Starting phenix.real_space_refine on Fri May 23 08:21:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bmy_44715/05_2025/9bmy_44715.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bmy_44715/05_2025/9bmy_44715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bmy_44715/05_2025/9bmy_44715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bmy_44715/05_2025/9bmy_44715.map" model { file = "/net/cci-nas-00/data/ceres_data/9bmy_44715/05_2025/9bmy_44715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bmy_44715/05_2025/9bmy_44715.cif" } resolution = 2.86 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= 0.053 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: 13.56, per 1000 atoms: 0.57 Number of scatterers: 23707 At special positions: 0 Unit cell: (143.505, 112.258, 208.314, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 117 16.00 P 9 15.00 Mg 2 11.99 O 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: 5.98 Conformation dependent library (CDL) restraints added in 2.8 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: 4.06 Creating SS restraints... Processing helix chain 'A' and resid 1457 through 1471 Processing helix chain 'A' and resid 1489 through 1509 removed outlier: 3.545A pdb=" N LYS A1508 " --> pdb=" O VAL A1504 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A1509 " --> pdb=" O SER A1505 " (cutoff:3.500A) Processing helix chain 'A' and resid 1510 through 1514 removed outlier: 4.152A pdb=" N LYS A1514 " --> pdb=" O PRO A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1554 removed outlier: 3.914A pdb=" N VAL A1536 " --> pdb=" O ALA A1532 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A1546 " --> pdb=" O ARG A1542 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A1554 " --> pdb=" O ILE A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1561 removed outlier: 4.068A pdb=" N HIS A1559 " --> pdb=" O ALA A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1585 Processing helix chain 'A' and resid 1587 through 1593 Processing helix chain 'A' and resid 1596 through 1614 Processing helix chain 'A' and resid 1615 through 1626 removed outlier: 3.954A pdb=" N SER A1624 " --> pdb=" O GLU A1620 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER A1625 " --> pdb=" O ARG A1621 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A1626 " --> pdb=" O GLU A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1632 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1646 through 1652 removed outlier: 3.585A pdb=" N GLN A1651 " --> pdb=" O ALA A1648 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1658 removed outlier: 3.641A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1728 removed outlier: 3.592A pdb=" N TRP A1701 " --> pdb=" O LYS A1697 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 3.873A 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: 3.504A pdb=" N SER A1986 " --> pdb=" O LEU A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2034 Processing helix chain 'A' and resid 2045 through 2058 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix removed outlier: 3.506A pdb=" N GLU A2078 " --> pdb=" O LYS A2074 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2117 removed outlier: 3.679A 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: 3.630A pdb=" N ARG A2358 " --> pdb=" O ALA A2354 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2385 Processing helix chain 'A' and resid 2411 through 2424 Processing helix chain 'A' and resid 2425 through 2428 removed outlier: 3.670A 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: 3.642A pdb=" N LEU A2443 " --> pdb=" O HIS A2439 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 Processing helix chain 'A' and resid 2482 through 2504 removed outlier: 3.998A pdb=" N ARG A2492 " --> pdb=" O ARG A2488 " (cutoff:3.500A) Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2549 through 2552 Processing helix chain 'A' and resid 2558 through 2562 removed outlier: 3.950A pdb=" N VAL A2562 " --> pdb=" O THR A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2587 Processing helix chain 'A' and resid 2600 through 2611 removed outlier: 3.812A 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: 5.061A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2784 Processing helix chain 'A' and resid 2795 through 2809 removed outlier: 3.779A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 Processing helix chain 'A' and resid 2839 through 2858 removed outlier: 3.738A pdb=" N ASP A2851 " --> pdb=" O ASP A2847 " (cutoff:3.500A) Processing helix chain 'A' and resid 2862 through 2868 Processing helix chain 'A' and resid 2885 through 2904 removed outlier: 3.575A 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: 3.516A pdb=" N GLU A3006 " --> pdb=" O SER A3002 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A3007 " --> pdb=" O GLY A3003 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A3010 " --> pdb=" O GLU A3006 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A3013 " --> pdb=" O ASN A3009 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3040 removed outlier: 3.536A 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: 4.229A 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: 3.562A pdb=" N LEU A3154 " --> pdb=" O VAL A3150 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS A3155 " --> pdb=" O HIS A3151 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 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: 3.610A 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: 3.605A 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: 3.613A 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: 3.632A pdb=" N GLN A4108 " --> pdb=" O GLY A4104 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A4115 " --> pdb=" O LYS A4111 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4142 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.590A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4175 through 4194 removed outlier: 3.769A pdb=" N LEU A4194 " --> pdb=" O ILE A4190 " (cutoff:3.500A) Processing helix chain 'A' and resid 4196 through 4201 removed outlier: 3.880A pdb=" N TRP A4201 " --> pdb=" O ALA A4197 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4227 Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 removed outlier: 3.521A 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: 3.567A pdb=" N TYR A4520 " --> pdb=" O VAL A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4535 through 4537 No H-bonds generated for 'chain 'A' and resid 4535 through 4537' Processing helix chain 'A' and resid 4631 through 4638 removed outlier: 3.577A pdb=" N PHE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1477 through 1480 removed outlier: 3.884A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1663 through 1666 removed outlier: 7.566A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.382A 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: 7.871A pdb=" N LEU A2039 " --> pdb=" O GLY A1901 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER A1903 " --> pdb=" O LEU A2039 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1931 removed outlier: 6.324A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASP A1958 " --> pdb=" O LEU A1928 " (cutoff:3.500A) removed outlier: 6.239A 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: 7.425A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 6.373A 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: 6.291A 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: 7.855A 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: 6.684A 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: 7.414A pdb=" N ILE A2936 " --> pdb=" O PHE A3094 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3610 through 3613 Processing sheet with id=AB7, first strand: chain 'A' and resid 3653 through 3656 Processing sheet with id=AB8, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.246A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.763A 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: 6.129A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A4587 " --> pdb=" O THR A4546 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4564 through 4571 removed outlier: 7.191A pdb=" N ILE A4581 " --> pdb=" O GLY A4567 " (cutoff:3.500A) removed outlier: 9.584A 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: 9.941A