Starting phenix.real_space_refine on Fri May 23 08:20:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bmr_44708/05_2025/9bmr_44708.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bmr_44708/05_2025/9bmr_44708.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/9bmr_44708/05_2025/9bmr_44708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bmr_44708/05_2025/9bmr_44708.map" model { file = "/net/cci-nas-00/data/ceres_data/9bmr_44708/05_2025/9bmr_44708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bmr_44708/05_2025/9bmr_44708.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= 0.062 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 15068 2.51 5 N 4090 2.21 5 O 4421 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: 23707 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 23593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2937, 23593 Classifications: {'peptide': 2937} Link IDs: {'PTRANS': 131, 'TRANS': 2805} 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: 13.74, per 1000 atoms: 0.58 Number of scatterers: 23707 At special positions: 0 Unit cell: (143, 119.9, 209, 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 4421 8.00 N 4090 7.00 C 15068 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: 6.03 Conformation dependent library (CDL) restraints added in 3.1 seconds 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5588 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: 3.89 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: 4.131A 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: 3.915A pdb=" N VAL A1536 " --> pdb=" O ALA A1532 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 3.650A 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: 4.009A 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: 4.204A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 3.873A 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: 3.991A 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: 3.503A 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: 3.507A pdb=" N GLU A2078 " --> pdb=" O LYS A2074 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2117 removed outlier: 3.679A 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: 3.876A 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: 3.520A 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: 3.631A 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: 3.783A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) removed outlier: 3.643A 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: 3.949A 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: 3.812A 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: 3.739A 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: 3.575A pdb=" N VAL A2899 " --> pdb=" O ALA A2895 " (cutoff:3.500A) removed outlier: 3.515A 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: 4.300A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) removed outlier: 3.517A 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: 3.563A pdb=" N THR A3010 " --> pdb=" O GLU A3006 " (cutoff:3.500A) removed outlier: 3.556A 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: 3.519A 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: 3.801A pdb=" N HIS A3155 " --> pdb=" O HIS A3151 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 3242 removed outlier: 3.623A 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: 3.635A 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: 3.591A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4175 through 4194 removed outlier: 3.769A pdb=" N LEU A4194 " --> pdb=" O ILE A4190 " (cutoff:3.500A) Processing helix chain 'A' and resid 4196 through 4201 removed outlier: 3.881A 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: 3.521A 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: 3.568A 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: 11.568A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.382A 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: 7.872A 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: 7.006A 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: 7.342A 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: 6.381A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 8.140A 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: 6.123A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 8.069A 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: 7.854A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.404A 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: 7.625A 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: 6.538A pdb=" N PHE A3094 " --> pdb=" O LEU A2934 " (cutoff:3.500A) removed outlier: 7.415A 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: 7.763A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.554A 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: 7.161A 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: 6.130A 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: 7.190A pdb=" N ILE A4581 " --> pdb=" O GLY A4567 " (cutoff:3.500A) removed outlier: 9.584A 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: 9.942A 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: 7.052A 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: 6.495A pdb=" N LEU A4607 " --> pdb=" O THR A4621 " (cutoff:3.500A) removed outlier: 4.494A 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) 1415 hydrogen bonds defined for protein. 4098 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: 13.56 Time building geometry restraints manager: 7.01 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: 7817 1.34 - 1.46: 4781 1.46 - 1.58: 11405 1.58 - 1.69: 14 1.69 - 1.81: 196 Bond restraints: 24213 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 3.01e+01 bond pdb=" C4 ADP A4701 " pdb=" C5 ADP A4701 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.93e+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 2.92e+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 1.74e+01 bond pdb=" C5 ADP A4701 " pdb=" C6 ADP A4701 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.72e+01 ... (remaining 24208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 32469 2.45 - 4.91: 324 4.91 - 7.36: 28 7.36 - 9.81: 10 9.81 - 12.27: 7 Bond angle restraints: 32838 Sorted by residual: angle pdb=" PB ATP A4702 " pdb=" O3B ATP A4702 " pdb=" PG ATP A4702 " ideal model delta sigma weight residual 139.87 134.14 5.73 1.00e+00 1.00e+00 3.28e+01 angle pdb=" PA ADP A4704 " pdb=" O3A ADP A4704 " pdb=" PB ADP A4704 " ideal model delta sigma weight residual 120.50 132.77 -12.27 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 120.50 132.68 -12.18 3.00e+00 1.11e-01 1.65e+01 angle pdb=" PA ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PB ADP A4701 " ideal model delta sigma weight residual 120.50 131.52 -11.02 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 111.00 100.16 10.84 3.00e+00 1.11e-01 1.31e+01 ... (remaining 32833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.15: 14305 31.15 - 62.30: 316 62.30 - 93.45: 68 93.45 - 124.60: 2 124.60 - 155.75: 2 Dihedral angle restraints: 14693 sinusoidal: 6090 harmonic: 8603 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 95.74 -155.75 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 300.00 174.39 125.61 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 50.57 -110.57 1 2.00e+01 2.50e-03 3.24e+01 ... (remaining 14690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2754 0.042 - 0.083: 708 0.083 - 0.124: 204 0.124 - 0.166: 21 0.166 - 0.207: 5 