Starting phenix.real_space_refine on Sat May 24 03:21:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9blz_44682/05_2025/9blz_44682.cif Found real_map, /net/cci-nas-00/data/ceres_data/9blz_44682/05_2025/9blz_44682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9blz_44682/05_2025/9blz_44682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9blz_44682/05_2025/9blz_44682.map" model { file = "/net/cci-nas-00/data/ceres_data/9blz_44682/05_2025/9blz_44682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9blz_44682/05_2025/9blz_44682.cif" } resolution = 2.2 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= 0.003 sd= 0.039 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 14834 2.51 5 N 4022 2.21 5 O 6205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 1.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25189 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 23218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2889, 23218 Classifications: {'peptide': 2889} Link IDs: {'PTRANS': 131, 'TRANS': 2757} Chain breaks: 3 Chain: "A" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1863, 1971 Unusual residues: {' MG': 2, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 6, 'water': 1857} Link IDs: {None: 1862} Time building chain proxies: 13.85, per 1000 atoms: 0.55 Number of scatterers: 25189 At special positions: 0 Unit cell: (147.264, 117.728, 175.552, 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 6205 8.00 N 4022 7.00 C 14834 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: 5.94 Conformation dependent library (CDL) restraints added in 2.7 seconds 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5492 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 20 sheets defined 63.2% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.11 Creating SS restraints... Processing helix chain 'A' and resid 1457 through 1473 removed outlier: 3.679A pdb=" N THR A1472 " --> pdb=" O GLU A1468 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1508 removed outlier: 3.592A pdb=" N LYS A1508 " --> pdb=" O VAL A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1513 through 1515 No H-bonds generated for 'chain 'A' and resid 1513 through 1515' Processing helix chain 'A' and resid 1516 through 1553 removed outlier: 3.659A pdb=" N ASP A1535 " --> pdb=" O MET A1531 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A1553 " --> pdb=" O GLY A1549 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1561 removed outlier: 3.899A 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 1615 Processing helix chain 'A' and resid 1615 through 1626 removed outlier: 3.654A pdb=" N SER A1625 " --> pdb=" O ARG A1621 " (cutoff:3.500A) removed outlier: 3.501A 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: 3.582A pdb=" N LYS A1649 " --> pdb=" O ASN A1646 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1658 removed outlier: 3.569A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1728 removed outlier: 3.525A pdb=" N THR A1722 " --> pdb=" O ALA A1718 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE A1727 " --> pdb=" O GLU A1723 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 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 1798 removed outlier: 3.702A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) 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: 4.022A pdb=" N GLN A1973 " --> pdb=" O SER A1969 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN A1974 " --> pdb=" O ALA A1970 " (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: 3.523A pdb=" N LEU A2080 " --> pdb=" O CYS A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2118 removed outlier: 3.543A 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 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2293 through 2297 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 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: 3.829A 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: 3.808A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A2443 " --> pdb=" O HIS A2439 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.656A pdb=" N CYS A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2504 removed outlier: 3.588A 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: 3.868A pdb=" N VAL A2562 " --> pdb=" O THR A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.768A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2611 removed outlier: 3.587A pdb=" N ALA A2611 " --> pdb=" O SER A2607 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.369A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2690 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: 5.090A 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 2833 Processing helix chain 'A' and resid 2834 through 2837 Processing helix chain 'A' and resid 2839 through 2858 Processing helix chain 'A' and resid 2862 through 2868 removed outlier: 3.595A pdb=" N ALA A2866 " --> pdb=" O ASP A2862 " (cutoff:3.500A) Processing helix chain 'A' and resid 2885 through 2904 removed outlier: 3.513A pdb=" N VAL A2899 " --> pdb=" O ALA A2895 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A2902 " --> pdb=" O LYS A2898 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2927 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: 3.937A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A3010 " --> pdb=" O GLU A3006 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3040 Processing helix chain 'A' and resid 3046 through 3061 Processing helix chain 'A' and resid 3071 through 3082 removed outlier: 3.656A pdb=" N ALA A3080 " --> pdb=" O LYS A3076 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3087 Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3164 removed outlier: 3.505A pdb=" N LEU A3154 " --> pdb=" O VAL A3150 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS A3155 " --> pdb=" O HIS A3151 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 3217 removed outlier: 3.654A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3473 through 3482 Processing helix chain 'A' and resid 3482 through 3495 Processing helix chain 'A' and resid 3495 through 3517 removed outlier: 4.594A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLY A3505 " --> pdb=" O SER A3501 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3554 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 removed outlier: 3.725A pdb=" N GLU A3598 " --> pdb=" O GLY A3594 " (cutoff:3.500A) 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: 3.568A 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 3755 Processing helix chain 'A' and resid 3763 through 3799 removed outlier: 3.619A pdb=" N ILE A3767 " --> pdb=" O ASP A3763 " (cutoff:3.500A) Processing helix chain 