pdb=" N ASN A4571 " --> pdb=" O LEU A4577 " (cutoff:3.500A) removed outlier: 10.187A pdb=" N LEU A4577 " --> pdb=" O ASN A4571 " (cutoff:3.500A) removed outlier: 7.052A 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: 6.594A 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: 14.58 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: 7818 1.34 - 1.46: 4905 1.46 - 1.58: 11280 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 3.05e+01 bond pdb=" C4 ADP A4701 " pdb=" C5 ADP A4701 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C4 ADP A4703 " pdb=" C5 ADP A4703 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C5 ADP A4703 " pdb=" C6 ADP A4703 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C5 ADP A4701 " pdb=" C6 ADP A4701 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.70e+01 ... (remaining 24208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 32468 2.45 - 4.91: 325 4.91 - 7.36: 28 7.36 - 9.82: 10 9.82 - 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 139.87 134.09 5.78 1.00e+00 1.00e+00 3.34e+01 angle pdb=" PA ADP A4704 " pdb=" O3A ADP A4704 " pdb=" PB ADP A4704 " ideal model delta sigma weight residual 120.50 132.77 -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 120.50 131.51 -11.01 3.00e+00 1.11e-01 1.35e+01 angle pdb=" C1' ADP A4701 " pdb=" C2' ADP A4701 " pdb=" C3' ADP A4701 " ideal model delta sigma weight residual 111.00 100.18 10.82 3.00e+00 1.11e-01 1.30e+01 ... (remaining 32833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.16: 14305 31.16 - 62.31: 316 62.31 - 93.47: 68 93.47 - 124.63: 2 124.63 - 155.78: 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 95.78 -155.78 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 300.00 174.37 125.63 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 50.60 -110.59 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: 2756 0.042 - 0.083: 709 0.083 - 0.125: 201 0.125 - 0.167: 21 0.167 - 0.208: 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 1.09e+00 chirality pdb=" CA LEU A2668 " pdb=" N LEU A2668 " pdb=" C LEU A2668 " pdb=" CB LEU A2668 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.82e-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 8.57e-01 ... (remaining 3689 not shown) Planarity restraints: 4206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A4195 " -0.448 9.50e-02 1.11e+02 2.01e-01 2.47e+01 pdb=" NE ARG A4195 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A4195 " 0.004 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 1.35e-02 4.58e+00 pdb=" CG TRP A1537 " 0.034 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 " -0.005 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: 1.74 - 2.38: 31 2.38 - 3.01: 12566 3.01 - 3.64: 37797 3.64 - 4.27: 58429 4.27 - 4.90: 93734 Nonbonded interactions: 202557 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 202552 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: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.970 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 59.390 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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= 0.209 Angle : 0.620 12.271 32838 Z= 0.327 Chirality : 0.041 0.208 3692 Planarity : 0.005 0.201 4206 Dihedral : 14.217 155.782 9105 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 6.64 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: 0.09 (0.34), residues: 235 loop : 0.77 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A1537 HIS 0.015 0.001 HIS A1810 PHE 0.017 0.002 PHE A1960 TYR 0.018 0.002 TYR A2472 ARG 0.008 0.001 ARG A2492 Details of bonding type rmsd hydrogen bonds : bond 0.20841 ( 1415) hydrogen bonds : angle 6.47155 ( 4098) covalent geometry : bond 0.00384 (24213) covalent geometry : angle 0.61997 (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 634 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 634 time to evaluate : 2.571 Fit side-chains revert: symmetry clash REVERT: A 2222 MET cc_start: 0.8470 (mtm) cc_final: 0.8148 (mtm) REVERT: A 2331 GLU cc_start: 0.7962 (tt0) cc_final: 0.7548 (tt0) REVERT: A 3784 VAL cc_start: 0.7964 (t) cc_final: 0.7627 (m) REVERT: A 3875 MET cc_start: 0.8897 (mtp) cc_final: 0.8668 (mtm) REVERT: A 4095 MET cc_start: 0.8459 (ttp) cc_final: 0.8132 (ttm) outliers start: 0 outliers final: 1 residues processed: 634 average time/residue: 1.5926 time to fit residues: 1139.5664 Evaluate side-chains 310 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 309 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1473 TYR 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: 3.9990 chunk 123 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 229 optimal weight: 6.9990 chunk 88 optimal weight: 0.3980 chunk 139 optimal weight: 0.5980 chunk 170 optimal weight: 0.5980 chunk 266 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1748 GLN A1784 ASN A1832 ASN A1855 GLN A1931 ASN A2187 GLN A2212 GLN A2430 ASN A2442 GLN A2713 ASN A2849 ASN A2954 ASN A2987 ASN A3087 ASN A3092 ASN A3104 GLN A3119 ASN A3523 GLN A3636 GLN A3735 GLN A3751 GLN ** A3754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3826 GLN A3906 GLN A4038 ASN A4062 GLN A4079 GLN A4397 HIS A4425 GLN A4444 GLN A4544 ASN ** A4573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.138908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109938 restraints weight = 29688.919| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.94 r_work: 0.3205 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24213 Z= 0.143 Angle : 0.567 8.430 32838 Z= 0.289 Chirality : 0.041 0.157 3692 Planarity : 0.004 0.066 4206 Dihedral : 7.245 159.805 3263 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.53 % Allowed : 11.55 % Favored : 85.91 % 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: 2.01 (0.16), residues: 2929 helix: 1.94 (0.12), residues: 1722 sheet: -0.09 (0.34), residues: 234 loop : 0.77 (0.21), residues: 973 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 A2708 TYR 0.019 0.001 TYR A2748 ARG 0.006 0.001 ARG A3759 Details of bonding type rmsd hydrogen bonds : bond 0.05463 ( 1415) hydrogen bonds : angle 4.57449 ( 4098) covalent geometry : bond 0.00314 (24213) covalent geometry : angle 0.56740 (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 394 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 328 time to evaluate : 2.626 Fit side-chains revert: symmetry clash REVERT: A 1560 LEU cc_start: 0.7994 (tp) cc_final: 0.7585 (mm) REVERT: A 1564 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.5792 (mp0) REVERT: A 1889 TYR cc_start: 0.8648 (m-10) cc_final: 0.8389 (m-10) REVERT: A 1980 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7352 (mt-10) REVERT: A 2018 MET cc_start: 0.9128 (mtm) cc_final: 0.8835 (mtp) REVERT: A 2043 LYS cc_start: 0.8707 (mmtt) cc_final: 0.8351 (mtpp) REVERT: A 2175 MET cc_start: 0.7748 (mtp) cc_final: 0.7292 (mtt) REVERT: A 2187 GLN cc_start: 0.8055 (mt0) cc_final: 0.7811 (tt0) REVERT: A 2222 MET cc_start: 0.8875 (mtm) cc_final: 0.8500 (mtm) REVERT: A 2286 LYS cc_start: 0.8854 (tttm) cc_final: 0.8534 (ttpp) REVERT: A 2331 GLU cc_start: 0.8495 (tt0) cc_final: 0.8012 (tt0) REVERT: A 2763 ARG cc_start: 0.8261 (mmm-85) cc_final: 0.7683 (mmm-85) REVERT: A 2841 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7280 (tm-30) REVERT: A 2977 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7107 (mtp180) REVERT: A 3022 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7947 (mt-10) REVERT: A 3199 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7301 (ttp) REVERT: A 3598 GLU cc_start: 0.7720 (tp30) cc_final: 0.7253 (pt0) REVERT: A 3746 GLU cc_start: 0.7605 (tp30) cc_final: 0.7183 (tt0) REVERT: A 3788 ASP cc_start: 0.6922 (m-30) cc_final: 0.6711 (m-30) REVERT: A 3791 MET cc_start: 0.7706 (tpt) cc_final: 0.7485 (mmm) REVERT: A 4108 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7755 (mt0) REVERT: A 4426 ASP cc_start: 0.7631 (m-30) cc_final: 0.7402 (m-30) REVERT: A 4447 TYR cc_start: 0.8078 (t80) cc_final: 0.7738 (t80) outliers start: 66 outliers final: 17 residues processed: 364 average time/residue: 1.4645 time to fit residues: 609.5198 Evaluate side-chains 295 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 274 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1564 GLU Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 2106 GLU Chi-restraints excluded: chain A residue 