Chirality restraints: 3692 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 1.08e+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 9.95e-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 8.85e-01 ... (remaining 3689 not shown) Planarity restraints: 4206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A4195 " 0.449 9.50e-02 1.11e+02 2.01e-01 2.48e+01 pdb=" NE ARG A4195 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A4195 " -0.004 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 4.65e+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 4.68e-02 3.50e+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 4203 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 31 2.38 - 3.01: 12568 3.01 - 3.64: 37801 3.64 - 4.27: 58426 4.27 - 4.90: 93728 Nonbonded interactions: 202554 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 2.095 2.170 nonbonded pdb=" O3B ADP A4701 " pdb="MG MG A4705 " model vdw 2.102 2.170 ... (remaining 202549 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=0.00 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: 4.800 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: 1.060 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 58.630 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: 0.000 Load rotamer database and sin/cos tables:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 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 24213 Z= 0.211 Angle : 0.621 12.268 32838 Z= 0.328 Chirality : 0.041 0.207 3692 Planarity : 0.005 0.201 4206 Dihedral : 14.217 155.747 9105 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.54 % Favored : 98.40 % 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: 2929 helix: 1.48 (0.12), residues: 1704 sheet: 0.08 (0.34), residues: 235 loop : 0.76 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A1537 HIS 0.014 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 0.20841 ( 1415) hydrogen bonds : angle 6.47179 ( 4098) covalent geometry : bond 0.00386 (24213) covalent geometry : angle 0.62059 (32838) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 602 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1531 MET cc_start: 0.8839 (tpp) cc_final: 0.8520 (mmm) REVERT: A 1709 MET cc_start: 0.8726 (ttp) cc_final: 0.8395 (ttp) REVERT: A 1941 MET cc_start: 0.8160 (mmm) cc_final: 0.7750 (mmm) REVERT: A 2273 ARG cc_start: 0.8333 (mmm160) cc_final: 0.8111 (mmm160) REVERT: A 3169 MET cc_start: 0.8553 (mmt) cc_final: 0.8318 (mmp) REVERT: A 3483 SER cc_start: 0.6291 (t) cc_final: 0.6001 (m) REVERT: A 4590 LEU cc_start: 0.8373 (mt) cc_final: 0.8150 (mp) outliers start: 0 outliers final: 1 residues processed: 602 average time/residue: 1.6495 time to fit residues: 1118.2078 Evaluate side-chains 342 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 341 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3077 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 247 optimal weight: 0.9980 chunk 222 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 chunk 266 optimal weight: 0.0470 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1471 ASN A1643 ASN A1646 ASN A1670 ASN A2713 ASN A3092 ASN A3542 GLN A3602 ASN A3709 GLN A3735 GLN A3826 GLN A3985 GLN A4062 GLN A4079 GLN A4108 GLN A4307 GLN A4386 ASN A4393 GLN A4404 ASN A4506 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.143762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.116632 restraints weight = 29487.244| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.60 r_work: 0.3299 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24213 Z= 0.141 Angle : 0.554 6.992 32838 Z= 0.285 Chirality : 0.041 0.148 3692 Planarity : 0.004 0.044 4206 Dihedral : 7.347 154.310 3263 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.30 % Allowed : 10.60 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.16), residues: 2929 helix: 1.91 (0.12), residues: 1732 sheet: -0.03 (0.32), residues: 253 loop : 0.71 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.012 0.001 HIS A1810 PHE 0.025 0.002 PHE A4413 TYR 0.021 0.001 TYR A4196 ARG 0.010 0.001 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.05085 ( 1415) hydrogen bonds : angle 4.47705 ( 4098) covalent geometry : bond 0.00307 (24213) covalent geometry : angle 0.55429 (32838) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 367 time to evaluate : 2.774 Fit side-chains revert: symmetry clash REVERT: A 1462 PHE cc_start: 0.6908 (OUTLIER) cc_final: 0.6392 (m-10) REVERT: A 1566 GLN cc_start: 0.7324 (mm110) cc_final: 0.7123 (mm-40) REVERT: A 1589 MET cc_start: 0.7561 (mmm) cc_final: 0.7293 (mmm) REVERT: A 1709 MET cc_start: 0.8993 (ttp) cc_final: 0.8555 (ttp) REVERT: A 1941 MET cc_start: 0.8874 (mmm) cc_final: 0.8356 (mmm) REVERT: A 1980 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7373 (mt-10) REVERT: A 2051 GLN cc_start: 0.7956 (tm130) cc_final: 0.7718 (tt0) REVERT: A 2074 LYS cc_start: 0.8039 (mptt) cc_final: 0.7834 (mptt) REVERT: A 2133 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7375 (mt-10) REVERT: A 2152 GLU cc_start: 0.7650 (pm20) cc_final: 0.7066 (mt-10) REVERT: A 2205 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8121 (mm-30) REVERT: A 2412 MET cc_start: 0.7039 (tpp) cc_final: 0.6691 (tpt) REVERT: A 2603 MET cc_start: 0.8398 (ttp) cc_final: 0.7965 (ttp) REVERT: A 2616 GLU cc_start: 0.7924 (tt0) cc_final: 0.7392 (pt0) REVERT: A 2629 GLU cc_start: 0.7810 (tp30) cc_final: 0.7576 (tp30) REVERT: A 2640 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7949 (pp20) REVERT: A 2643 ARG cc_start: 0.7878 (mtp85) cc_final: 0.7653 (mmt-90) REVERT: A 3006 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7843 (tm-30) REVERT: A 3048 GLU cc_start: 0.7255 (pm20) cc_final: 0.6990 (tp30) REVERT: A 3156 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.6566 (mp-120) REVERT: A 3169 MET cc_start: 0.8855 (mmt) cc_final: 0.8354 (mmp) REVERT: A 3191 ARG cc_start: 0.7436 (ttm170) cc_final: 0.7152 (mmm-85) REVERT: A 3220 ARG cc_start: 0.6136 (tpp-160) cc_final: 0.5861 (mmm-85) REVERT: A 3558 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7423 (tt0) REVERT: A 3595 GLN cc_start: 0.7939 (mp10) cc_final: 0.7239 (pp30) REVERT: A 3895 THR cc_start: 0.7711 (m) cc_final: 0.7487 (p) REVERT: A 4023 GLN cc_start: 0.7547 (mm-40) cc_final: 0.7079 (mm-40) REVERT: A 4075 GLU cc_start: 0.7769 (tp30) cc_final: 0.7176 (pm20) REVERT: A 4224 ASP cc_start: 0.7930 (m-30) cc_final: 0.7693 (m-30) REVERT: A 4281 GLU cc_start: 0.7472 (mm-30) cc_final: 0.6863 (pp20) REVERT: A 4301 ARG cc_start: 0.7522 (ttm-80) cc_final: 0.6961 (ptt90) REVERT: A 4415 ARG cc_start: 0.7537 (mtp180) cc_final: 0.6739 (ttp-110) REVERT: A 4422 LYS cc_start: 0.7131 (tttt) cc_final: 0.6815 (tppt) REVERT: A 4571 ASN cc_start: 0.7276 (t0) cc_final: 0.6994 (t0) REVERT: A 4583 THR cc_start: 0.8244 (m) cc_final: 0.7865 (p) REVERT: A 4591 ARG cc_start: 0.7601 (ttt180) cc_final: 0.7110 (ttt90) REVERT: A 4617 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7477 (p0) outliers start: 60 outliers final: 19 residues processed: 404 average time/residue: 1.6350 time to fit residues: 745.9524 Evaluate side-chains 336 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 311 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1462 PHE Chi-restraints excluded: chain A residue 1465 GLN Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1799 GLU Chi-restraints excluded: chain A residue 2110 LYS Chi-restraints excluded: chain A residue 2133 GLU Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2654 GLN Chi-restraints excluded: chain A residue 2746 GLN Chi-restraints excluded: chain A residue 2764 THR Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2847 ASP Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3156 GLN Chi-restraints excluded: chain A residue 3680 SER Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3928 THR Chi-restraints excluded: chain A residue 4073 SER Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4204 LYS Chi-restraints excluded: chain A residue 4311 LEU Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 106 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 26 optimal weight: 0.1980 chunk 257 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 237 optimal weight: 0.9990 chunk 222 optimal weight: 0.9980 chunk 180 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1832 ASN A3063 HIS A3542 GLN A3754 ASN A3837 HIS A3906 GLN A4108 GLN A4232 ASN A4307 GLN A4572 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.142361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.114505 restraints weight = 29349.980| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.67 r_work: 0.3281 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24213 Z= 0.131 Angle : 0.504 6.707 32838 Z= 0.256 Chirality : 0.040 0.145 3692 Planarity : 0.004 0.042 4206 Dihedral : 6.896 146.397 3261 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.61 % Allowed : 12.09 % Favored : 85.30 % 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: 2.09 (0.16), residues: 2929 helix: 2.05 (0.12), residues: 1736 sheet: -0.03 (0.33), residues: 253 loop : 0.68 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.009 0.001 HIS A1810 PHE 0.020 0.002 PHE A4413 TYR 0.015 0.001 TYR A2748 ARG 0.009 0.001 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.04604 ( 1415) hydrogen bonds : angle 4.18074 ( 4098) covalent geometry : bond 0.00289 (24213) covalent geometry : angle 0.50412 (32838) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 346 time to evaluate : 2.710 Fit side-chains REVERT: A 1462 PHE cc_start: 0.6962 (OUTLIER) cc_final: 0.6387 (m-10) REVERT: A 1558 LYS cc_start: 0.7767 (tmmt) cc_final: 0.7561 (tmmt) REVERT: A 1564 GLU cc_start: 0.7559 (mp0) cc_final: 0.7355 (mp0) REVERT: A 1566 GLN cc_start: 0.7150 (mm110) cc_final: 0.6924 (mm-40) REVERT: A 1583 SER cc_start: 0.7749 (t) cc_final: 0.7402 (p) REVERT: A 1709 MET cc_start: 0.8963 (ttp) cc_final: 0.8526 (ttp) REVERT: A 1892 MET cc_start: 0.8658 (mmp) cc_final: 0.8333 (mmp) REVERT: A 1941 MET cc_start: 0.8920 (mmm) cc_final: 0.8719 (mmm) REVERT: A 2051 GLN cc_start: 0.7996 (tm130) cc_final: 0.7701 (tt0) REVERT: A 2133 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7428 (mt-10) REVERT: A 2152 GLU cc_start: 0.7742 (pm20) cc_final: 0.7159 (mt-10) REVERT: A 2310 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8316 (mt-10) REVERT: A 2412 MET cc_start: 0.7058 (tpp) cc_final: 0.6845 (tpt) REVERT: A 2508 LEU cc_start: 0.7905 (tp) cc_final: 0.7243 (pt) REVERT: A 2616 GLU cc_start: 0.7926 (tt0) cc_final: 0.7449 (pt0) REVERT: A 2629 GLU cc_start: 0.7988 (tp30) cc_final: 0.7681 (tp30) REVERT: A 2804 ARG cc_start: 0.8488 (tpt170) cc_final: 0.8201 (tpt170) REVERT: A 2848 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7936 (pt0) REVERT: A 3048 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.7073 (tp30) REVERT: A 3068 MET cc_start: 0.9305 (ptm) cc_final: 0.8932 (ptp) REVERT: A 3160 ARG cc_start: 0.7150 (mtp180) cc_final: 0.6857 (mtp-110) REVERT: A 3169 MET cc_start: 0.8861 (mmt) cc_final: 0.8462 (mmp) REVERT: A 3191 ARG cc_start: 0.7403 (ttm170) cc_final: 0.7117 (mmm-85) REVERT: A 3595 GLN cc_start: 0.7999 (mp10) cc_final: 0.7273 (pp30) REVERT: A 3747 LYS cc_start: 0.7460 (ttpt) cc_final: 0.7221 (tttt) REVERT: A 4023 GLN cc_start: 0.7512 (mm-40) cc_final: 0.7195 (mm-40) REVERT: A 4075 GLU cc_start: 0.7785 (tp30) cc_final: 0.7084 (pm20) REVERT: A 4128 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8671 (pmm) REVERT: A 4270 GLU cc_start: 0.7927 (pt0) cc_final: 0.7687 (mt-10) REVERT: A 4281 GLU cc_start: 0.7504 (mm-30) cc_final: 0.6820 (pp20) REVERT: A 4422 LYS cc_start: 0.7188 (tttt) cc_final: 0.6959 (tppt) REVERT: A 4456 VAL cc_start: 0.8084 (t) cc_final: 0.7590 (m) REVERT: A 4460 LEU cc_start: 0.8242 (tp) cc_final: 0.7944 (tm) REVERT: A 4546 THR cc_start: 0.6623 (m) cc_final: 0.6411 (p) REVERT: A 4572 ASN cc_start: 0.7616 (t0) cc_final: 0.7181 (t0) REVERT: A 4583 THR cc_start: 0.8221 (m) cc_final: 0.7640 (p) REVERT: A 4591 ARG cc_start: 0.7631 (ttt180) cc_final: 0.7171 (ttt90) outliers start: 68 outliers final: 24 residues processed: 387 average time/residue: 1.5815 time to fit residues: 694.1316 Evaluate side-chains 339 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 311 time to evaluate : 2.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1462 PHE Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1556 ASP Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1878 LYS Chi-restraints excluded: chain A residue 2133 GLU Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2847 ASP Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3048 GLU Chi-restraints excluded: chain A residue 3087 ASN Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3928 THR Chi-restraints excluded: chain A residue 3959 ILE Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4204 LYS Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4311 LEU Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4540 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 259 optimal weight: 0.4980 chunk 162 optimal weight: 3.9990 chunk 246 optimal weight: 0.9990 chunk 174 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 282 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2296 GLN A2476 HIS A2781 GLN A3542 GLN A4108 GLN A4232 ASN A4307 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.141646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.114563 restraints weight = 29571.924| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.66 r_work: 0.3277 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24213 Z= 0.131 Angle : 0.498 6.501 32838 Z= 0.252 Chirality : 0.040 0.146 3692 Planarity : 0.004 0.050 4206 Dihedral : 6.768 138.689 3261 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.38 % Allowed : 13.13 % Favored : 84.49 % 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: 2929 helix: 2.14 (0.12), residues: 1727 sheet: -0.01 (0.32), residues: 251 loop : 0.71 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.008 0.001 HIS A1810 PHE 0.017 0.001 PHE A2912 TYR 0.016 0.001 TYR A2748 ARG 0.010 0.001 ARG A2863 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 1415) hydrogen bonds : angle 4.07213 ( 4098) covalent geometry : bond 0.00298 (24213) covalent geometry : angle 0.49801 (32838) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 328 time to evaluate : 2.724 Fit side-chains REVERT: A 1462 PHE cc_start: 0.6968 (OUTLIER) cc_final: 0.6451 (m-10) REVERT: A 1464 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7576 (mtpt) REVERT: A 1566 GLN cc_start: 0.7062 (mm110) cc_final: 0.6849 (mm-40) REVERT: A 1583 SER cc_start: 0.7726 (t) cc_final: 0.7361 (p) REVERT: A 1584 LYS cc_start: 0.7501 (mmtp) cc_final: 0.7184 (ptpt) REVERT: A 1685 MET cc_start: 0.8627 (mmm) cc_final: 0.8394 (mmm) REVERT: A 1709 MET cc_start: 0.8929 (ttp) cc_final: 0.8505 (ttp) REVERT: A 2047 GLN cc_start: 0.8408 (tm-30) cc_final: 0.8038 (tp40) REVERT: A 2051 GLN cc_start: 0.7949 (tm130) cc_final: 0.7676 (tt0) REVERT: A 2133 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7315 (mm-30) REVERT: A 2310 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8332 (mt-10) REVERT: A 2412 MET