'A' and resid 3801 through 3818 Processing helix chain 'A' and resid 3819 through 3821 No H-bonds generated for 'chain 'A' and resid 3819 through 3821' Processing helix chain 'A' and resid 3828 through 3842 removed outlier: 3.672A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3847 removed outlier: 3.500A pdb=" N LYS A3847 " --> pdb=" O PRO A3844 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 removed outlier: 3.515A pdb=" N PHE A3864 " --> pdb=" O THR A3860 " (cutoff:3.500A) Processing helix chain 'A' and resid 3876 through 3894 removed outlier: 3.503A pdb=" N HIS A3880 " --> pdb=" O LEU A3876 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE A3881 " --> pdb=" O HIS A3877 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N THR A3882 " --> pdb=" O GLN A3878 " (cutoff:3.500A) 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 3970 removed outlier: 4.106A pdb=" N VAL A3970 " --> pdb=" O GLU A3967 " (cutoff:3.500A) 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 removed outlier: 3.513A pdb=" N MET A4021 " --> pdb=" O MET A4018 " (cutoff:3.500A) Processing helix chain 'A' and resid 4026 through 4034 removed outlier: 3.696A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) 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: 3.578A pdb=" N GLN A4108 " --> pdb=" O GLY A4104 " (cutoff:3.500A) removed outlier: 3.623A 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 Processing helix chain 'A' and resid 4175 through 4196 removed outlier: 3.589A pdb=" N LEU A4194 " --> pdb=" O ILE A4190 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG A4195 " --> pdb=" O GLN A4191 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TYR A4196 " --> pdb=" O GLU A4192 " (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 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 4346 Processing helix chain 'A' and resid 4375 through 4391 Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4457 Processing helix chain 'A' and resid 4474 through 4498 removed outlier: 3.859A pdb=" N SER A4480 " --> pdb=" O ILE A4476 " (cutoff:3.500A) Processing helix chain 'A' and resid 4500 through 4505 removed outlier: 3.625A pdb=" N LYS A4505 " --> pdb=" O LYS A4502 " (cutoff:3.500A) Processing helix chain 'A' and resid 4516 through 4532 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 Processing sheet with id=AA1, first strand: chain 'A' and resid 1476 through 1480 removed outlier: 4.238A pdb=" N ASP A1476 " --> pdb=" O ARG A1488 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1663 through 1666 removed outlier: 7.279A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.658A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.416A 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: 6.638A pdb=" N GLY A1901 " --> pdb=" O ARG A2037 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LEU A2039 " --> pdb=" O GLY A1901 " (cutoff:3.500A) removed outlier: 6.554A 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: 6.254A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ASP A1958 " --> pdb=" O LEU A1928 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE A1930 " --> pdb=" O ASP A1958 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N THR A2017 " --> pdb=" O GLY A1955 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE A1957 " --> pdb=" O THR A2017 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 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 removed outlier: 6.640A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE A2303 " --> pdb=" O GLU A2344 " (cutoff:3.500A) 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 2540 removed outlier: 3.760A pdb=" N GLU A2544 " --> pdb=" O SER A2540 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 6.356A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 6.280A 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: 6.727A pdb=" N VAL A2648 " --> pdb=" O LYS A2702 " (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: 6.248A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU A2935 " --> pdb=" O MET A3068 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N HIS A2932 " --> pdb=" O VAL A3090 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASN A3092 " --> pdb=" O HIS A2932 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU A2934 " --> pdb=" O ASN A3092 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE A3094 " --> pdb=" O LEU A2934 " (cutoff:3.500A) removed outlier: 7.515A 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: 6.250A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU A4042 " --> pdb=" O PHE A4145 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N PHE A4147 " --> pdb=" O LEU A4042 " (cutoff:3.500A) removed outlier: 6.600A 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: 6.278A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A4587 " --> pdb=" O THR A4546 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4575 through 4584 removed outlier: 9.357A pdb=" N ASN A4579 " --> pdb=" O THR A4569 " (cutoff:3.500A) removed outlier: 9.558A pdb=" N THR A4569 " --> pdb=" O ASN A4579 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ILE A4581 " --> pdb=" O GLY A4567 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL A4605 " --> pdb=" O ASP A4623 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASP A4623 " --> pdb=" O VAL A4605 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU A4607 " --> pdb=" O THR A4621 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N THR A4621 " --> pdb=" O LEU A4607 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL A4609 " --> pdb=" O ILE A4619 " (cutoff:3.500A) 1374 hydrogen bonds defined for protein. 3972 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.88 Time building geometry restraints manager: 6.80 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: 7682 1.34 - 1.46: 4655 1.46 - 1.58: 11290 1.58 - 1.69: 14 1.69 - 1.81: 196 Bond restraints: 23837 Sorted by residual: bond pdb=" C4 ADP A4704 " pdb=" C5 ADP A4704 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+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 2.96e+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 A4701 " pdb=" C6 ADP A4701 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+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 1.70e+01 ... (remaining 23832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 31859 2.31 - 4.62: 414 4.62 - 6.93: 36 6.93 - 9.24: 16 9.24 - 11.55: 10 Bond angle restraints: 32335 Sorted by residual: angle pdb=" PB ATP A4702 " pdb=" O3B ATP A4702 " pdb=" PG ATP A4702 " ideal model delta sigma weight residual 139.87 131.91 7.96 1.00e+00 1.00e+00 6.33e+01 angle pdb=" PA ATP A4702 " pdb=" O3A ATP A4702 " pdb=" PB ATP A4702 " ideal model