2172 ARG Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2804 ARG Chi-restraints excluded: chain A residue 2977 ARG Chi-restraints excluded: chain A residue 2986 LYS Chi-restraints excluded: chain A residue 3199 MET Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3765 THR Chi-restraints excluded: chain A residue 4108 GLN Chi-restraints excluded: chain A residue 4465 SER Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4582 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 106 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 237 optimal weight: 0.9990 chunk 222 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2005 GLN A2827 HIS A3584 ASN A3636 GLN ** A3754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4038 ASN A4079 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.132407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103947 restraints weight = 29999.910| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.93 r_work: 0.3111 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 24213 Z= 0.210 Angle : 0.585 9.513 32838 Z= 0.295 Chirality : 0.043 0.168 3692 Planarity : 0.004 0.056 4206 Dihedral : 7.194 167.709 3261 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.84 % Allowed : 12.59 % Favored : 84.57 % 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: 1.86 (0.15), residues: 2929 helix: 1.86 (0.12), residues: 1723 sheet: -0.22 (0.32), residues: 248 loop : 0.67 (0.21), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A2500 HIS 0.014 0.001 HIS A1810 PHE 0.020 0.002 PHE A2343 TYR 0.025 0.002 TYR A2748 ARG 0.008 0.001 ARG A2863 Details of bonding type rmsd hydrogen bonds : bond 0.05033 ( 1415) hydrogen bonds : angle 4.36224 ( 4098) covalent geometry : bond 0.00500 (24213) covalent geometry : angle 0.58482 (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 388 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 314 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1461 GLU cc_start: 0.7675 (tp30) cc_final: 0.7350 (tp30) REVERT: A 1498 LYS cc_start: 0.7846 (mttm) cc_final: 0.7391 (mmtt) REVERT: A 1560 LEU cc_start: 0.8079 (tp) cc_final: 0.7808 (mm) REVERT: A 1564 GLU cc_start: 0.6565 (OUTLIER) cc_final: 0.6004 (mp0) REVERT: A 1573 THR cc_start: 0.8860 (m) cc_final: 0.8543 (p) REVERT: A 1617 GLU cc_start: 0.7486 (mp0) cc_final: 0.7143 (pt0) REVERT: A 1829 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.7787 (mmtm) REVERT: A 1967 MET cc_start: 0.8842 (mmt) cc_final: 0.8478 (mmt) REVERT: A 1980 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7384 (mt-10) REVERT: A 2000 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8067 (tm-30) REVERT: A 2018 MET cc_start: 0.9149 (mtm) cc_final: 0.8826 (mtp) REVERT: A 2043 LYS cc_start: 0.8764 (mmtt) cc_final: 0.8369 (mtpp) REVERT: A 2175 MET cc_start: 0.7816 (mtp) cc_final: 0.7403 (mtt) REVERT: A 2222 MET cc_start: 0.8956 (mtm) cc_final: 0.8743 (mtm) REVERT: A 2286 LYS cc_start: 0.8843 (tttm) cc_final: 0.8377 (ttpp) REVERT: A 2331 GLU cc_start: 0.8610 (tt0) cc_final: 0.8226 (tt0) REVERT: A 2841 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7311 (tm-30) REVERT: A 2847 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8633 (m-30) REVERT: A 2977 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.7203 (mtp180) REVERT: A 3022 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8142 (mt-10) REVERT: A 3164 ARG cc_start: 0.7707 (ptp-110) cc_final: 0.6882 (tmm160) REVERT: A 3563 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8212 (mp10) REVERT: A 3584 ASN cc_start: 0.7986 (m110) cc_final: 0.7674 (m110) REVERT: A 3598 GLU cc_start: 0.7829 (tp30) cc_final: 0.7387 (pt0) REVERT: A 3606 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8444 (p0) REVERT: A 3779 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7078 (mm-30) REVERT: A 3788 ASP cc_start: 0.7096 (m-30) cc_final: 0.6842 (m-30) REVERT: A 4270 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7841 (mm-30) REVERT: A 4338 ASP cc_start: 0.8214 (t0) cc_final: 0.7829 (m-30) REVERT: A 4447 TYR cc_start: 0.8090 (t80) cc_final: 0.7739 (t80) REVERT: A 4591 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7460 (ttp-110) outliers start: 74 outliers final: 25 residues processed: 361 average time/residue: 1.4899 time to fit residues: 612.9352 Evaluate side-chains 314 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 280 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1564 GLU Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1677 SER Chi-restraints excluded: chain A residue 1829 LYS Chi-restraints excluded: chain A residue 2022 TYR Chi-restraints excluded: chain A residue 2172 ARG Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2804 ARG Chi-restraints excluded: chain A residue 2847 ASP Chi-restraints excluded: chain A residue 2977 ARG Chi-restraints excluded: chain A residue 3022 GLU Chi-restraints excluded: chain A residue 3112 LYS Chi-restraints excluded: chain A residue 3211 THR Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3606 ASP Chi-restraints excluded: chain A residue 3624 GLU Chi-restraints excluded: chain A residue 3680 SER Chi-restraints excluded: chain A residue 3765 THR Chi-restraints excluded: chain A residue 3779 GLU Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4108 GLN Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4347 GLN Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4465 SER Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4582 SER Chi-restraints excluded: chain A residue 4591 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 259 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 246 optimal weight: 0.4980 chunk 174 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 282 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1867 ASN A2430 ASN ** A3754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4079 GLN A4573 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.133934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.105486 restraints weight = 30003.177| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.94 r_work: 0.3131 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24213 Z= 0.134 Angle : 0.518 8.066 32838 Z= 0.260 Chirality : 0.040 0.143 3692 Planarity : 0.004 0.043 4206 Dihedral : 7.006 170.108 3261 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.57 % Allowed : 14.24 % Favored : 83.19 % 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: 2.04 (0.16), residues: 2929 helix: 2.04 (0.12), residues: 1726 sheet: -0.26 (0.32), residues: 257 loop : 0.69 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.009 0.001 HIS A1810 PHE 0.014 0.001 PHE A2912 TYR 0.022 0.001 TYR A2748 ARG 0.008 0.000 ARG A2863 Details of bonding type rmsd hydrogen bonds : bond 0.04323 ( 1415) hydrogen bonds : angle 4.19054 ( 4098) covalent geometry : bond 0.00305 (24213) covalent geometry : angle 0.51769 (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 362 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 295 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1461 GLU cc_start: 0.7721 (tp30) cc_final: 0.7356 (tp30) REVERT: A 1478 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7855 (m) REVERT: A 1498 LYS cc_start: 0.8046 (mttm) cc_final: 0.7564 (mmtt) REVERT: A 1560 LEU cc_start: 0.8009 (tp) cc_final: 0.7752 (mm) REVERT: A 1564 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6002 (mp0) REVERT: A 1573 THR cc_start: 0.8854 (m) cc_final: 0.8559 (p) REVERT: A 1579 MET cc_start: 0.8597 (mmp) cc_final: 0.8338 (mmm) REVERT: A 1617 GLU cc_start: 0.7449 (mp0) cc_final: 0.7080 (pt0) REVERT: A 1669 ASP cc_start: 0.7143 (OUTLIER) cc_final: 0.6899 (m-30) REVERT: A 1745 TYR cc_start: 0.8818 (m-80) cc_final: 0.8458 (m-80) REVERT: A 1967 MET cc_start: 0.8864 (mmt) cc_final: 0.8601 (mmt) REVERT: A 1980 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7403 (mt-10) REVERT: A 2000 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8033 (tm-30) REVERT: A 2018 MET cc_start: 0.9053 (mtm) cc_final: 0.8715 (mtp) REVERT: A 2043 LYS cc_start: 0.8753 (mmtt) cc_final: 0.8330 (mtpp) REVERT: A 2074 LYS cc_start: 0.8428 (ttpt) cc_final: 0.8191 (tmmm) REVERT: A 2138 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8286 (tt) REVERT: A 2172 ARG cc_start: 0.6976 (OUTLIER) cc_final: 0.6657 (ttm-80) REVERT: A 2175 MET cc_start: 0.7877 (mtp) cc_final: 0.7430 (mtt) REVERT: A 2222 MET cc_start: 