cc_start: 0.7109 (tpp) cc_final: 0.6884 (tpt) REVERT: A 2513 GLU cc_start: 0.6969 (tm-30) cc_final: 0.6711 (mm-30) REVERT: A 2629 GLU cc_start: 0.7989 (tp30) cc_final: 0.7697 (tp30) REVERT: A 2759 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7850 (mm) REVERT: A 2848 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7920 (pt0) REVERT: A 3048 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.7006 (tp30) REVERT: A 3068 MET cc_start: 0.9319 (ptm) cc_final: 0.8942 (ptp) REVERT: A 3156 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.6869 (mp10) REVERT: A 3164 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6984 (ttp-110) REVERT: A 3169 MET cc_start: 0.8891 (mmt) cc_final: 0.8486 (mmp) REVERT: A 3188 HIS cc_start: 0.7743 (t70) cc_final: 0.6971 (m-70) REVERT: A 3191 ARG cc_start: 0.7364 (ttm170) cc_final: 0.7103 (mmm-85) REVERT: A 3542 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7882 (mt0) REVERT: A 3595 GLN cc_start: 0.8012 (mp10) cc_final: 0.7251 (pp30) REVERT: A 3904 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7916 (mp0) REVERT: A 3906 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7637 (tm-30) REVERT: A 4023 GLN cc_start: 0.7477 (mm-40) cc_final: 0.7078 (mm-40) REVERT: A 4075 GLU cc_start: 0.7763 (tp30) cc_final: 0.7034 (pm20) REVERT: A 4128 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8684 (pmm) REVERT: A 4209 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7359 (tp30) REVERT: A 4281 GLU cc_start: 0.7505 (mm-30) cc_final: 0.6843 (pp20) REVERT: A 4422 LYS cc_start: 0.7181 (tttt) cc_final: 0.6946 (tppt) REVERT: A 4572 ASN cc_start: 0.7574 (t0) cc_final: 0.7187 (t0) REVERT: A 4583 THR cc_start: 0.8237 (m) cc_final: 0.7626 (p) REVERT: A 4591 ARG cc_start: 0.7517 (ttt180) cc_final: 0.7073 (ttt90) outliers start: 62 outliers final: 23 residues processed: 363 average time/residue: 1.6680 time to fit residues: 686.2530 Evaluate side-chains 333 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 300 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1462 PHE Chi-restraints excluded: chain A residue 1464 LYS Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2133 GLU Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2759 ILE Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2847 ASP Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3048 GLU Chi-restraints excluded: chain A residue 3087 ASN Chi-restraints excluded: chain A residue 3156 GLN Chi-restraints excluded: chain A residue 3164 ARG Chi-restraints excluded: chain A residue 3718 LYS Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3904 GLU Chi-restraints excluded: chain A residue 3906 GLN Chi-restraints excluded: chain A residue 3928 THR Chi-restraints excluded: chain A residue 3959 ILE Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4204 LYS Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4311 LEU Chi-restraints excluded: chain A residue 4377 MET Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4507 ILE Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 114 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 275 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 249 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1612 GLN A2476 HIS A3854 GLN A4108 GLN A4232 ASN A4307 GLN A4397 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.140808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113512 restraints weight = 29651.304| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.67 r_work: 0.3265 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24213 Z= 0.143 Angle : 0.506 6.447 32838 Z= 0.256 Chirality : 0.041 0.151 3692 Planarity : 0.004 0.057 4206 Dihedral : 6.697 123.967 3261 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.57 % Allowed : 13.44 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.17 (0.16), residues: 2929 helix: 2.15 (0.12), residues: 1726 sheet: 0.01 (0.32), residues: 251 loop : 0.64 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.007 0.001 HIS A1810 PHE 0.017 0.002 PHE A1568 TYR 0.017 0.001 TYR A1546 ARG 0.011 0.001 ARG A2243 Details of bonding type rmsd hydrogen bonds : bond 0.04259 ( 1415) hydrogen bonds : angle 4.04581 ( 4098) covalent geometry : bond 0.00330 (24213) covalent geometry : angle 0.50647 (32838) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 323 time to evaluate : 2.932 Fit side-chains REVERT: A 1462 PHE cc_start: 0.6931 (OUTLIER) cc_final: 0.6458 (m-80) REVERT: A 1566 GLN cc_start: 0.7017 (mm110) cc_final: 0.6784 (mm-40) REVERT: A 1583 SER cc_start: 0.7820 (t) cc_final: 0.7392 (p) REVERT: A 1584 LYS cc_start: 0.7447 (mmtp) cc_final: 0.7170 (ptpt) REVERT: A 1612 GLN cc_start: 0.8364 (tt0) cc_final: 0.8086 (tt0) REVERT: A 1709 MET cc_start: 0.8874 (ttp) cc_final: 0.8534 (ttp) REVERT: A 2051 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7681 (tt0) REVERT: A 2133 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7492 (mm-30) REVERT: A 2310 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8375 (mt-10) REVERT: A 2412 MET cc_start: 0.7178 (tpp) cc_final: 0.6943 (tpt) REVERT: A 2629 GLU cc_start: 0.8024 (tp30) cc_final: 0.7783 (tp30) REVERT: A 2755 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8814 (ptt) REVERT: A 2759 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7841 (mm) REVERT: A 2804 ARG cc_start: 0.8446 (tpt170) cc_final: 0.8166 (tpt170) REVERT: A 2848 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7837 (pt0) REVERT: A 2953 MET cc_start: 0.8528 (mtp) cc_final: 0.8306 (mtp) REVERT: A 3048 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6950 (tp30) REVERT: A 3156 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.6821 (mp10) REVERT: A 3164 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6930 (ttp-110) REVERT: A 3169 MET cc_start: 0.8896 (mmt) cc_final: 0.8530 (mmp) REVERT: A 3178 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8017 (m-30) REVERT: A 3191 ARG cc_start: 0.7315 (ttm170) cc_final: 0.7036 (mmm-85) REVERT: A 3595 GLN cc_start: 0.7977 (mp10) cc_final: 0.7273 (pp30) REVERT: A 3729 SER cc_start: 0.8000 (m) cc_final: 0.7448 (p) REVERT: A 3790 VAL cc_start: 0.7637 (m) cc_final: 0.7436 (p) REVERT: A 3802 LEU cc_start: 0.8151 (mp) cc_final: 0.7415 (mp) REVERT: A 3893 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7248 (pttp) REVERT: A 3906 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7659 (tm-30) REVERT: A 4023 GLN cc_start: 0.7417 (mm-40) cc_final: 0.7105 (mm-40) REVERT: A 4075 GLU cc_start: 0.7742 (tp30) cc_final: 0.6869 (pm20) REVERT: A 4128 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8738 (pmm) REVERT: A 4281 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6733 (pp20) REVERT: A 4422 LYS cc_start: 0.7226 (tttt) cc_final: 0.6940 (tppt) REVERT: A 4456 VAL cc_start: 0.8049 (t) cc_final: 0.7641 (m) REVERT: A 4460 LEU cc_start: 0.8299 (tp) cc_final: 0.7969 (tm) REVERT: A 4572 ASN cc_start: 0.7597 (t0) cc_final: 0.7252 (t0) REVERT: A 4583 THR cc_start: 0.8212 (m) cc_final: 0.7884 (t) REVERT: A 4590 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7951 (mt) REVERT: A 4617 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7541 (p0) outliers start: 67 outliers final: 25 residues processed: 362 average time/residue: 1.6625 time to fit residues: 682.5800 Evaluate side-chains 344 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 305 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1462 PHE Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1556 ASP Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1878 LYS Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2051 