delta sigma weight residual 136.83 132.12 4.71 1.00e+00 1.00e+00 2.22e+01 angle pdb=" N PRO A4632 " pdb=" CA PRO A4632 " pdb=" C PRO A4632 " ideal model delta sigma weight residual 113.81 107.37 6.44 1.45e+00 4.76e-01 1.98e+01 angle pdb=" C THR A4628 " pdb=" CA THR A4628 " pdb=" CB THR A4628 " ideal model delta sigma weight residual 116.54 111.68 4.86 1.15e+00 7.56e-01 1.79e+01 angle pdb=" PA ADP A4704 " pdb=" O3A ADP A4704 " pdb=" PB ADP A4704 " ideal model delta sigma weight residual 120.50 132.05 -11.55 3.00e+00 1.11e-01 1.48e+01 ... (remaining 32330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.93: 14000 28.93 - 57.87: 332 57.87 - 86.80: 108 86.80 - 115.73: 4 115.73 - 144.67: 2 Dihedral angle restraints: 14446 sinusoidal: 5988 harmonic: 8458 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 84.66 -144.67 1 2.00e+01 2.50e-03 4.36e+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 300.00 172.52 127.49 1 2.00e+01 2.50e-03 3.86e+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 51.74 -111.74 1 2.00e+01 2.50e-03 3.29e+01 ... (remaining 14443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2857 0.048 - 0.096: 607 0.096 - 0.145: 157 0.145 - 0.193: 9 0.193 - 0.241: 2 Chirality restraints: 3632 Sorted by residual: chirality pdb=" CB ILE A1538 " pdb=" CA ILE A1538 " pdb=" CG1 ILE A1538 " pdb=" CG2 ILE A1538 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA VAL A4622 " pdb=" N VAL A4622 " pdb=" C VAL A4622 " pdb=" CB VAL A4622 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA VAL A2568 " pdb=" N VAL A2568 " pdb=" C VAL A2568 " pdb=" CB VAL A2568 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.17e-01 ... (remaining 3629 not shown) Planarity restraints: 4141 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1537 " 0.029 2.00e-02 2.50e+03 3.00e-02 2.25e+01 pdb=" CG TRP A1537 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP A1537 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP A1537 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A1537 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP A1537 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A1537 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1537 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1537 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A1537 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A2801 " -0.250 9.50e-02 1.11e+02 1.12e-01 7.70e+00 pdb=" NE ARG A2801 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A2801 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A2801 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A2801 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A2774 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C VAL A2774 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL A2774 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU A2775 " -0.013 2.00e-02 2.50e+03 ... (remaining 4138 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 550 2.48 - 3.09: 18956 3.09 - 3.69: 45043 3.69 - 4.30: 67076 4.30 - 4.90: 102082 Nonbonded interactions: 233707 Sorted by model distance: nonbonded pdb=" OG SER A2231 " pdb="MG MG A4706 " model vdw 1.876 2.170 nonbonded pdb=" O2G ATP A4702 " pdb="MG MG A4706 " model vdw 1.907 2.170 nonbonded pdb="MG MG A4705 " pdb=" O HOH A5554 " model vdw 2.070 2.170 nonbonded pdb="MG MG A4705 " pdb=" O HOH A5188 " model vdw 2.072 2.170 nonbonded pdb=" OE2 GLU A2344 " pdb="MG MG A4706 " model vdw 2.078 2.170 ... (remaining 233702 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.910 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 60.360 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 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 0.109 23837 Z= 0.223 Angle : 0.663 11.554 32335 Z= 0.369 Chirality : 0.043 0.241 3632 Planarity : 0.005 0.112 4141 Dihedral : 14.009 144.667 8954 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.04 % Allowed : 0.16 % 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: 1.39 (0.16), residues: 2881 helix: 1.39 (0.13), residues: 1661 sheet: -0.03 (0.31), residues: 260 loop : 0.60 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP A1537 HIS 0.010 0.001 HIS A1500 PHE 0.019 0.002 PHE A1960 TYR 0.016 0.001 TYR A1546 ARG 0.008 0.001 ARG A1806 Details of bonding type rmsd hydrogen bonds : bond 0.12541 ( 1374) hydrogen bonds : angle 5.81468 ( 3972) covalent geometry : bond 0.00375 (23837) covalent geometry : angle 0.66348 (32335) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 397 time to evaluate : 2.751 Fit side-chains REVERT: A 2484 GLU cc_start: 0.6326 (tm-30) cc_final: 0.6110 (tm-30) REVERT: A 3624 GLU cc_start: 0.8211 (tt0) cc_final: 0.7803 (mt-10) outliers start: 1 outliers final: 1 residues processed: 397 average time/residue: 1.7078 time to fit residues: 770.2197 Evaluate side-chains 329 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 328 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1571 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 6.9990 chunk 218 optimal weight: 0.0020 chunk 121 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 116 optimal weight: 0.0670 chunk 225 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 168 optimal weight: 0.0570 chunk 261 optimal weight: 8.9990 overall best weight: 1.4248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1612 GLN A1646 ASN A1761 ASN A1779 HIS A2442 GLN A2554 GLN A2577 HIS A2677 GLN A3092 ASN A3198 GLN A3202 ASN A3523 GLN A3527 ASN ** A3650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3826 GLN A3838 ASN A4012 ASN A4137 ASN A4262 GLN A4266 ASN A4295 GLN A4477 GLN A4491 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.168112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.137241 restraints weight = 24187.945| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.32 r_work: 0.3467 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23837 Z= 0.137 Angle : 0.563 8.025 32335 Z= 0.290 Chirality : 0.041 0.182 3632 Planarity : 0.004 0.053 4141 Dihedral : 7.457 151.802 3211 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.44 % Allowed : 7.13 % Favored : 91.43 % 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: 2881 helix: 2.00 (0.13), residues: 1675 sheet: -0.05 (0.31), residues: 250 loop : 0.67 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A4222 HIS 0.006 0.001 HIS A2689 PHE 0.021 0.002 PHE A1960 TYR 0.020 0.002 TYR A1546 ARG 0.006 0.001 ARG A1488 Details of bonding type rmsd hydrogen bonds : bond 0.04764 ( 1374) hydrogen bonds : angle 4.37757 ( 3972) covalent geometry : bond 0.00285 (23837) covalent geometry : angle 0.56289 (32335) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 363 time to evaluate : 2.786 Fit side-chains revert: symmetry clash REVERT: A 