0.8909 (mtm) cc_final: 0.8603 (mtm) REVERT: A 2286 LYS cc_start: 0.8791 (tttm) cc_final: 0.8510 (ttpp) REVERT: A 2331 GLU cc_start: 0.8569 (tt0) cc_final: 0.8282 (tt0) REVERT: A 2763 ARG cc_start: 0.8344 (mmm-85) cc_final: 0.7708 (ptt90) REVERT: A 2839 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: A 2841 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7228 (tm-30) REVERT: A 2847 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8625 (m-30) REVERT: A 2863 ARG cc_start: 0.7821 (ttm110) cc_final: 0.6990 (ttt90) REVERT: A 2977 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7094 (mtp180) REVERT: A 3022 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8152 (mt-10) REVERT: A 3078 ARG cc_start: 0.8153 (tpp-160) cc_final: 0.7726 (mmt90) REVERT: A 3141 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.7693 (mm-30) REVERT: A 3163 LYS cc_start: 0.7287 (pttp) cc_final: 0.7082 (mttp) REVERT: A 3164 ARG cc_start: 0.7526 (ptp-110) cc_final: 0.6762 (tmm160) REVERT: A 3584 ASN cc_start: 0.7954 (m110) cc_final: 0.7674 (m110) REVERT: A 3598 GLU cc_start: 0.7807 (tp30) cc_final: 0.7389 (pt0) REVERT: A 3788 ASP cc_start: 0.7139 (m-30) cc_final: 0.6850 (m-30) REVERT: A 4075 GLU cc_start: 0.7800 (mp0) cc_final: 0.7484 (pm20) REVERT: A 4108 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7863 (mt0) REVERT: A 4270 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7934 (mm-30) REVERT: A 4447 TYR cc_start: 0.8104 (t80) cc_final: 0.7800 (t80) REVERT: A 4561 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.8893 (p) REVERT: A 4591 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8231 (mmm-85) outliers start: 67 outliers final: 28 residues processed: 335 average time/residue: 1.5520 time to fit residues: 593.0886 Evaluate side-chains 319 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 279 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1478 VAL Chi-restraints excluded: chain A residue 1491 ASP Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1564 GLU Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 2022 TYR Chi-restraints excluded: chain A residue 2106 GLU Chi-restraints excluded: chain A residue 2138 ILE Chi-restraints excluded: chain A residue 2172 ARG Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2612 LEU Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2804 ARG Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 2847 ASP Chi-restraints excluded: chain A residue 2977 ARG Chi-restraints excluded: chain A residue 3141 GLU Chi-restraints excluded: chain A residue 3211 THR Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3723 ASP Chi-restraints excluded: chain A residue 3750 LEU Chi-restraints excluded: chain A residue 3946 ASP Chi-restraints excluded: chain A residue 3959 ILE Chi-restraints excluded: chain A residue 4108 GLN Chi-restraints excluded: chain A residue 4344 LEU Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4465 SER Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4582 SER Chi-restraints excluded: chain A residue 4591 ARG 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: 2.9990 chunk 54 optimal weight: 0.8980 chunk 275 optimal weight: 0.0670 chunk 47 optimal weight: 3.9990 chunk 249 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 71 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 194 optimal weight: 0.0040 overall best weight: 0.3930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2187 GLN A2430 ASN A3063 HIS A3636 GLN A3735 GLN ** A3754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4079 GLN A4573 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.135429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.106172 restraints weight = 30079.204| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.96 r_work: 0.3151 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24213 Z= 0.106 Angle : 0.486 7.632 32838 Z= 0.244 Chirality : 0.039 0.136 3692 Planarity : 0.004 0.044 4206 Dihedral : 6.764 169.015 3261 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.42 % Allowed : 14.93 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.16), residues: 2929 helix: 2.18 (0.12), residues: 1739 sheet: -0.28 (0.32), residues: 257 loop : 0.72 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.006 0.001 HIS A1810 PHE 0.017 0.001 PHE A3996 TYR 0.018 0.001 TYR A2748 ARG 0.009 0.000 ARG A3654 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 1415) hydrogen bonds : angle 4.02385 ( 4098) covalent geometry : bond 0.00226 (24213) covalent geometry : angle 0.48612 (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 363 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 300 time to evaluate : 2.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1461 GLU cc_start: 0.7664 (tp30) cc_final: 0.7235 (tp30) REVERT: A 1498 LYS cc_start: 0.8050 (mttm) cc_final: 0.7564 (mmtt) REVERT: A 1560 LEU cc_start: 0.7976 (tp) cc_final: 0.7721 (mm) REVERT: A 1564 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.5882 (mp0) REVERT: A 1573 THR cc_start: 0.8788 (m) cc_final: 0.8497 (p) REVERT: A 1579 MET cc_start: 0.8616 (mmp) cc_final: 0.8407 (mmm) REVERT: A 1617 GLU cc_start: 0.7473 (mp0) cc_final: 0.7069 (pt0) REVERT: A 1745 TYR cc_start: 0.8760 (m-80) cc_final: 0.8385 (m-80) REVERT: A 1967 MET cc_start: 0.8878 (mmt) cc_final: 0.8485 (mmt) REVERT: A 1980 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7385 (mt-10) REVERT: A 2000 GLU cc_start: 0.8415 (tm-30) cc_final: 0.7968 (tm-30) REVERT: A 2018 MET cc_start: 0.8968 (mtm) cc_final: 0.8599 (mtp) REVERT: A 2043 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8292 (mtpp) REVERT: A 2074 LYS cc_start: 0.8400 (ttpt) cc_final: 0.8157 (tmmm) REVERT: A 2138 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8342 (tt) REVERT: A 2172 ARG cc_start: 0.6951 (mtp85) cc_final: 0.6680 (ttm-80) REVERT: A 2175 MET cc_start: 0.7890 (mtp) cc_final: 0.7372 (mtt) REVERT: A 2222 MET cc_start: 0.8901 (mtm) cc_final: 0.8533 (mtm) REVERT: A 2286 LYS cc_start: 0.8755 (tttm) cc_final: 0.8519 (ttpp) REVERT: A 2331 GLU cc_start: 0.8502 (tt0) cc_final: 0.8191 (tt0) REVERT: A 2763 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7746 (ptt90) REVERT: A 2839 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: A 2863 ARG cc_start: 0.7817 (ttm110) cc_final: 0.6996 (ttt90) REVERT: A 2879 LYS cc_start: 0.8406 (pmtt) cc_final: 0.7949 (pptt) REVERT: A 2902 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8011 (mp0) REVERT: A 2977 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7077 (mtp180) REVERT: A 3022 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8237 (mt-10) REVERT: A 3052 LYS cc_start: 0.8428 (mttp) cc_final: 0.8215 (mttm) REVERT: A 3078 ARG cc_start: 0.8093 (tpp-160) cc_final: 0.7786 (mmt90) REVERT: A 3141 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.7687 (mm-30) REVERT: A 3164 ARG cc_start: 0.7500 (ptp-110) cc_final: 0.6883 (tmm160) REVERT: A 3598 GLU cc_start: 0.7816 (tp30) cc_final: 0.7364 (pt0) REVERT: A 3788 ASP cc_start: 0.7197 (m-30) cc_final: 0.6880 (m-30) REVERT: A 4065 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7334 (mt0) REVERT: A 4075 GLU cc_start: 0.7814 (mp0) cc_final: 0.7481 (pm20) REVERT: A 4108 GLN cc_start: 0.8307 (tt0) cc_final: 0.7820 (mt0) REVERT: A 4213 ARG cc_start: 0.7789 (mmp80) cc_final: 0.7551 (mtp85) REVERT: A 4270 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7946 (mm-30) REVERT: A 4399 LYS cc_start: 0.6653 (tmtt) cc_final: 0.5908 (tmtt) REVERT: A 4447 TYR cc_start: 0.8178 (t80) cc_final: 0.7923 (t80) REVERT: A 4484 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: A 4561 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8853 (p) REVERT: A 4591 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7374 (ttp-110) outliers start: 63 outliers final: 23 residues processed: 342 average time/residue: 1.5323 time to fit residues: 595.8952 Evaluate side-chains 309 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 276 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1564 GLU Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 2022 TYR Chi-restraints excluded: chain A residue 2106 GLU Chi-restraints excluded: chain A residue 2138 ILE Chi-restraints excluded: chain A residue 2612 LEU Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2804 ARG Chi-restraints excluded: chain A residue 2811 ARG Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 