GLN Chi-restraints excluded: chain A residue 2133 GLU Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2759 ILE Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2847 ASP Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 3048 GLU Chi-restraints excluded: chain A residue 3087 ASN Chi-restraints excluded: chain A residue 3156 GLN Chi-restraints excluded: chain A residue 3164 ARG Chi-restraints excluded: chain A residue 3178 ASP Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3718 LYS Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3893 LYS Chi-restraints excluded: chain A residue 3906 GLN Chi-restraints excluded: chain A residue 3928 THR Chi-restraints excluded: chain A residue 3959 ILE Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4204 LYS Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4311 LEU Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4590 LEU Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 144 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 275 optimal weight: 0.5980 chunk 249 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 288 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 131 optimal weight: 0.4980 chunk 150 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1810 HIS A2476 HIS A3499 GLN A3542 GLN A4054 HIS A4232 ASN A4307 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.139844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112698 restraints weight = 29445.568| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.61 r_work: 0.3255 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24213 Z= 0.157 Angle : 0.518 6.727 32838 Z= 0.261 Chirality : 0.041 0.157 3692 Planarity : 0.004 0.060 4206 Dihedral : 6.660 115.099 3261 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.07 % Allowed : 13.32 % Favored : 83.61 % 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: 2.14 (0.16), residues: 2929 helix: 2.13 (0.12), residues: 1726 sheet: 0.02 (0.32), residues: 251 loop : 0.64 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.007 0.001 HIS A1810 PHE 0.017 0.002 PHE A2912 TYR 0.016 0.001 TYR A2748 ARG 0.014 0.001 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.04290 ( 1415) hydrogen bonds : angle 4.05701 ( 4098) covalent geometry : bond 0.00368 (24213) covalent geometry : angle 0.51787 (32838) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 320 time to evaluate : 2.835 Fit side-chains revert: symmetry clash REVERT: A 1462 PHE cc_start: 0.6907 (OUTLIER) cc_final: 0.6466 (m-10) REVERT: A 1566 GLN cc_start: 0.7081 (mm110) cc_final: 0.6845 (mm-40) REVERT: A 1583 SER cc_start: 0.7862 (t) cc_final: 0.7410 (p) REVERT: A 1584 LYS cc_start: 0.7364 (mmtp) cc_final: 0.7044 (ptpt) REVERT: A 1709 MET cc_start: 0.8917 (ttp) cc_final: 0.8539 (ttp) REVERT: A 1750 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8135 (m) REVERT: A 2051 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: A 2310 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8407 (mt-10) REVERT: A 2412 MET cc_start: 0.7295 (tpp) cc_final: 0.7057 (tpt) REVERT: A 2763 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7501 (mtp85) REVERT: A 2848 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7909 (pt0) REVERT: A 2863 ARG cc_start: 0.7746 (ttt-90) cc_final: 0.6883 (ttt90) REVERT: A 2953 MET cc_start: 0.8533 (mtp) cc_final: 0.8256 (mtp) REVERT: A 3038 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7368 (tm-30) REVERT: A 3048 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6941 (tp30) REVERT: A 3156 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.6848 (mp10) REVERT: A 3163 LYS cc_start: 0.7680 (ttmm) cc_final: 0.7319 (mtmm) REVERT: A 3164 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.6881 (ttp-110) REVERT: A 3169 MET cc_start: 0.8890 (mmt) cc_final: 0.8532 (mmp) REVERT: A 3178 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8023 (m-30) REVERT: A 3191 ARG cc_start: 0.7416 (ttm170) cc_final: 0.7072 (mmm-85) REVERT: A 3542 GLN cc_start: 0.8382 (mm-40) cc_final: 0.7830 (mt0) REVERT: A 3595 GLN cc_start: 0.7989 (mp10) cc_final: 0.7275 (pp30) REVERT: A 3715 GLU cc_start: 0.8191 (tp30) cc_final: 0.7789 (tp30) REVERT: A 3729 SER cc_start: 0.8148 (m) cc_final: 0.7634 (p) REVERT: A 3795 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6768 (mm-30) REVERT: A 3893 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7194 (pttp) REVERT: A 3904 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: A 3906 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7656 (tm-30) REVERT: A 4022 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7579 (pt0) REVERT: A 4023 GLN cc_start: 0.7362 (mm-40) cc_final: 0.7086 (mm-40) REVERT: A 4075 GLU cc_start: 0.7761 (tp30) cc_final: 0.6914 (pm20) REVERT: A 4209 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7329 (tp30) REVERT: A 4281 GLU cc_start: 0.7410 (mm-30) cc_final: 0.6837 (pp20) REVERT: A 4415 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7359 (mtp180) REVERT: A 4422 LYS cc_start: 0.7220 (tttt) cc_final: 0.6880 (tppt) REVERT: A 4456 VAL cc_start: 0.8066 (t) cc_final: 0.7663 (m) REVERT: A 4460 LEU cc_start: 0.8370 (tp) cc_final: 0.8055 (tm) REVERT: A 4572 ASN cc_start: 0.7667 (t0) cc_final: 0.7357 (t0) REVERT: A 4583 THR cc_start: 0.8307 (m) cc_final: 0.7952 (t) REVERT: A 4590 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7960 (mt) outliers start: 80 outliers final: 33 residues processed: 368 average time/residue: 1.6297 time to fit residues: 685.4229 Evaluate side-chains 353 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 305 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1462 PHE Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1556 ASP Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1601 LEU Chi-restraints excluded: chain A residue 1635 GLU Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1878 LYS Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2051 GLN Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2746 GLN Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3038 GLN Chi-restraints excluded: chain A residue 3048 GLU Chi-restraints excluded: chain A residue 3087 ASN Chi-restraints excluded: chain A residue 3156 GLN Chi-restraints excluded: chain A residue 3164 ARG Chi-restraints excluded: chain A residue 3178 ASP Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3718 LYS Chi-restraints excluded: chain A residue 3755 GLU Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3893 LYS Chi-restraints excluded: chain A residue 3904 GLU Chi-restraints excluded: chain A residue 3906 GLN Chi-restraints excluded: chain A residue 3928 THR Chi-restraints excluded: chain A residue 3959 ILE Chi-restraints excluded: chain A residue 4022 GLU Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4311 LEU Chi-restraints excluded: chain A residue 4415 ARG Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4530 GLN Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4590 LEU Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 180 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 204 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 218 optimal weight: 0.7980 chunk 233 optimal weight: 0.6980 chunk 215 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: A1612 GLN A2476 HIS A4012 ASN A4232 ASN A4307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.140926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.114049 restraints weight = 29604.673| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.61 r_work: 0.3266 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24213 Z= 0.122 Angle : 0.495 6.497 32838 Z= 0.249 Chirality : 0.040 0.150 3692 Planarity : 0.004 0.063 4206 Dihedral : 6.516 114.920 3261 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.19 % Allowed : 14.66 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.25 (0.16), residues: 2929 helix: 2.24 (0.12), residues: 1725 sheet: -0.09 (0.32), residues: 256 loop : 0.68 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.002 0.001 HIS A3151 PHE 0.016 0.001 PHE A2912 TYR 0.018 0.001 TYR A2748 ARG 0.014 0.000 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 1415) hydrogen bonds : angle 3.97955 ( 4098) covalent geometry : bond 0.00275 (24213) covalent geometry : angle 0.49457 (32838) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 319 time to evaluate : 3.009 Fit side-chains revert: symmetry clash REVERT: A 1462 PHE cc_start: 0.6938 (OUTLIER) cc_final: 0.6505 (m-10) REVERT: A 1566 GLN cc_start: 0.7049 (mm110) cc_final: 0.6791 (mm-40) REVERT: A 1569 GLN cc_start: 0.7640 (tp40) cc_final: 0.6999 (tm-30) REVERT: A 1583 SER cc_start: 0.7723 (t) cc_final: 0.7244 (p) REVERT: A 1584 LYS cc_start: 0.7347 (mmtp) cc_final: 0.7030 (ptpt) REVERT: A 1709 MET cc_start: 0.8869 (ttp) cc_final: 0.8522 (ttp) REVERT: A 1750 VAL cc_start: 0.8449 (OUTLIER) cc_final: 0.8192 (m) REVERT: A 2051 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: A 2310 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8411 (mt-10) REVERT: A 2412 MET cc_start: 0.7213 (tpp) cc_final: 0.6981 (tpt) REVERT: A 2763 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7566 (mtp85) REVERT: A 2804 ARG cc_start: 0.8505 (tpt170) cc_final: 0.8239 (tpt170) REVERT: A 2848 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7924 (pt0) REVERT: A 2863 ARG cc_start: 0.7746 (ttt-90) cc_final: 0.6895 (ttt90) REVERT: A 2864 GLU cc_start: 0.7860 (tp30) cc_final: 0.6720 (mp0) REVERT: A 2953 MET cc_start: 0.8518 (mtp) cc_final: 0.8248 (mtp) REVERT: A 3048 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6890 (tp30) REVERT: A 3156 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7106 (mp10) REVERT: A 3163 LYS cc_start: 0.7693 (ttmm) cc_final: 0.7342 (mtmm) REVERT: A 3169 MET cc_start: 0.8907 (mmt) cc_final: 0.8544 (mmp) REVERT: A 3191 ARG cc_start: 0.7404 (ttm170) cc_final: 0.7065 (mmm-85) REVERT: A 3595 GLN cc_start: 0.7964 (mp10) cc_final: 0.7329 (pp30) REVERT: A 3715 GLU cc_start: 0.8205 (tp30) cc_final: 0.7836 (tp30) REVERT: A 3729 SER cc_start: 0.8140 (m) cc_final: 0.7714 (p) REVERT: A 3795 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6818 (mm-30) REVERT: A 3904 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: A 4023 GLN cc_start: 0.7407 (mm-40) cc_final: 0.7103 (mm-40) REVERT: A 4075 GLU cc_start: 0.7751 (tp30) cc_final: 0.6909 (pm20) REVERT: A 4128 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8672 (pmm) REVERT: A 4209 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7434 (tp30) REVERT: A 4301 ARG cc_start: 0.7606 (ttm-80) cc_final: 0.7060 (mtm-85) REVERT: A 4415 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7001 (ttp-110) REVERT: A 4422 LYS cc_start: 0.7238 (tttt) cc_final: 0.6920 (tppt) REVERT: A 4456 VAL cc_start: 0.8067 (t) cc_final: 0.7680 (m) REVERT: A 4460 LEU cc_start: 0.8388 (tp) cc_final: 0.8089 (tm) REVERT: A 4572 ASN cc_start: 0.7701 (t0) cc_final: 0.7408 (t0) REVERT: A 4583 THR cc_start: 0.8219 (m) cc_final: 0.7899 (t) REVERT: A 4617 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7737 (p0) outliers start: 57 outliers final: 27 residues processed: 355 average time/residue: 1.5681 time to fit residues: 631.4819 Evaluate side-chains 342 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 305 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1462 PHE Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1601 LEU Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1878 LYS Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2051 GLN Chi-restraints excluded: chain A residue 2063 GLU Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2221 MET Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2847 ASP Chi-restraints excluded: chain A residue 3048 GLU Chi-restraints excluded: chain A residue 3087 ASN Chi-restraints excluded: chain A residue 3156 GLN Chi-restraints excluded: chain A residue 3164 ARG Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3718 LYS Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3904 GLU Chi-restraints excluded: chain A residue 3928 THR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4311 LEU Chi-restraints excluded: chain A residue 4415 ARG Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 48 optimal weight: 3.9990 chunk 286 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 175 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 213 optimal weight: 0.6980 chunk 236 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 263 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1612 GLN A2476 HIS A2849 ASN A3542 GLN A4054 HIS A4232 ASN A4307 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.141332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.114443 restraints weight = 29530.025| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.65 r_work: 0.3279 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24213 Z= 0.118 Angle : 0.493 6.460 32838 Z= 0.247 Chirality : 0.039 0.151 3692 Planarity : 0.004 0.064 4206 Dihedral : 6.434 113.567 3261 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.11 % Allowed : 14.89 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.16), residues: 2929 helix: 2.28 (0.12), residues: 1726 sheet: -0.04 (0.32), residues: 251 loop : 0.69 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.003 0.001 HIS A3151 PHE 0.016 0.001 PHE A2912 TYR 0.017 0.001 TYR A2748 ARG 0.012 0.000 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 1415) hydrogen bonds : angle 3.94191 ( 4098) covalent geometry : bond 0.00265 (24213) covalent geometry : angle 0.49251 (32838) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 326 time to evaluate : 2.614 Fit side-chains revert: symmetry clash REVERT: A 1462 PHE cc_start: 0.6961 (OUTLIER) cc_final: 0.6538 (m-80) REVERT: A 1566 GLN cc_start: 0.7046 (mm110) cc_final: 0.6760 (mm-40) REVERT: A 1569 GLN cc_start: 0.7604 (tp40) cc_final: 0.6965 (tm-30) REVERT: A 1576 LEU cc_start: 0.8143 (mt) cc_final: 0.7727 (mt) REVERT: A 1583 SER cc_start: 0.7833 (t) cc_final: 0.7389 (p) REVERT: A 1584 LYS cc_start: 0.7338 (mmtp) cc_final: 0.7008 (ptpt) REVERT: A 1709 MET cc_start: 0.8835 (ttp) cc_final: 0.8510 (ttp) REVERT: A 1750 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8170 (m) REVERT: A 2051 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7643 (tt0) REVERT: A 2310 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8408 (mt-10) REVERT: A 2412 MET cc_start: 0.7319 (tpp) cc_final: 0.7078 (tpt) REVERT: A 2763 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7555 (mtp85) REVERT: A 2848 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7921 (pt0) REVERT: A 2863 ARG cc_start: 0.7828 (ttt-90) cc_final: 0.7541 (tmt90) REVERT: A 2953 MET cc_start: 0.8443 (mtp) cc_final: 0.8210 (mtp) REVERT: A 3048 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6862 (tp30) REVERT: A 3156 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7125 (mp10) REVERT: A 3163 LYS cc_start: 0.7683 (ttmm) cc_final: 0.7337 (mtmm) REVERT: A 3169 MET cc_start: 0.8897 (mmt) cc_final: 0.8538 (mmp) REVERT: A 3191 ARG cc_start: 0.7351 (ttm170) cc_final: 0.7014 (mmm-85) REVERT: A 3595 GLN cc_start: 0.7837 (mp10) cc_final: 0.7184 (pp30) REVERT: A 3715 GLU cc_start: 0.8235 (tp30) cc_final: 0.7867 (tp30) REVERT: A 3729 SER cc_start: 0.8101 (m) cc_final: 0.7730 (p) REVERT: A 3795 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6756 (mm-30) REVERT: A 3904 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: A 3906 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7752 (tm-30) REVERT: A 4075 GLU cc_start: 0.7730 (tp30) cc_final: 0.6879 (pm20) REVERT: A 4128 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8552 (pmm) REVERT: A 4209 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7385 (tp30) REVERT: A 4301 ARG cc_start: 0.7578 (ttm-80) cc_final: 0.7030 (mtm-85) REVERT: A 4422 LYS cc_start: 0.7260 (tttt) cc_final: 0.6976 (tppt) REVERT: A 4456 VAL cc_start: 0.8056 (t) cc_final: 0.7649 (m) REVERT: A 4460 LEU cc_start: 0.8367 (tp) cc_final: 0.8087 (tm) REVERT: A 4572 ASN cc_start: 0.7644 (t0) cc_final: 0.7346 (t0) REVERT: A 4583 THR cc_start: 0.8206 (m) cc_final: 0.7891 (t) REVERT: A 4590 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7960 (mt) outliers start: 55 outliers final: 32 residues processed: 361 average time/residue: 1.5324 time to fit residues: 632.4233 Evaluate side-chains 348 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 306 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1462 PHE Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1601 LEU Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1878 LYS Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2051 GLN Chi-restraints excluded: chain A residue 2063 GLU Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2221 MET Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2847 ASP Chi-restraints excluded: chain A residue 3048 GLU Chi-restraints excluded: chain A residue 3087 ASN Chi-restraints excluded: chain A residue 3156 GLN Chi-restraints excluded: chain A residue 3164 ARG Chi-restraints excluded: chain A residue 3224 ILE Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3718 LYS Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3904 GLU Chi-restraints excluded: chain A residue 3906 GLN Chi-restraints excluded: chain A residue 3928 THR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4311 LEU Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4590 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 4 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 287 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 184 optimal weight: 0.7980 chunk 206 optimal weight: 4.9990 chunk 254 optimal weight: 4.9990 chunk 112 optimal weight: 0.0270 chunk 174 optimal weight: 4.9990 chunk 103 optimal weight: 0.0020 overall best weight: 0.7248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1612 GLN A2476 HIS A3542 GLN A4054 HIS A4232 ASN A4307 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.141139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.114307 restraints weight = 29455.612| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.61 r_work: 0.3273 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24213 Z= 0.120 Angle : 0.496 6.675 32838 Z= 0.249 Chirality : 0.040 0.154 3692 Planarity : 0.004 0.066 4206 Dihedral : 6.415 112.911 3261 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.19 % Allowed : 15.12 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.16), residues: 2929 helix: 2.29 (0.12), residues: 1727 sheet: -0.13 (0.32), residues: 256 loop : 0.70 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.003 0.001 HIS A3151 PHE 0.016 0.001 PHE A2912 TYR 0.017 0.001 TYR A2748 ARG 0.015 0.000 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 1415) hydrogen bonds : angle 3.93330 ( 4098) covalent geometry : bond 0.00272 (24213) covalent geometry : angle 0.49560 (32838) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 318 time to evaluate : 2.694 Fit side-chains REVERT: A 1462 PHE cc_start: 0.6998 (OUTLIER) cc_final: 0.6597 (m-80) REVERT: A 1566 GLN cc_start: 0.7055 (mm110) cc_final: 0.6769 (mm-40) REVERT: A 1569 GLN cc_start: 0.7615 (tp40) cc_final: 0.6978 (tm-30) REVERT: A 1576 LEU cc_start: 0.8166 (mt) cc_final: 0.7748 (mt) REVERT: A 1583 SER cc_start: 0.7714 (t) cc_final: 0.7237 (p) REVERT: A 1584 LYS cc_start: 0.7349 (mmtp) cc_final: 0.7053 (ptpt) REVERT: A 1709 MET cc_start: 0.8839 (ttp) cc_final: 0.8524 (ttp) REVERT: A 1750 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8198 (m) REVERT: A 2051 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: A 2175 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7283 (mtt) REVERT: A 2310 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8429 (mt-10) REVERT: A 2412 MET cc_start: 0.7263 (tpp) cc_final: 0.7040 (tpt) REVERT: A 2763 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7567 (mtp85) REVERT: A 2848 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7949 (pt0) REVERT: A 2863 ARG cc_start: 0.7821 (ttt-90) cc_final: 0.7549 (tmt90) REVERT: A 2953 MET cc_start: 0.8461 (mtp) cc_final: 0.8218 (mtp) REVERT: A 3048 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6883 (tp30) REVERT: A 3156 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7142 (mp10) REVERT: A 3163 LYS cc_start: 0.7685 (ttmm) cc_final: 0.7340 (mtmm) REVERT: A 3169 MET cc_start: 0.8904 (mmt) cc_final: 0.8543 (mmp) REVERT: A 3191 ARG cc_start: 0.7377 (ttm170) cc_final: 0.7046 (mmm-85) REVERT: A 3595 GLN cc_start: 0.7834 (mp10) cc_final: 0.7195 (pp30) REVERT: A 3715 GLU cc_start: 0.8258 (tp30) cc_final: 0.7899 (tp30) REVERT: A 3729 SER cc_start: 0.8156 (m) cc_final: 0.7828 (p) REVERT: A 3795 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6738 (mm-30) REVERT: A 3893 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7075 (pttp) REVERT: A 3904 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: A 3906 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: A 4022 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7278 (pm20) REVERT: A 4075 GLU cc_start: 0.7755 (tp30) cc_final: 0.6914 (pm20) REVERT: A 4128 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8574 (pmm) REVERT: A 4209 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7408 (tp30) REVERT: A 4301 ARG cc_start: 0.7602 (ttm-80) cc_final: 0.7049 (mtm-85) REVERT: A 4422 LYS cc_start: 0.7273 (tttt) cc_final: 0.6990 (tppt) REVERT: A 4456 VAL cc_start: 0.8072 (t) cc_final: 0.7669 (m) REVERT: A 4460 LEU cc_start: 0.8408 (tp) cc_final: 0.8153 (tm) REVERT: A 4572 ASN cc_start: 0.7640 (t0) cc_final: 0.7401 (t0) REVERT: A 4583 THR cc_start: 0.8224 (m) cc_final: 0.7911 (t) REVERT: A 4590 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7956 (mt) outliers start: 57 outliers final: 31 residues processed: 353 average time/residue: 1.5746 time to fit residues: 630.3597 Evaluate side-chains 350 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 306 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1462 PHE Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1601 LEU Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1878 LYS Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2051 GLN Chi-restraints excluded: chain A residue 2063 GLU Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2221 MET Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2847 ASP Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3048 GLU Chi-restraints excluded: chain A residue 3087 ASN Chi-restraints excluded: chain A residue 3156 GLN Chi-restraints excluded: chain A residue 3224 ILE Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3718 LYS Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3893 LYS Chi-restraints excluded: chain A residue 3904 GLU Chi-restraints excluded: chain A residue 3906 GLN Chi-restraints