 1573 THR cc_start: 0.8023 (OUTLIER) cc_final: 0.7765 (p) REVERT: A 1580 LYS cc_start: 0.7723 (mmmt) cc_final: 0.7220 (mttt) REVERT: A 1602 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7983 (mt-10) REVERT: A 1613 LYS cc_start: 0.8304 (mmtm) cc_final: 0.8085 (mmtm) REVERT: A 1635 GLU cc_start: 0.8169 (tp30) cc_final: 0.7720 (tm-30) REVERT: A 1892 MET cc_start: 0.8834 (mmp) cc_final: 0.8533 (mmp) REVERT: A 2012 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8353 (tmt) REVERT: A 2060 ARG cc_start: 0.8020 (mtm110) cc_final: 0.7490 (ptt90) REVERT: A 2074 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8232 (mmmt) REVERT: A 2106 GLU cc_start: 0.7485 (pt0) cc_final: 0.7084 (mt-10) REVERT: A 2113 ARG cc_start: 0.6822 (mtm-85) cc_final: 0.6408 (mtm-85) REVERT: A 2175 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7579 (mtt) REVERT: A 2188 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8141 (pt0) REVERT: A 2617 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.9100 (p) REVERT: A 2801 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8370 (ttp-170) REVERT: A 2855 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7596 (mm) REVERT: A 2867 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7726 (mtp) REVERT: A 2898 LYS cc_start: 0.8689 (tttt) cc_final: 0.8209 (tttm) REVERT: A 3016 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7860 (pt0) REVERT: A 3464 ASP cc_start: 0.6035 (t0) cc_final: 0.5648 (m-30) REVERT: A 3551 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7791 (mm-30) REVERT: A 3746 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6817 (tp30) REVERT: A 3747 LYS cc_start: 0.7226 (mtpp) cc_final: 0.6864 (tppt) REVERT: A 3756 VAL cc_start: 0.7089 (p) cc_final: 0.6669 (p) REVERT: A 3775 ARG cc_start: 0.7862 (ttm-80) cc_final: 0.7328 (ttp-110) REVERT: A 3793 GLU cc_start: 0.6873 (tm-30) cc_final: 0.6592 (tt0) REVERT: A 3795 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6598 (tt0) REVERT: A 3902 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7554 (m-30) REVERT: A 3985 GLN cc_start: 0.7724 (tt0) cc_final: 0.7394 (tt0) REVERT: A 3990 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6577 (tp) REVERT: A 4020 ILE cc_start: 0.7983 (mm) cc_final: 0.7390 (mp) REVERT: A 4081 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.8024 (t70) REVERT: A 4159 ARG cc_start: 0.7748 (ttm170) cc_final: 0.7424 (ttm170) REVERT: A 4171 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7342 (mmmt) REVERT: A 4329 ARG cc_start: 0.7312 (ttm110) cc_final: 0.6624 (mtm-85) REVERT: A 4343 MET cc_start: 0.8716 (mtp) cc_final: 0.8417 (mtp) REVERT: A 4424 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7790 (tp) REVERT: A 4481 ASP cc_start: 0.7567 (t0) cc_final: 0.6968 (t0) REVERT: A 4574 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6624 (mttm) REVERT: A 4589 GLN cc_start: 0.7958 (mt0) cc_final: 0.7657 (mt0) outliers start: 59 outliers final: 32 residues processed: 338 average time/residue: 1.6799 time to fit residues: 640.7126 Evaluate side-chains 355 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 307 time to evaluate : 2.731 ------------------------------------------------------------------------------- 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 1579 MET Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1973 GLN 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 2175 MET 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 2616 GLU Chi-restraints excluded: chain A residue 2617 VAL 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 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 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 4043 MET 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 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: 0.6980 chunk 52 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 241 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 160 optimal weight: 0.5980 chunk 239 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2047 GLN A2187 GLN A2654 GLN A3087 ASN ** A3145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3523 GLN ** A3584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3800 GLN A4063 ASN A4108 GLN A4466 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.152712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.111843 restraints weight = 25096.097| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.72 r_work: 0.3071 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24195 Z= 0.127 Angle : 0.508 15.535 32815 Z= 0.253 Chirality : 0.040 0.161 3690 Planarity : 0.004 0.097 4203 Dihedral : 6.741 127.800 3259 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.11 % Allowed : 16.37 % Favored : 81.52 % 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: 2.29 (0.16), residues: 2927 helix: 2.32 (0.12), residues: 1726 sheet: -0.16 (0.32), residues: 240 loop : 0.61 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2234 HIS 0.006 0.001 HIS A1810 PHE 0.025 0.001 PHE A4008 TYR 0.021 0.001 TYR A2748 ARG 0.010 0.000 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 1414) hydrogen bonds : angle 4.01267 ( 4095) covalent geometry : bond 0.00289 (24195) covalent geometry : angle 0.50767 (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 363 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 308 time to evaluate : 2.710 Fit side-chains REVERT: A 1471 ASN cc_start: 0.7757 (m-40) cc_final: 0.7431 (m110) REVERT: A 1556 ASP cc_start: 0.7535 (p0) cc_final: 0.7016 (p0) REVERT: A 1569 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7244 (mm-40) REVERT: A 1573 THR cc_start: 0.8011 (OUTLIER) cc_final: 0.7765 (p) REVERT: A 1580 LYS cc_start: 0.7713 (mmmt) cc_final: 0.7215 (mttt) REVERT: A 1602 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7976 (mt-10) REVERT: A 1613 LYS cc_start: 0.8278 (mmtm) cc_final: 0.8061 (mmtm) REVERT: A 1635 GLU cc_start: 0.8150 (tp30) cc_final: 0.7697 (tm-30) REVERT: A 1892 MET cc_start: 0.8812 (mmp) cc_final: 0.8506 (mmp) REVERT: A 2012 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8345 (tmt) REVERT: A 2060 ARG cc_start: 0.8025 (mtm110) cc_final: 0.7488 (ptt90) REVERT: A 2074 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8208 (mmmt) REVERT: A 2106 GLU cc_start: 0.7487 (pt0) cc_final: 0.7083 (mt-10) REVERT: A 2113 ARG cc_start: 0.6802 (mtm-85) cc_final: 0.6374 (mtm-85) REVERT: A 2175 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7526 (mtt) REVERT: A 2188 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8155 (pt0) REVERT: A 2617 VAL cc_start: 0.9343 (OUTLIER) cc_final: 0.9105 (p) REVERT: A 2801 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8352 (ttp-170) REVERT: A 2855 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7625 (mm) REVERT: A 2867 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7727 (mtp) REVERT: A 2898 LYS cc_start: 0.8685 (tttt) cc_final: 0.8206 (tttm) REVERT: A 3016 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7850 (pt0) REVERT: A 3217 GLU cc_start: 0.7013 (pp20) cc_final: 0.6263 (tt0) REVERT: A 3464 ASP cc_start: 0.6038 (t0) cc_final: 0.5649 (m-30) REVERT: A 3523 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7755 (tp-100) REVERT: A 3551 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7783 (mm-30) REVERT: A 3746 GLU cc_start: 0.7326 (mm-30) cc_final: 0.6862 (tp30) REVERT: A 3747 LYS cc_start: 0.7253 (mtpp) cc_final: 0.6848 (tppt) REVERT: A 3756 VAL cc_start: 0.6922 (p) cc_final: 0.6504 (p) REVERT: A 3775 ARG cc_start: 0.7794 (ttm-80) cc_final: 0.7359 (ttp-110) REVERT: A 3793 GLU cc_start: 0.6892 (tm-30) cc_final: 0.6619 (tt0) REVERT: A 3795 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6583 (tm-30) REVERT: A 3902 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7671 (m-30) REVERT: A 3985 GLN cc_start: 0.7738 (tt0) cc_final: 0.7410 (tt0) REVERT: A 3990 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6573 (tp) REVERT: A 4020 ILE cc_start: 0.7975 (mm) cc_final: 0.7388 (mp) REVERT: A 4081 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.8023 (t70) REVERT: A 4159 ARG cc_start: 0.7746 (ttm170) cc_final: 0.7422 (ttm170) REVERT: A 4171 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7315 (mmmt) REVERT: A 4329 ARG cc_start: 0.7312 (ttm110) cc_final: 0.6624 (mtm-85) REVERT: A 4343 MET cc_start: 0.8716 (mtp) cc_final: 0.8413 (mtp) REVERT: A 4424 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7806 (tp) REVERT: A 4481 ASP cc_start: 0.7605 (t0) cc_final: 0.6986 (t0) REVERT: A 4574 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6630 (mttm) REVERT: A 4589 GLN cc_start: 0.7974 (mt0) cc_final: 0.7735 (mt0) outliers start: 55 outliers final: 30 residues processed: 337 average time/residue: 1.6573 time to fit residues: 631.9299 Evaluate side-chains 351 residues out of total 2603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 304 time to evaluate : 2.478 ------------------------------------------------------------------------------- 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 1973 GLN 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 2175 MET Chi-restraints excluded: chain A residue 2220 LEU 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 2617 VAL 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 3016 GLU Chi-restraints excluded: chain A residue 3121 ILE Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3523 GLN 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 4043 MET 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 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: 5.9990 chunk 251 optimal weight: 0.0770 chunk 131 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 279 optimal weight: 5.9990 chunk 281 optimal weight: 5.9990 chunk 254 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 164 optimal weight: 0.0170 chunk 282 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.5576 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3523 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.152722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.112019 restraints weight = 24896.274| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.70 r_work: 0.3055 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.130 24195 Z= 0.143 Angle : 0.683 59.200 32815 Z= 0.373 Chirality : 0.039 0.159 3690 Planarity : 0.004 0.098 4203 Dihedral : 6.739 127.800 3259 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.04 % Allowed : 16.48 % Favored : 81.48 % Cbeta Deviations : 0.04 % 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: 2.29 (0.16), residues: 2927 helix: 2.31 (0.12), residues: 1726 sheet: -0.17 (0.32), residues: 240 loop : 0.61 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2234 HIS 0.005 0.001 HIS A1810 PHE 0.023 0.001 PHE A4008 TYR 0.021 0.001 TYR A2748 ARG 0.007 0.000 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 1414) hydrogen bonds : angle 4.01296 ( 4095) covalent geometry : bond 0.00309 (24195) covalent geometry : angle 0.68275 (32815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20699.88 seconds wall clock time: 357 minutes 55.29 seconds (21475.29 seconds total)