2970 GLU Chi-restraints excluded: chain A residue 2977 ARG Chi-restraints excluded: chain A residue 3141 GLU Chi-restraints excluded: chain A residue 3161 LEU Chi-restraints excluded: chain A residue 3211 THR Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3680 SER Chi-restraints excluded: chain A residue 3723 ASP Chi-restraints excluded: chain A residue 4065 GLN Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4347 GLN Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4465 SER Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4591 ARG 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: 0.8980 chunk 27 optimal weight: 0.3980 chunk 275 optimal weight: 0.9980 chunk 249 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 288 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2187 GLN A2430 ASN A2834 GLN ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3584 ASN A3602 ASN ** A3754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4079 GLN A4573 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.134453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.105728 restraints weight = 29833.652| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.90 r_work: 0.3139 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24213 Z= 0.129 Angle : 0.506 10.517 32838 Z= 0.252 Chirality : 0.040 0.142 3692 Planarity : 0.004 0.046 4206 Dihedral : 6.702 168.781 3261 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.61 % Allowed : 15.47 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.16), residues: 2929 helix: 2.19 (0.12), residues: 1740 sheet: -0.30 (0.32), residues: 257 loop : 0.70 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.008 0.001 HIS A1810 PHE 0.015 0.001 PHE A1568 TYR 0.022 0.001 TYR A2748 ARG 0.011 0.000 ARG A3654 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 1415) hydrogen bonds : angle 4.01781 ( 4098) covalent geometry : bond 0.00298 (24213) covalent geometry : angle 0.50566 (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 363 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 295 time to evaluate : 2.930 Fit side-chains revert: symmetry clash REVERT: A 1460 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7267 (mm-30) REVERT: A 1498 LYS cc_start: 0.8070 (mttm) cc_final: 0.7577 (mmtt) REVERT: A 1560 LEU cc_start: 0.7958 (tp) cc_final: 0.7617 (mm) REVERT: A 1564 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.5868 (mp0) REVERT: A 1573 THR cc_start: 0.8778 (m) cc_final: 0.8512 (p) REVERT: A 1688 THR cc_start: 0.8542 (m) cc_final: 0.8109 (p) REVERT: A 1745 TYR cc_start: 0.8783 (m-80) cc_final: 0.8402 (m-80) REVERT: A 1831 ASP cc_start: 0.8805 (p0) cc_final: 0.8566 (p0) REVERT: A 1967 MET cc_start: 0.8871 (mmt) cc_final: 0.8635 (mmt) REVERT: A 1980 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7387 (mt-10) REVERT: A 2000 GLU cc_start: 0.8438 (tm-30) cc_final: 0.7986 (tm-30) REVERT: A 2018 MET cc_start: 0.9017 (mtm) cc_final: 0.8632 (mtp) REVERT: A 2043 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8242 (mtpp) REVERT: A 2074 LYS cc_start: 0.8378 (ttpt) cc_final: 0.8123 (tmmm) REVERT: A 2138 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8321 (tt) REVERT: A 2172 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6694 (ttm-80) REVERT: A 2175 MET cc_start: 0.7922 (mtp) cc_final: 0.7477 (mtt) REVERT: A 2222 MET cc_start: 0.8919 (mtm) cc_final: 0.8545 (mtm) REVERT: A 2286 LYS cc_start: 0.8782 (tttm) cc_final: 0.8553 (ttpp) REVERT: A 2331 GLU cc_start: 0.8542 (tt0) cc_final: 0.8230 (tt0) REVERT: A 2763 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7742 (ptt90) REVERT: A 2839 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: A 2879 LYS cc_start: 0.8482 (pmtt) cc_final: 0.8034 (pptt) REVERT: A 2902 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8034 (mp0) REVERT: A 3022 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8303 (mt-10) REVERT: A 3052 LYS cc_start: 0.8475 (mttp) cc_final: 0.8266 (mttm) REVERT: A 3078 ARG cc_start: 0.8041 (tpp-160) cc_final: 0.7773 (mmt90) REVERT: A 3141 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7736 (mm-30) REVERT: A 3598 GLU cc_start: 0.7816 (tp30) cc_final: 0.7337 (pt0) REVERT: A 3726 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6890 (pp20) REVERT: A 3788 ASP cc_start: 0.7187 (m-30) cc_final: 0.6950 (m-30) REVERT: A 3791 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7248 (tpp) REVERT: A 3793 GLU cc_start: 0.6844 (tm-30) cc_final: 0.6512 (tp30) REVERT: A 4065 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7362 (mt0) REVERT: A 4075 GLU cc_start: 0.7801 (mp0) cc_final: 0.7591 (pm20) REVERT: A 4108 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7808 (mt0) REVERT: A 4270 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7951 (mm-30) REVERT: A 4419 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.6747 (ptm) REVERT: A 4441 LYS cc_start: 0.8289 (mppt) cc_final: 0.8022 (mppt) REVERT: A 4447 TYR cc_start: 0.8159 (t80) cc_final: 0.7872 (t80) REVERT: A 4561 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.8902 (p) REVERT: A 4591 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7484 (ttp-110) outliers start: 68 outliers final: 30 residues processed: 333 average time/residue: 1.6202 time to fit residues: 615.8082 Evaluate side-chains 319 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 276 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1564 GLU Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2022 TYR Chi-restraints excluded: chain A residue 2138 ILE Chi-restraints excluded: chain A residue 2172 ARG Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2612 LEU Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2804 ARG Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 2970 GLU Chi-restraints excluded: chain A residue 3141 GLU Chi-restraints excluded: chain A residue 3211 THR Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3545 THR Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3624 GLU Chi-restraints excluded: chain A residue 3680 SER Chi-restraints excluded: chain A residue 3723 ASP Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 3750 LEU Chi-restraints excluded: chain A residue 3765 THR Chi-restraints excluded: chain A residue 3791 MET Chi-restraints excluded: chain A residue 3948 ILE Chi-restraints excluded: chain A residue 4065 GLN Chi-restraints excluded: chain A residue 4108 GLN Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4419 MET Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4465 SER Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4582 SER Chi-restraints excluded: chain A residue 4591 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 180 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 247 optimal weight: 0.7980 chunk 224 optimal weight: 0.8980 chunk 218 optimal weight: 0.8980 chunk 233 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2187 GLN A2430 ASN ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3584 ASN ** A3754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4079 GLN A4573 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.134444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.105605 restraints weight = 30070.641| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.04 r_work: 0.3115 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24213 Z= 0.129 Angle : 0.514 10.074 32838 Z= 0.256 Chirality : 0.040 0.155 3692 Planarity : 0.004 0.050 4206 Dihedral : 6.652 169.289 3261 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.46 % Allowed : 15.93 % Favored : 81.61 % 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: 2.24 (0.16), residues: 2929 helix: 2.24 (0.12), residues: 1734 sheet: -0.33 (0.32), residues: 257 loop : 0.72 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.007 0.001 HIS A1810 PHE 0.015 0.001 PHE A1568 TYR 0.021 0.001 TYR A2748 ARG 0.013 0.000 ARG A3654 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 1415) hydrogen bonds : angle 3.99582 ( 4098) covalent geometry : bond 0.00299 (24213) covalent geometry : angle 0.51371 (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 351 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 287 time to evaluate : 2.710 Fit side-chains revert: symmetry clash REVERT: A 1460 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7218 (mm-30) REVERT: A 1488 ARG cc_start: 0.8225 (mtm110) cc_final: 