excluded: chain A residue 3928 THR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4022 GLU Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4311 LEU Chi-restraints excluded: chain A residue 4377 MET Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4590 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 163 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 251 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 224 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 266 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1612 GLN A2476 HIS A3542 GLN A4054 HIS A4232 ASN A4307 GLN A4466 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.140511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.113745 restraints weight = 29535.734| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.59 r_work: 0.3266 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24213 Z= 0.132 Angle : 0.510 7.595 32838 Z= 0.256 Chirality : 0.040 0.157 3692 Planarity : 0.004 0.065 4206 Dihedral : 6.443 111.282 3261 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.96 % Allowed : 15.47 % Favored : 82.57 % 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: 2929 helix: 2.24 (0.12), residues: 1727 sheet: -0.14 (0.32), residues: 256 loop : 0.71 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.003 0.001 HIS A3151 PHE 0.016 0.001 PHE A1568 TYR 0.016 0.001 TYR A2748 ARG 0.015 0.000 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 1415) hydrogen bonds : angle 3.95612 ( 4098) covalent geometry : bond 0.00306 (24213) covalent geometry : angle 0.51004 (32838) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 310 time to evaluate : 2.649 Fit side-chains revert: symmetry clash REVERT: A 1462 PHE cc_start: 0.6997 (OUTLIER) cc_final: 0.6599 (m-80) REVERT: A 1566 GLN cc_start: 0.7110 (mm110) cc_final: 0.6783 (mm-40) REVERT: A 1569 GLN cc_start: 0.7643 (tp40) cc_final: 0.7012 (tm-30) REVERT: A 1576 LEU cc_start: 0.8227 (mt) cc_final: 0.7785 (mt) REVERT: A 1583 SER cc_start: 0.7749 (t) cc_final: 0.7275 (p) REVERT: A 1584 LYS cc_start: 0.7367 (mmtp) cc_final: 0.7078 (ptpt) REVERT: A 1612 GLN cc_start: 0.8099 (tt0) cc_final: 0.7865 (tt0) REVERT: A 1709 MET cc_start: 0.8893 (ttp) cc_final: 0.8571 (ttp) REVERT: A 1750 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8189 (m) REVERT: A 2051 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: A 2175 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7290 (mtt) REVERT: A 2310 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8414 (mt-10) REVERT: A 2412 MET cc_start: 0.7332 (tpp) cc_final: 0.7112 (tpt) REVERT: A 2763 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7565 (mtp85) REVERT: A 2848 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7970 (pt0) REVERT: A 2863 ARG cc_start: 0.7865 (ttt-90) cc_final: 0.7595 (tmt90) REVERT: A 2953 MET cc_start: 0.8462 (mtp) cc_final: 0.8217 (mtp) REVERT: A 3048 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6925 (tp30) REVERT: A 3156 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7179 (mp10) REVERT: A 3163 LYS cc_start: 0.7709 (ttmm) cc_final: 0.7366 (mtmm) REVERT: A 3169 MET cc_start: 0.8921 (mmt) cc_final: 0.8565 (mmp) REVERT: A 3191 ARG cc_start: 0.7383 (ttm170) cc_final: 0.7042 (mmm-85) REVERT: A 3478 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6627 (tt) REVERT: A 3595 GLN cc_start: 0.7954 (mp10) cc_final: 0.7349 (pp30) REVERT: A 3715 GLU cc_start: 0.8288 (tp30) cc_final: 0.7939 (tp30) REVERT: A 3729 SER cc_start: 0.8177 (m) cc_final: 0.7858 (p) REVERT: A 3795 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6784 (mm-30) REVERT: A 3893 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7046 (pttm) REVERT: A 3904 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: A 3906 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: A 4004 MET cc_start: 0.8457 (tpt) cc_final: 0.7886 (tpt) REVERT: A 4022 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7404 (pm20) REVERT: A 4075 GLU cc_start: 0.7771 (tp30) cc_final: 0.6950 (pm20) REVERT: A 4128 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8604 (pmm) REVERT: A 4209 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7440 (tp30) REVERT: A 4301 ARG cc_start: 0.7621 (ttm-80) cc_final: 0.7098 (mtm-85) REVERT: A 4414 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7152 (pp20) REVERT: A 4415 ARG cc_start: 0.7722 (mtp85) cc_final: 0.7173 (mtp180) REVERT: A 4456 VAL cc_start: 0.8097 (t) cc_final: 0.7685 (m) REVERT: A 4460 LEU cc_start: 0.8426 (tp) cc_final: 0.8186 (tm) REVERT: A 4572 ASN cc_start: 0.7695 (t0) cc_final: 0.7485 (t0) REVERT: A 4583 THR cc_start: 0.8250 (m) cc_final: 0.7936 (t) REVERT: A 4590 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7988 (mt) outliers start: 51 outliers final: 33 residues processed: 342 average time/residue: 1.5936 time to fit residues: 620.0679 Evaluate side-chains 349 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 301 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1462 PHE Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1601 LEU Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1878 LYS Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2051 GLN Chi-restraints excluded: chain A residue 2063 GLU Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2221 MET Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2847 ASP Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 3001 ASP Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3048 GLU Chi-restraints excluded: chain A residue 3087 ASN Chi-restraints excluded: chain A residue 3156 GLN Chi-restraints excluded: chain A residue 3164 ARG Chi-restraints excluded: chain A residue 3224 ILE Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3718 LYS Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3893 LYS Chi-restraints excluded: chain A residue 3904 GLU Chi-restraints excluded: chain A residue 3906 GLN Chi-restraints excluded: chain A residue 3928 THR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4022 GLU Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4311 LEU Chi-restraints excluded: chain A residue 4393 GLN Chi-restraints excluded: chain A residue 4414 GLU Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4590 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 84 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 chunk 278 optimal weight: 0.9990 chunk 242 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1867 ASN A2476 HIS A4054 HIS A4307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.140811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.113931 restraints weight = 29402.644| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.60 r_work: 0.3265 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24213 Z= 0.132 Angle : 0.509 7.025 32838 Z= 0.255 Chirality : 0.040 0.157 3692 Planarity : 0.004 0.065 4206 Dihedral : 6.445 111.280 3261 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.03 % Allowed : 15.66 % Favored : 82.30 % 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: 2929 helix: 2.24 (0.12), residues: 1728 sheet: -0.14 (0.32), residues: 256 loop : 0.72 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.003 0.001 HIS A3151 PHE 0.016 0.001 PHE A1568 TYR 0.018 0.001 TYR A1546 ARG 0.015 0.000 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.03938 ( 1415) hydrogen bonds : angle 3.95268 ( 4098) covalent geometry : bond 0.00305 (24213) covalent geometry : angle 0.50873 (32838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20154.58 seconds wall clock time: 348 minutes 49.93 seconds (20929.93 seconds total)