1621 ARG cc_start: 0.7913 (ttp80) cc_final: 0.7526 (mtp-110) REVERT: A 2484 GLU cc_start: 0.6301 (tm-30) cc_final: 0.6002 (tm-30) REVERT: A 2516 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6847 (pt0) REVERT: A 2561 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7728 (mtpp) REVERT: A 2763 ARG cc_start: 0.6733 (ttp80) cc_final: 0.5964 (tpm-80) REVERT: A 2865 LYS cc_start: 0.6782 (ttpp) cc_final: 0.6379 (tptp) REVERT: A 3035 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7054 (pp20) REVERT: A 3169 MET cc_start: 0.8673 (mmt) cc_final: 0.8470 (mmt) REVERT: A 4043 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8182 (mtp) REVERT: A 4331 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8182 (tp) REVERT: A 4491 ASN cc_start: 0.7968 (m-40) cc_final: 0.7732 (m110) outliers start: 37 outliers final: 14 residues processed: 379 average time/residue: 1.6602 time to fit residues: 713.7202 Evaluate side-chains 341 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 323 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1571 ILE Chi-restraints excluded: chain A residue 2064 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2449 LEU Chi-restraints excluded: chain A residue 2561 LYS Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2822 ILE Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2994 MET Chi-restraints excluded: chain A residue 3035 GLU Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3796 THR Chi-restraints excluded: chain A residue 3842 GLU Chi-restraints excluded: chain A residue 4043 MET Chi-restraints excluded: chain A residue 4331 LEU Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4645 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 50 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 257 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 256 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 chunk 213 optimal weight: 6.9990 chunk 226 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1612 GLN A1646 ASN A1779 HIS A1931 ASN A2471 GLN A2554 GLN A2752 ASN A3069 ASN A3202 ASN A3538 GLN ** A3650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4137 ASN A4295 GLN A4477 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.164240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.131589 restraints weight = 23958.024| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.35 r_work: 0.3434 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 23837 Z= 0.209 Angle : 0.634 8.020 32335 Z= 0.329 Chirality : 0.045 0.189 3632 Planarity : 0.005 0.069 4141 Dihedral : 7.429 157.690 3211 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.99 % Allowed : 8.92 % Favored : 89.09 % 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: 1.84 (0.15), residues: 2881 helix: 1.91 (0.12), residues: 1670 sheet: -0.23 (0.31), residues: 239 loop : 0.55 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A4222 HIS 0.008 0.001 HIS A2689 PHE 0.024 0.003 PHE A1534 TYR 0.024 0.002 TYR A4196 ARG 0.009 0.001 ARG A3721 Details of bonding type rmsd hydrogen bonds : bond 0.05610 ( 1374) hydrogen bonds : angle 4.44969 ( 3972) covalent geometry : bond 0.00470 (23837) covalent geometry : angle 0.63397 (32335) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 351 time to evaluate : 2.691 Fit side-chains revert: symmetry clash REVERT: A 1566 GLN cc_start: 0.6889 (tm-30) cc_final: 0.6193 (tm-30) REVERT: A 1621 ARG cc_start: 0.7985 (ttp80) cc_final: 0.7768 (ttp-170) REVERT: A 1760 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: A 1829 LYS cc_start: 0.7891 (mptm) cc_final: 0.7438 (mptt) REVERT: A 2043 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8139 (mptt) REVERT: A 2332 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7288 (pmm-80) REVERT: A 2484 GLU cc_start: 0.6196 (tm-30) cc_final: 0.5770 (tm-30) REVERT: A 2516 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6712 (pt0) REVERT: A 2561 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7697 (mtpp) REVERT: A 2688 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: A 2763 ARG cc_start: 0.6723 (ttp80) cc_final: 0.5730 (tpm-80) REVERT: A 3006 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7112 (tp30) REVERT: A 3035 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6935 (pp20) REVERT: A 3620 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7785 (tpp-160) REVERT: A 3799 GLN cc_start: 0.8072 (mm110) cc_final: 0.7620 (mm-40) REVERT: A 4276 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7379 (mmp-170) outliers start: 51 outliers final: 24 residues processed: 380 average time/residue: 1.6926 time to fit residues: 731.7203 Evaluate side-chains 357 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 324 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1697 LYS Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1835 SER Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2043 LYS Chi-restraints excluded: chain A residue 2064 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2212 GLN Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2332 ARG Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2554 GLN Chi-restraints excluded: chain A residue 2561 LYS Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2616 GLU Chi-restraints excluded: chain A residue 2688 GLU Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 2994 MET Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3035 GLU Chi-restraints excluded: chain A residue 3161 LEU Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3620 ARG Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3796 THR Chi-restraints excluded: chain A residue 3842 GLU Chi-restraints excluded: chain A residue 4237 LYS Chi-restraints excluded: chain A residue 4276 ARG Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4645 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 95 optimal weight: 0.0270 chunk 246 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 174 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1646 ASN A1779 HIS A1931 ASN A2102 ASN A2442 GLN A2554 GLN A2930 GLN A3202 ASN A3650 ASN A3754 ASN A4023 GLN A4137 ASN A4295 GLN A4444 GLN A4477 GLN A4491 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.168695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.136032 restraints weight = 24449.118| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.39 r_work: 0.3488 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23837 Z= 0.111 Angle : 0.510 6.833 32335 Z= 0.261 Chirality : 0.039 0.193 3632 Planarity : 0.004 0.044 4141 Dihedral : 7.031 155.883 3209 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.64 % Allowed : 10.28 % Favored : 88.08 % 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: 2.22 (0.16), residues: 2881 helix: 2.23 (0.12), residues: 1663 sheet: -0.10 (0.32), residues: 240 loop : 0.69 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.004 0.001 HIS A1985 PHE 0.016 0.001 PHE A2912 TYR 0.020 0.001 TYR A4527 ARG 0.004 0.000 ARG A1806 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 1374) hydrogen bonds : angle 4.14418 ( 3972) covalent geometry : bond 0.00225 (23837) covalent geometry : angle 0.51001 (32335) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 356 time to evaluate : 2.609 Fit side-chains revert: symmetry clash REVERT: A 1566 GLN cc_start: 0.6690 (tm-30) cc_final: 0.5991 (tm-30) REVERT: A 1610 LYS cc_start: 0.7858 (mttm) cc_final: 0.7389 (mppt) REVERT: A 1621 ARG cc_start: 0.7811 (ttp80) cc_final: 0.7191 (mtp-110) REVERT: A 1829 LYS cc_start: 0.7792 (mptm) cc_final: 0.7247 (mptt) REVERT: A 2332 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7168 (pmm-80) REVERT: A 2471 GLN cc_start: 0.6969 (OUTLIER) cc_final: 0.6139 (tm-30) REVERT: A 2484 GLU cc_start: 0.6099 (tm-30) cc_final: 0.5651 (tm-30) REVERT: A 2516 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6546 (pt0) REVERT: A 2661 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8479 (mp) REVERT: A 2688 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: A 2763 ARG cc_start: 0.6605 (ttp80) cc_final: 0.5362 (tpm-80) REVERT: A 2855 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6777 (mp) REVERT: A 2994 MET cc_start: 0.8413 (ttp) cc_final: 0.8099 (ptm) REVERT: A 3035 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6697 (pp20) REVERT: A 3078 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7489 (tpt170) REVERT: A 3611 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7256 (ttm110) REVERT: A 3620 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7575 (tpp-160) REVERT: A 3799 GLN cc_start: 0.7979 (mm110) cc_final: 0.7445 (mm-40) REVERT: A 3906 GLN cc_start: 0.7481 (tp40) cc_final: 0.6849 (tm-30) REVERT: A 4276 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7062 (mmp-170) REVERT: A 4279 ASP cc_start: 0.6660 (m-30) cc_final: 0.5858 (m-30) REVERT: A 4491 ASN cc_start: 0.7778 (m-40) cc_final: 0.7557 (m110) outliers start: 42 outliers final: 15 residues processed: 376 average time/residue: 1.7364 time to fit residues: 739.7224 Evaluate side-chains 353 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 328 time to evaluate : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1571 ILE Chi-restraints excluded: chain A residue 1697 LYS Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2212 GLN Chi-restraints excluded: chain A residue 2332 ARG Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2444 GLU Chi-restraints excluded: chain A residue 2449 LEU Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2554 GLN Chi-restraints excluded: chain A residue 2661 LEU Chi-restraints excluded: chain A residue 2688 GLU Chi-restraints excluded: chain A residue 2822 ILE Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 3035 GLU Chi-restraints excluded: chain A residue 3078 ARG Chi-restraints excluded: chain A residue 3161 LEU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3611 ARG Chi-restraints excluded: chain A residue 3620 ARG Chi-restraints excluded: chain A residue 3796 THR Chi-restraints excluded: chain A residue 3842 GLU Chi-restraints excluded: chain A residue 4276 ARG Chi-restraints excluded: chain A residue 4645 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 35 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 286 optimal weight: 10.0000 chunk 210 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 206 optimal weight: 9.9990 chunk 283 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1612 GLN A1779 HIS A1931 ASN A2187 GLN A2554 GLN A2713 ASN A2954 ASN A3155 HIS A3202 ASN A3535 HIS A4137 ASN A4295 GLN A4477 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.162310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.130004 restraints weight = 24058.396| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.34 r_work: 0.3395 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 23837 Z= 0.255 Angle : 0.665 8.139 32335 Z= 0.346 Chirality : 0.047 0.229 3632 Planarity : 0.006 0.068 4141 Dihedral : 7.478 156.494 3209 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.38 % Allowed : 10.60 % Favored : 87.03 % 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: 1.79 (0.15), residues: 2881 helix: 1.87 (0.12), residues: 1665 sheet: -0.30 (0.31), residues: 239 loop : 0.55 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A4222 HIS 0.007 0.001 HIS A2588 PHE 0.026 0.003 PHE A1534 TYR 0.022 0.003 TYR A4196 ARG 0.008 0.001 ARG A2729 Details of bonding type rmsd hydrogen bonds : bond 0.05803 ( 1374) hydrogen bonds : angle 4.47716 ( 3972) covalent geometry : bond 0.00581 (23837) covalent geometry : angle 0.66457 (32335) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 333 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1566 GLN cc_start: 0.6975 (tm-30) cc_final: 0.6275 (tm-30) REVERT: A 1601 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7638 (mm) REVERT: A 1829 LYS cc_start: 0.7914 (mptm) cc_final: 0.7411 (mptt) REVERT: A 1980 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7455 (mm-30) REVERT: A 2332 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7558 (pmm-80) REVERT: A 2471 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6407 (tm-30) REVERT: A 2484 GLU cc_start: 0.6234 (tm-30) cc_final: 0.5796 (tm-30) REVERT: A 2516 GLU cc_start: 0.7494 (mt-10) cc_final: 0.6848 (pt0) REVERT: A 2688 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: A 2763 ARG cc_start: 0.6796 (ttp80) cc_final: 0.5881 (tpm-80) REVERT: A 2848 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7270 (tp30) REVERT: A 2863 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7470 (ttt-90) REVERT: A 3006 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7188 (tp30) REVERT: A 3035 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7082 (pp20) REVERT: A 3078 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7682 (tpt170) REVERT: A 3611 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7561 (ttm110) REVERT: A 3620 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7892 (tpp-160) REVERT: A 3799 GLN cc_start: 0.8115 (mm110) cc_final: 0.7627 (mm-40) REVERT: A 4276 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7543 (mmp-170) REVERT: A 4279 ASP cc_start: 0.6973 (m-30) cc_final: 0.6443 (m-30) REVERT: A 4331 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8140 (tp) outliers start: 61 outliers final: 27 residues processed: 364 average time/residue: 1.7099 time to fit residues: 709.1566 Evaluate side-chains 360 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 320 