0.8017 (mpp80) REVERT: A 1498 LYS cc_start: 0.8077 (mttm) cc_final: 0.7592 (mmtt) REVERT: A 1560 LEU cc_start: 0.7969 (tp) cc_final: 0.7609 (mm) REVERT: A 1564 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.5982 (mp0) REVERT: A 1573 THR cc_start: 0.8789 (m) cc_final: 0.8533 (p) REVERT: A 1688 THR cc_start: 0.8573 (m) cc_final: 0.8134 (p) REVERT: A 1745 TYR cc_start: 0.8802 (m-80) cc_final: 0.8428 (m-80) REVERT: A 1831 ASP cc_start: 0.8821 (p0) cc_final: 0.8590 (p0) REVERT: A 1967 MET cc_start: 0.8901 (mmt) cc_final: 0.8661 (mmt) REVERT: A 1980 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7419 (mt-10) REVERT: A 2000 GLU cc_start: 0.8462 (tm-30) cc_final: 0.7959 (tm-30) REVERT: A 2018 MET cc_start: 0.8965 (mtm) cc_final: 0.8614 (mtp) REVERT: A 2043 LYS cc_start: 0.8782 (mmtt) cc_final: 0.8258 (mtpp) REVERT: A 2074 LYS cc_start: 0.8382 (ttpt) cc_final: 0.8147 (tmmm) REVERT: A 2078 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7645 (mt-10) REVERT: A 2138 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8352 (tt) REVERT: A 2172 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6706 (ttm-80) REVERT: A 2175 MET cc_start: 0.7930 (mtp) cc_final: 0.7455 (mtt) REVERT: A 2222 MET cc_start: 0.8934 (mtm) cc_final: 0.8596 (mtm) REVERT: A 2286 LYS cc_start: 0.8808 (tttm) cc_final: 0.8573 (ttpp) REVERT: A 2331 GLU cc_start: 0.8602 (tt0) cc_final: 0.8312 (tt0) REVERT: A 2763 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7743 (ptt90) REVERT: A 2839 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: A 2863 ARG cc_start: 0.7938 (ttm110) cc_final: 0.7069 (ttt90) REVERT: A 2879 LYS cc_start: 0.8499 (pmtt) cc_final: 0.8055 (pptt) REVERT: A 2902 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8078 (mp0) REVERT: A 3022 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8353 (mt-10) REVERT: A 3052 LYS cc_start: 0.8522 (mttp) cc_final: 0.8317 (mttm) REVERT: A 3078 ARG cc_start: 0.7991 (tpp-160) cc_final: 0.7753 (mmt90) REVERT: A 3141 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7788 (mm-30) REVERT: A 3164 ARG cc_start: 0.8081 (ttp-110) cc_final: 0.7276 (ttp-170) REVERT: A 3482 LEU cc_start: 0.7581 (mp) cc_final: 0.7379 (mm) REVERT: A 3598 GLU cc_start: 0.7848 (tp30) cc_final: 0.7384 (pt0) REVERT: A 3755 GLU cc_start: 0.7432 (mm-30) cc_final: 0.6981 (mp0) REVERT: A 3972 TYR cc_start: 0.7581 (t80) cc_final: 0.7176 (t80) REVERT: A 4065 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7383 (mt0) REVERT: A 4075 GLU cc_start: 0.7849 (mp0) cc_final: 0.7638 (pm20) REVERT: A 4108 GLN cc_start: 0.8311 (tt0) cc_final: 0.7829 (mt0) REVERT: A 4270 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7999 (mm-30) REVERT: A 4399 LYS cc_start: 0.6897 (tmtt) cc_final: 0.6360 (ttpp) REVERT: A 4419 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.6774 (ptm) REVERT: A 4441 LYS cc_start: 0.8296 (mppt) cc_final: 0.8018 (mppt) REVERT: A 4447 TYR cc_start: 0.8167 (t80) cc_final: 0.7895 (t80) REVERT: A 4484 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: A 4561 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8948 (p) REVERT: A 4591 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7509 (ttp-110) REVERT: A 4595 GLN cc_start: 0.7993 (tp40) cc_final: 0.7781 (tp40) outliers start: 64 outliers final: 29 residues processed: 324 average time/residue: 1.5523 time to fit residues: 571.7508 Evaluate side-chains 314 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 274 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1564 GLU Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2022 TYR Chi-restraints excluded: chain A residue 2138 ILE Chi-restraints excluded: chain A residue 2172 ARG Chi-restraints excluded: chain A residue 2221 MET Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2612 LEU Chi-restraints excluded: chain A residue 2671 MET Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2743 SER Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2804 ARG Chi-restraints excluded: chain A residue 2811 ARG Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 2970 GLU Chi-restraints excluded: chain A residue 3141 GLU Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3545 THR Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3680 SER Chi-restraints excluded: chain A residue 3723 ASP Chi-restraints excluded: chain A residue 3750 LEU Chi-restraints excluded: chain A residue 3765 THR Chi-restraints excluded: chain A residue 4065 GLN Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4419 MET Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4465 SER Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4582 SER Chi-restraints excluded: chain A residue 4591 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 48 optimal weight: 2.9990 chunk 286 optimal weight: 3.9990 chunk 53 optimal weight: 0.0000 chunk 175 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 236 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 263 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN A1922 GLN A2187 GLN A2430 ASN ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3473 ASN A3584 ASN A3735 GLN ** A3754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4079 GLN A4573 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.134818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.106017 restraints weight = 29942.120| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.93 r_work: 0.3145 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24213 Z= 0.120 Angle : 0.509 9.725 32838 Z= 0.254 Chirality : 0.039 0.173 3692 Planarity : 0.004 0.052 4206 Dihedral : 6.533 168.958 3261 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.00 % Allowed : 16.70 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.16), residues: 2929 helix: 2.31 (0.12), residues: 1728 sheet: -0.39 (0.31), residues: 262 loop : 0.73 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.006 0.001 HIS A1810 PHE 0.014 0.001 PHE A1568 TYR 0.020 0.001 TYR A2748 ARG 0.014 0.000 ARG A3654 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 1415) hydrogen bonds : angle 3.95741 ( 4098) covalent geometry : bond 0.00275 (24213) covalent geometry : angle 0.50913 (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 342 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 290 time to evaluate : 2.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1460 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7218 (mm-30) REVERT: A 1488 ARG cc_start: 0.8211 (mtm110) cc_final: 0.7985 (mpp80) REVERT: A 1498 LYS cc_start: 0.8052 (mttm) cc_final: 0.7562 (mmtt) REVERT: A 1560 LEU cc_start: 0.7989 (tp) cc_final: 0.7626 (mm) REVERT: A 1564 GLU cc_start: 0.6468 (OUTLIER) cc_final: 0.5934 (mp0) REVERT: A 1573 THR cc_start: 0.8769 (m) cc_final: 0.8517 (p) REVERT: A 1688 THR cc_start: 0.8558 (m) cc_final: 0.8130 (p) REVERT: A 1745 TYR cc_start: 0.8753 (m-80) cc_final: 0.8376 (m-80) REVERT: A 1831 ASP cc_start: 0.8782 (p0) cc_final: 0.8516 (p0) REVERT: A 1967 MET cc_start: 0.8872 (mmt) cc_final: 0.8636 (mmt) REVERT: A 1980 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7448 (mt-10) REVERT: A 2000 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7919 (tm-30) REVERT: A 2018 MET cc_start: 0.8915 (mtm) cc_final: 0.8555 (mtp) REVERT: A 2043 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8213 (mtpp) REVERT: A 2051 GLN cc_start: 0.8668 (tt0) cc_final: 0.8440 (tt0) REVERT: A 2074 LYS cc_start: 0.8308 (ttpt) cc_final: 0.8071 (tmmm) REVERT: A 2078 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7623 (mt-10) REVERT: A 2138 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8304 (tt) REVERT: A 2172 ARG cc_start: 0.6953 (mtp85) cc_final: 0.6700 (ttm-80) REVERT: A 2175 MET cc_start: 0.7913 (mtp) cc_final: 0.7513 (mtt) REVERT: A 2222 MET cc_start: 0.8920 (mtm) cc_final: 0.8540 (mtm) REVERT: A 2286 LYS cc_start: 0.8779 (tttm) cc_final: 0.8544 (ttpp) REVERT: A 2331 GLU cc_start: 0.8554 (tt0) cc_final: 0.8264 (tt0) REVERT: A 2616 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7996 (pt0) REVERT: A 2763 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7720 (ptt90) REVERT: A 2839 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: A 2863 ARG cc_start: 0.7903 (ttm110) cc_final: 0.7043 (ttt90) REVERT: A 2879 LYS cc_start: 0.8445 (pmtt) cc_final: 0.8079 (pptt) REVERT: A 2902 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8046 (mp0) REVERT: A 3006 GLU cc_start: 0.8573 (tp30) cc_final: 0.8327 (mm-30) REVERT: A 3022 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8383 (mt-10) REVERT: A 3078 ARG cc_start: 0.7984 (tpp-160) cc_final: 0.7755 (mmt90) REVERT: A 3108 GLU cc_start: 0.8455 (tp30) cc_final: 0.8146 (tm-30) REVERT: A 3141 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7718 (mm-30) REVERT: A 3598 GLU cc_start: 0.7792 (tp30) cc_final: 0.7334 (pt0) REVERT: A 3726 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6845 (pp20) REVERT: A 3755 GLU cc_start: 0.7400 (mm-30) cc_final: 0.6967 (mp0) REVERT: A 3972 TYR cc_start: 0.7503 (t80) cc_final: 0.7109 (t80) REVERT: A 4004 MET cc_start: 0.8330 (tpt) cc_final: 0.8097 (tpt) REVERT: A 4075 GLU cc_start: 0.7796 (mp0) cc_final: 0.7586 (pm20) REVERT: A 4108 GLN cc_start: 0.8283 (tt0) cc_final: 0.7808 (mt0) REVERT: A 4419 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.6722 (ptm) REVERT: A 4447 TYR cc_start: 0.8153 (t80) cc_final: 0.7895 (t80) REVERT: A 4484 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: A 4561 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8887 (p) REVERT: A 4591 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7498 (ttp-110) REVERT: A 4595 GLN cc_start: 0.8080 (tp40) cc_final: 0.7835 (tp40) outliers start: 52 outliers final: 24 residues processed: 319 average time/residue: 1.5791 time to fit residues: 579.2010 Evaluate side-chains 306 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 271 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1564 GLU Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 2022 TYR Chi-restraints excluded: chain A residue 2138 ILE Chi-restraints excluded: chain A residue 2221 MET Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2612 LEU Chi-restraints excluded: chain A residue 2616 GLU Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2743 SER Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2804 ARG Chi-restraints excluded: chain A residue 2811 ARG Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 2970 GLU Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3141 GLU Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3545 THR Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3680 SER Chi-restraints excluded: chain A residue 3723 ASP Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 3750 LEU Chi-restraints excluded: chain A residue 3765 THR Chi-restraints excluded: chain A residue 4419 MET Chi-restraints excluded: chain A residue 4465 SER Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4591 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 4 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 287 optimal weight: 7.9990 chunk 71 optimal weight: 0.5980 chunk 184 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 254 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1612 GLN A2109 GLN A2187 GLN A2430 ASN ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3584 ASN A3735 GLN A4079 GLN A4453 ASN A4573 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.133972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105617 restraints weight = 29875.382| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.87 r_work: 0.3123 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3830 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= 0.138 Angle : 0.526 9.622 32838 Z= 0.262 Chirality : 0.040 0.151 3692 Planarity : 0.004 0.059 4206 Dihedral : 6.509 169.097 3261 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.00 % Allowed : 17.08 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.16), residues: 2929 helix: 2.27 (0.12), residues: 1727 sheet: -0.41 (0.31), residues: 262 loop : 0.71 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.007 0.001 HIS A1810 PHE 0.015 0.001 PHE A1568 TYR 0.022 0.001 TYR A2748 ARG 0.014 0.000 ARG A3654 Details of bonding type rmsd hydrogen bonds : bond 0.03955 ( 1415) hydrogen bonds : angle 3.98559 ( 4098) covalent geometry : bond 0.00323 (24213) covalent geometry : angle 0.52581 (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 335 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 283 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1460 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7252 (mm-30) REVERT: A 1488 ARG cc_start: 0.8281 (mtm110) cc_final: 0.8023 (mpp80) REVERT: A 1498 LYS cc_start: 0.8110 (mttm) cc_final: 0.7550 (mmtt) REVERT: A 1560 LEU cc_start: 0.8031 (tp) cc_final: 0.7639 (mm) REVERT: A 1564 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.5990 (mp0) REVERT: A 1573 THR cc_start: 0.8780 (m) cc_final: 0.8536 (p) REVERT: A 1688 THR cc_start: 0.8597 (m) cc_final: 0.8160 (p) REVERT: A 1745 TYR cc_start: 0.8789 (m-80) cc_final: 0.8417 (m-80) REVERT: A 1967 MET cc_start: 0.8887 (mmt) cc_final: 0.8644 (mmt) REVERT: A 1980 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7499 (mt-10) REVERT: A 2000 GLU cc_start: 0.8470 (tm-30) cc_final: 0.7996 (tm-30) REVERT: A 2018 MET cc_start: 0.8969 (mtm) cc_final: 0.8616 (mtp) REVERT: A 2043 LYS cc_start: 0.8771 (mmtt) cc_final: 0.8265 (mtpp) REVERT: A 2051 GLN cc_start: 0.8689 (tt0) cc_final: 0.8470 (tt0) REVERT: A 2074 LYS cc_start: 0.8336 (ttpt) cc_final: 0.8111 (tmmm) REVERT: A 2138 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8332 (tt) REVERT: A 2172 ARG cc_start: 0.6956 (mtp85) cc_final: 0.6719 (ttm-80) REVERT: A 2175 MET cc_start: 0.7951 (mtp) cc_final: 0.7567 (mtt) REVERT: A 2222 MET cc_start: 0.8937 (mtm) cc_final: 0.8584 (mtm) REVERT: A 2286 LYS cc_start: 0.8818 (tttm) cc_final: 0.8578 (ttpp) REVERT: A 2331 GLU cc_start: 0.8586 (tt0) cc_final: 0.8305 (tt0) REVERT: A 2616 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8024 (pt0) REVERT: A 2763 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7744 (ptt90) REVERT: A 2839 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: A 2863 ARG cc_start: 0.7948 (ttm110) cc_final: 0.7077 (ttt90) REVERT: A 2879 LYS cc_start: 0.8433 (pmtt) cc_final: 0.8082 (pptt) REVERT: A 2902 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8073 (mp0) REVERT: A 3006 GLU cc_start: 0.8593 (tp30) cc_final: 0.8374 (mm-30) REVERT: A 3022 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8463 (mt-10) REVERT: A 3078 ARG cc_start: 0.8045 (tpp-160) cc_final: 0.7827 (mmt90) REVERT: A 3108 GLU cc_start: 0.8486 (tp30) cc_final: 0.8187 (tm-30) REVERT: A 3141 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.7753 (mm-30) REVERT: A 3598 GLU cc_start: 0.7824 (tp30) cc_final: 0.7393 (pt0) REVERT: A 3606 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8276 (p0) REVERT: A 3726 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6937 (pp20) REVERT: A 3755 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6895 (mp0) REVERT: A 3791 MET cc_start: 0.7518 (tpt) cc_final: 0.7283 (tpp) REVERT: A 3972 TYR cc_start: 0.7444 (t80) cc_final: 0.7048 (t80) REVERT: A 4004 MET cc_start: 0.8348 (tpt) cc_final: 0.8108 (tpt) REVERT: A 4075 GLU cc_start: 0.7815 (mp0) cc_final: 0.7601 (pm20) REVERT: A 4108 GLN cc_start: 0.8305 (tt0) cc_final: 0.7837 (mt0) REVERT: A 4270 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7977 (mm-30) REVERT: A 4399 LYS cc_start: 0.6915 (tmtt) cc_final: 0.6505 (ttpp) REVERT: A 4419 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.6746 (ptm) REVERT: A 4447 TYR cc_start: 0.8156 (t80) cc_final: 0.7888 (t80) REVERT: A 4484 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: A 4561 THR cc_start: 0.9238 (OUTLIER) cc_final: 0.8967 (p) REVERT: A 4591 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7544 (ttp-110) REVERT: A 4595 GLN cc_start: 0.8099 (tp40) cc_final: 0.7872 (tp40) outliers start: 52 outliers final: 28 residues processed: 314 average time/residue: 1.5421 time to fit residues: 549.9475 Evaluate side-chains 314 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 274 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1564 GLU Chi-restraints excluded: chain A residue 1603 ARG Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 2022 TYR Chi-restraints excluded: chain A residue 2138 ILE Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2612 LEU Chi-restraints excluded: chain A residue 2616 GLU Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2743 SER Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2804 ARG Chi-restraints excluded: chain A residue 2811 ARG Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 2970 GLU Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3141 GLU Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3545 THR Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3606 ASP Chi-restraints excluded: chain A residue 3680 SER Chi-restraints excluded: chain A residue 3723 ASP Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 3750 LEU Chi-restraints excluded: chain A residue 3765 THR Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4419 MET Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4465 SER Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4518 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4582 SER Chi-restraints excluded: chain A residue 4591 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 163 optimal weight: 0.0050 chunk 114 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 251 optimal weight: 0.0050 chunk 52 optimal weight: 0.8980 chunk 224 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 266 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.4808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2187 GLN A2430 ASN ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3584 ASN ** A3754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4079 GLN A4573 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.135254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106907 restraints weight = 29934.212| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.95 r_work: 0.3155 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24213 Z= 0.109 Angle : 0.510 10.095 32838 Z= 0.253 Chirality : 0.039 0.154 3692 Planarity : 0.004 0.060 4206 Dihedral : 6.366 168.236 3261 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.46 % Allowed : 17.81 % Favored : 80.73 % 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: 2.37 (0.16), residues: 2929 helix: 2.39 (0.12), residues: 1721 sheet: -0.36 (0.31), residues: 262 loop : 0.73 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.005 0.001 HIS A1810 PHE 0.013 0.001 PHE A1568 TYR 0.018 0.001 TYR A2748 ARG 0.015 0.000 ARG A3654 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 1415) hydrogen bonds : angle 3.91338 ( 4098) covalent geometry : bond 0.00244 (24213) covalent geometry : angle 0.50960 (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 330 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 292 time to evaluate : 2.886 Fit side-chains revert: symmetry clash REVERT: A 1460 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7261 (mm-30) REVERT: A 1488 ARG cc_start: 0.8194 (mtm110) cc_final: 0.7925 (mpp80) REVERT: A 1498 LYS cc_start: 0.8047 (mttm) cc_final: 0.7495 (mmtt) REVERT: A 1560 LEU cc_start: 0.7976 (tp) cc_final: 0.7642 (mm) REVERT: A 1564 GLU cc_start: 0.6415 (OUTLIER) cc_final: 0.5890 (mp0) REVERT: A 1573 THR cc_start: 0.8728 (m) cc_final: 0.8491 (p) REVERT: A 1688 THR cc_start: 0.8557 (m) cc_final: 0.8140 (p) REVERT: A 1745 TYR cc_start: 0.8719 (m-80) cc_final: 0.8342 (m-80) REVERT: A 1967 MET cc_start: 0.8864 (mmt) cc_final: 0.8607 (mmt) REVERT: A 1980 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7451 (mt-10) REVERT: A 2000 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7933 (tm-30) REVERT: A 2018 MET cc_start: 0.8878 (mtm) cc_final: 0.8509 (mtp) REVERT: A 2043 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8211 (mtpp) REVERT: A 2051 GLN cc_start: 0.8665 (tt0) cc_final: 0.8435 (tt0) REVERT: A 2074 LYS cc_start: 0.8339 (ttpt) cc_final: 0.8102 (tmmm) REVERT: A 2138 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8312 (tt) REVERT: A 2175 MET cc_start: 0.7876 (mtp) cc_final: 0.7481 (mtt) REVERT: A 2222 MET cc_start: 0.8890 (mtm) cc_final: 0.8571 (mtm) REVERT: A 2286 LYS cc_start: 0.8773 (tttm) cc_final: 0.8557 (ttpp) REVERT: A 2331 GLU cc_start: 0.8507 (tt0) cc_final: 0.8223 (tt0) REVERT: A 2763 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7707 (ptt90) REVERT: A 2863 ARG cc_start: 0.8012 (ttm110) cc_final: 0.7123 (ttt90) REVERT: A 2902 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8035 (mp0) REVERT: A 3006 GLU cc_start: 0.8563 (tp30) cc_final: 0.8323 (mm-30) REVERT: A 3022 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8454 (mt-10) REVERT: A 3078 ARG cc_start: 0.8025 (tpp-160) cc_final: 0.7809 (mmt90) REVERT: A 3108 GLU cc_start: 0.8442 (tp30) cc_final: 0.8132 (tm-30) REVERT: A 3141 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7723 (mm-30) REVERT: A 3598 GLU cc_start: 0.7812 (tp30) cc_final: 0.7372 (pt0) REVERT: A 3606 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.8259 (p0) REVERT: A 3652 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7496 (mt-10) REVERT: A 3726 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6885 (pp20) REVERT: A 3755 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6864 (mp0) REVERT: A 3972 TYR cc_start: 0.7399 (t80) cc_final: 0.6996 (t80) REVERT: A 4075 GLU cc_start: 0.7767 (mp0) cc_final: 0.7488 (pm20) REVERT: A 4108 GLN cc_start: 0.8247 (tt0) cc_final: 0.7890 (mt0) REVERT: A 4270 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7936 (mm-30) REVERT: A 4399 LYS cc_start: 0.6906 (tmtt) cc_final: 0.5874 (mttt) REVERT: A 4419 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7359 (ttm) REVERT: A 4447 TYR cc_start: 0.8137 (t80) cc_final: 0.7903 (t80) REVERT: A 4484 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: A 4506 ASN cc_start: 0.8196 (m-40) cc_final: 0.7923 (m-40) REVERT: A 4561 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8868 (p) REVERT: A 4591 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7517 (ttp-110) outliers start: 38 outliers final: 20 residues processed: 317 average time/residue: 1.5407 time to fit residues: 562.5221 Evaluate side-chains 300 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 270 time to evaluate : 2.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1564 GLU Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 2022 TYR Chi-restraints excluded: chain A residue 2138 ILE Chi-restraints excluded: chain A residue 2612 LEU Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2804 ARG Chi-restraints excluded: chain A residue 2811 ARG Chi-restraints excluded: chain A residue 2970 GLU Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3141 GLU Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3606 ASP Chi-restraints excluded: chain A residue 3680 SER Chi-restraints excluded: chain A residue 3723 ASP Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 3750 LEU Chi-restraints excluded: chain A residue 3765 THR Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4419 MET Chi-restraints excluded: chain A residue 4465 SER Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4591 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 84 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 214 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 235 optimal weight: 2.9990 chunk 278 optimal weight: 4.9990 chunk 242 optimal weight: 0.2980 chunk 130 optimal weight: 0.9990 chunk 13 optimal weight: 0.0070 chunk 91 optimal weight: 0.9990 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2187 GLN ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3584 ASN ** A3754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4079 GLN A4573 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.135873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.107091 restraints weight = 29674.296| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.91 r_work: 0.3154 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24213 Z= 0.111 Angle : 0.514 11.424 32838 Z= 0.254 Chirality : 0.039 0.154 3692 Planarity : 0.004 0.068 4206 Dihedral : 6.278 166.881 3261 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.69 % Allowed : 17.70 % Favored : 80.61 % 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: 2.38 (0.16), residues: 2929 helix: 2.39 (0.12), residues: 1723 sheet: -0.34 (0.31), residues: 262 loop : 0.75 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.005 0.001 HIS A1810 PHE 0.013 0.001 PHE A1568 TYR 0.019 0.001 TYR A2748 ARG 0.017 0.000 ARG A3654 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 1415) hydrogen bonds : angle 3.90157 ( 4098) covalent geometry : bond 0.00248 (24213) covalent geometry : angle 0.51450 (32838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18180.36 seconds wall clock time: 313 minutes 3.48 seconds (18783.48 seconds total)