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1571 ILE Chi-restraints excluded: chain A residue 1601 LEU Chi-restraints excluded: chain A residue 1635 GLU Chi-restraints excluded: chain A residue 1697 LYS Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1835 SER Chi-restraints excluded: chain A residue 2064 VAL Chi-restraints excluded: chain A residue 2212 GLN Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2332 ARG Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2554 GLN Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2561 LYS Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2688 GLU Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2848 GLU Chi-restraints excluded: chain A residue 2863 ARG Chi-restraints excluded: chain A residue 2994 MET Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3035 GLU Chi-restraints excluded: chain A residue 3078 ARG Chi-restraints excluded: chain A residue 3161 LEU Chi-restraints excluded: chain A residue 3191 ARG Chi-restraints excluded: chain A residue 3597 THR Chi-restraints excluded: chain A residue 3611 ARG Chi-restraints excluded: chain A residue 3620 ARG Chi-restraints excluded: chain A residue 3796 THR Chi-restraints excluded: chain A residue 3842 GLU Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4276 ARG Chi-restraints excluded: chain A residue 4331 LEU Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4453 ASN Chi-restraints excluded: chain A residue 4626 ILE Chi-restraints excluded: chain A residue 4645 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 240 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 196 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 chunk 175 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 273 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1612 GLN A1779 HIS A2187 GLN A2554 GLN A3202 ASN A3535 HIS A3538 GLN A4137 ASN A4295 GLN A4491 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.164460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.132235 restraints weight = 24047.820| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.41 r_work: 0.3426 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23837 Z= 0.153 Angle : 0.564 7.380 32335 Z= 0.292 Chirality : 0.041 0.239 3632 Planarity : 0.004 0.046 4141 Dihedral : 7.243 154.658 3209 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.03 % Allowed : 11.06 % Favored : 86.91 % 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: 1.97 (0.15), residues: 2881 helix: 2.02 (0.12), residues: 1665 sheet: -0.25 (0.31), residues: 232 loop : 0.60 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A4222 HIS 0.005 0.001 HIS A2588 PHE 0.019 0.002 PHE A1568 TYR 0.021 0.002 TYR A4527 ARG 0.005 0.000 ARG A4449 Details of bonding type rmsd hydrogen bonds : bond 0.04919 ( 1374) hydrogen bonds : angle 4.29377 ( 3972) covalent geometry : bond 0.00334 (23837) covalent geometry : angle 0.56411 (32335) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 335 time to evaluate : 2.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1566 GLN cc_start: 0.6941 (tm-30) cc_final: 0.6253 (tm-30) REVERT: A 1601 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7528 (mm) REVERT: A 1829 LYS cc_start: 0.7897 (mptm) cc_final: 0.7380 (mptt) REVERT: A 2332 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7235 (pmm-80) REVERT: A 2471 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6368 (tm-30) REVERT: A 2484 GLU cc_start: 0.6194 (tm-30) cc_final: 0.5817 (tm-30) REVERT: A 2516 GLU cc_start: 0.7480 (mt-10) cc_final: 0.6823 (pt0) REVERT: A 2688 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7985 (tt0) REVERT: A 2763 ARG cc_start: 0.6776 (ttp80) cc_final: 0.5876 (tpm-80) REVERT: A 2855 LEU cc_start: 0.7225 (mm) cc_final: 0.6980 (mp) REVERT: A 2994 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8197 (ptm) REVERT: A 3006 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7143 (tp30) REVERT: A 3035 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7042 (pp20) REVERT: A 3078 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7664 (tpt170) REVERT: A 3611 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7502 (ttm110) REVERT: A 3620 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7807 (tpp-160) REVERT: A 3799 GLN cc_start: 0.8083 (mm110) cc_final: 0.7570 (mm-40) REVERT: A 3906 GLN cc_start: 0.7674 (tp40) cc_final: 0.7103 (tm-30) REVERT: A 4108 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7421 (mt0) REVERT: A 4276 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7399 (mmp-170) REVERT: A 4279 ASP cc_start: 0.6867 (m-30) cc_final: 0.6166 (m-30) REVERT: A 4406 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.6955 (mttm) REVERT: A 4491 ASN cc_start: 0.7894 (m-40) cc_final: 0.7676 (m110) outliers start: 52 outliers final: 23 residues processed: 367 average time/residue: 1.6901 time to fit residues: 704.2301 Evaluate side-chains 361 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 326 time to evaluate : 3.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1571 ILE Chi-restraints excluded: chain A residue 1601 LEU Chi-restraints excluded: chain A residue 1635 GLU Chi-restraints excluded: chain A residue 1697 LYS Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1835 SER Chi-restraints excluded: chain A residue 2064 VAL Chi-restraints excluded: chain A residue 2212 GLN Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2332 ARG Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2444 GLU Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2554 GLN Chi-restraints excluded: chain A residue 2561 LYS Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2688 GLU Chi-restraints excluded: chain A residue 2788 THR Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2979 VAL Chi-restraints excluded: chain A residue 2994 MET Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3035 GLU Chi-restraints excluded: chain A residue 3078 ARG Chi-restraints excluded: chain A residue 3161 LEU Chi-restraints excluded: chain A residue 3597 THR Chi-restraints excluded: chain A residue 3611 ARG Chi-restraints excluded: chain A residue 3620 ARG Chi-restraints excluded: chain A residue 3796 THR Chi-restraints excluded: chain A residue 3842 GLU Chi-restraints excluded: chain A residue 4276 ARG Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4406 LYS Chi-restraints excluded: chain A residue 4645 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 208 optimal weight: 9.9990 chunk 222 optimal weight: 9.9990 chunk 76 optimal weight: 30.0000 chunk 66 optimal weight: 30.0000 chunk 42 optimal weight: 0.2980 chunk 201 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 270 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 chunk 107 optimal weight: 0.3980 overall best weight: 2.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1612 GLN A1779 HIS A2187 GLN A2554 GLN A3202 ASN A4137 ASN A4295 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.163886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.131437 restraints weight = 24077.362| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.43 r_work: 0.3417 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23837 Z= 0.171 Angle : 0.581 7.532 32335 Z= 0.300 Chirality : 0.042 0.238 3632 Planarity : 0.005 0.047 4141 Dihedral : 7.252 154.421 3209 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.95 % Allowed : 11.30 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.15), residues: 2881 helix: 2.01 (0.12), residues: 1663 sheet: -0.31 (0.31), residues: 239 loop : 0.60 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A4222 HIS 0.005 0.001 HIS A2588 PHE 0.021 0.002 PHE A1568 TYR 0.021 0.002 TYR A4527 ARG 0.005 0.000 ARG A2729 Details of bonding type rmsd hydrogen bonds : bond 0.05052 ( 1374) hydrogen bonds : angle 4.30334 ( 3972) covalent geometry : bond 0.00380 (23837) covalent geometry : angle 0.58090 (32335) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 330 time to evaluate : 2.745 Fit side-chains revert: symmetry clash REVERT: A 1488 ARG cc_start: 0.8394 (ptt-90) cc_final: 0.8034 (ptt-90) REVERT: A 1566 GLN cc_start: 0.6959 (tm-30) cc_final: 0.6265 (tm-30) REVERT: A 1601 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7551 (mm) REVERT: A 1829 LYS cc_start: 0.7907 (mptm) cc_final: 0.7375 (mptt) REVERT: A 1980 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7434 (mm-30) REVERT: A 2332 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7259 (pmm-80) REVERT: A 2471 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.6346 (tm-30) REVERT: A 2484 GLU cc_start: 0.6205 (tm-30) cc_final: 0.5759 (tm-30) REVERT: A 2516 GLU cc_start: 0.7490 (mt-10) cc_final: 0.6840 (pt0) REVERT: A 2688 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: A 2763 ARG cc_start: 0.6770 (ttp80) cc_final: 0.5881 (tpm-80) REVERT: A 2855 LEU cc_start: 0.7246 (mm) cc_final: 0.6991 (mp) REVERT: A 2994 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8214 (ptm) REVERT: A 3006 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7150 (tp30) REVERT: A 3035 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7057 (pp20) REVERT: A 3078 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7633 (tpt170) REVERT: A 3611 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7545 (ttm110) REVERT: A 3620 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7793 (tpp-160) REVERT: A 3799 GLN cc_start: 0.8074 (mm110) cc_final: 0.7557 (mm-40) REVERT: A 3906 GLN cc_start: 0.7680 (tp40) cc_final: 0.7104 (tm-30) REVERT: A 4108 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7317 (mt0) REVERT: A 4276 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7437 (mmp-170) REVERT: A 4279 ASP cc_start: 0.6865 (m-30) cc_final: 0.6192 (m-30) REVERT: A 4406 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6978 (mttm) REVERT: A 4491 ASN cc_start: 0.7918 (m-40) cc_final: 0.7695 (m110) outliers start: 50 outliers final: 25 residues processed: 360 average time/residue: 1.8013 time to fit residues: 736.4510 Evaluate side-chains 362 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 325 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1571 ILE Chi-restraints excluded: chain A residue 1601 LEU Chi-restraints excluded: chain A residue 1635 GLU Chi-restraints excluded: chain A residue 1697 LYS Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1835 SER Chi-restraints excluded: chain A residue 2064 VAL Chi-restraints excluded: chain A residue 2212 GLN Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2332 ARG Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2444 GLU Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2554 GLN Chi-restraints excluded: chain A residue 2561 LYS Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2688 GLU Chi-restraints excluded: chain A residue 2788 THR Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2979 VAL Chi-restraints excluded: chain A residue 2994 MET Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3035 GLU Chi-restraints excluded: chain A residue 3078 ARG Chi-restraints excluded: chain A residue 3161 LEU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3597 THR Chi-restraints excluded: chain A residue 3611 ARG Chi-restraints excluded: chain A residue 3620 ARG Chi-restraints excluded: chain A residue 3796 THR Chi-restraints excluded: chain A residue 3842 GLU Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4276 ARG Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4406 LYS Chi-restraints excluded: chain A residue 4645 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 188 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 190 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1612 GLN A1779 HIS A2187 GLN A2442 GLN A2554 GLN A3202 ASN A4137 ASN A4295 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.164423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.132091 restraints weight = 24021.936| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.43 r_work: 0.3424 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23837 Z= 0.155 Angle : 0.568 8.708 32335 Z= 0.293 Chirality : 0.041 0.237 3632 Planarity : 0.004 0.044 4141 Dihedral : 7.178 153.775 3209 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.95 % Allowed : 11.49 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.15), residues: 2881 helix: 2.07 (0.12), residues: 1662 sheet: -0.25 (0.31), residues: 232 loop : 0.62 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A4222 HIS 0.004 0.001 HIS A1500 PHE 0.020 0.002 PHE A1568 TYR 0.022 0.002 TYR A4527 ARG 0.006 0.000 ARG A1543 Details of bonding type rmsd hydrogen bonds : bond 0.04876 ( 1374) hydrogen bonds : angle 4.25533 ( 3972) covalent geometry : bond 0.00341 (23837) covalent geometry : angle 0.56799 (32335) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 333 time to evaluate : 2.835 Fit side-chains revert: symmetry clash REVERT: A 1488 ARG cc_start: 0.8398 (ptt-90) cc_final: 0.8095 (ptt-90) REVERT: A 1566 GLN cc_start: 0.6969 (tm-30) cc_final: 0.6267 (tm-30) REVERT: A 1601 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7532 (mm) REVERT: A 1829 LYS cc_start: 0.7901 (mptm) cc_final: 0.7361 (mptt) REVERT: A 1980 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7423 (mm-30) REVERT: A 2332 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7236 (pmm-80) REVERT: A 2471 GLN cc_start: 0.7085 (OUTLIER) cc_final: 0.6324 (tm-30) REVERT: A 2484 GLU cc_start: 0.6186 (tm-30) cc_final: 0.5738 (tm-30) REVERT: A 2516 GLU cc_start: 0.7487 (mt-10) cc_final: 0.6838 (pt0) REVERT: A 2688 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: A 2763 ARG cc_start: 0.6758 (ttp80) cc_final: 0.5871 (tpm-80) REVERT: A 2855 LEU cc_start: 0.7211 (mm) cc_final: 0.6956 (mp) REVERT: A 2994 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8225 (ptm) REVERT: A 3006 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7140 (tp30) REVERT: A 3035 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7043 (pp20) REVERT: A 3078 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7645 (tpt170) REVERT: A 3611 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7527 (ttm110) REVERT: A 3620 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7780 (tpp-160) REVERT: A 3779 GLU cc_start: 0.7595 (pt0) cc_final: 0.7337 (pp20) REVERT: A 3906 GLN cc_start: 0.7680 (tp40) cc_final: 0.7101 (tm-30) REVERT: A 4108 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7312 (mt0) REVERT: A 4276 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7375 (mmp-170) REVERT: A 4279 ASP cc_start: 0.6837 (m-30) cc_final: 0.6102 (m-30) REVERT: A 4406 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.6979 (mttm) REVERT: A 4491 ASN cc_start: 0.7905 (m-40) cc_final: 0.7680 (m110) outliers start: 50 outliers final: 25 residues processed: 361 average time/residue: 1.7130 time to fit residues: 701.1426 Evaluate side-chains 355 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 318 time to evaluate : 2.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1601 LEU Chi-restraints excluded: chain A residue 1635 GLU Chi-restraints excluded: chain A residue 1697 LYS Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1835 SER Chi-restraints excluded: chain A residue 2064 VAL Chi-restraints excluded: chain A residue 2212 GLN Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2332 ARG Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2561 LYS Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2688 GLU Chi-restraints excluded: chain A residue 2788 THR Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2979 VAL Chi-restraints excluded: chain A residue 2994 MET Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3035 GLU Chi-restraints excluded: chain A residue 3078 ARG Chi-restraints excluded: chain A residue 3161 LEU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3597 THR Chi-restraints excluded: chain A residue 3611 ARG Chi-restraints excluded: chain A residue 3620 ARG Chi-restraints excluded: chain A residue 3691 ASP Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3796 THR Chi-restraints excluded: chain A residue 3842 GLU Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4276 ARG Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4406 LYS Chi-restraints excluded: chain A residue 4645 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 194 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 211 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 chunk 237 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 190 optimal weight: 20.0000 chunk 159 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1612 GLN A1779 HIS A2187 GLN A2442 GLN A3202 ASN A4079 GLN A4137 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.164042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131651 restraints weight = 24043.065| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.40 r_work: 0.3420 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23837 Z= 0.167 Angle : 0.584 11.620 32335 Z= 0.301 Chirality : 0.042 0.236 3632 Planarity : 0.004 0.048 4141 Dihedral : 7.193 154.013 3209 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.68 % Allowed : 12.00 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.15), residues: 2881 helix: 2.04 (0.12), residues: 1662 sheet: -0.25 (0.31), residues: 232 loop : 0.61 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A4222 HIS 0.005 0.001 HIS A2588 PHE 0.021 0.002 PHE A1568 TYR 0.022 0.002 TYR A4527 ARG 0.006 0.000 ARG A1543 Details of bonding type rmsd hydrogen bonds : bond 0.04974 ( 1374) hydrogen bonds : angle 4.28102 ( 3972) covalent geometry : bond 0.00370 (23837) covalent geometry : angle 0.58407 (32335) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 325 time to evaluate : 2.813 Fit side-chains revert: symmetry clash REVERT: A 1488 ARG cc_start: 0.8410 (ptt-90) cc_final: 0.8106 (ptt-90) REVERT: A 1566 GLN cc_start: 0.6982 (tm-30) cc_final: 0.6257 (tm-30) REVERT: A 1601 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7533 (mm) REVERT: A 1829 LYS cc_start: 0.7906 (mptm) cc_final: 0.7368 (mptt) REVERT: A 1980 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7419 (mm-30) REVERT: A 2332 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7245 (pmm-80) REVERT: A 2471 GLN cc_start: 0.7089 (OUTLIER) cc_final: 0.6326 (tm-30) REVERT: A 2484 GLU cc_start: 0.6187 (tm-30) cc_final: 0.5734 (tm-30) REVERT: A 2516 GLU cc_start: 0.7479 (mt-10) cc_final: 0.6835 (pt0) REVERT: A 2688 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: A 2763 ARG cc_start: 0.6778 (ttp80) cc_final: 0.5894 (tpm-80) REVERT: A 2855 LEU cc_start: 0.7216 (mm) cc_final: 0.6969 (mp) REVERT: A 3006 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7142 (tp30) REVERT: A 3035 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7046 (pp20) REVERT: A 3078 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7640 (tpt170) REVERT: A 3611 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7536 (ttm110) REVERT: A 3620 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7799 (tpp-160) REVERT: A 3779 GLU cc_start: 0.7584 (pt0) cc_final: 0.7297 (pp20) REVERT: A 3842 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8130 (pm20) REVERT: A 3906 GLN cc_start: 0.7678 (tp40) cc_final: 0.7077 (tm-30) REVERT: A 4108 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7312 (mt0) REVERT: A 4276 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7442 (mmp-170) REVERT: A 4279 ASP cc_start: 0.6853 (m-30) cc_final: 0.6221 (m-30) REVERT: A 4406 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6969 (mttm) REVERT: A 4491 ASN cc_start: 0.7902 (m-40) cc_final: 0.7676 (m110) outliers start: 43 outliers final: 24 residues processed: 353 average time/residue: 1.7239 time to fit residues: 696.3945 Evaluate side-chains 354 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 318 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1601 LEU Chi-restraints excluded: chain A residue 1635 GLU Chi-restraints excluded: chain A residue 1697 LYS Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1835 SER Chi-restraints excluded: chain A residue 2064 VAL Chi-restraints excluded: chain A residue 2212 GLN Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2332 ARG Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2561 LYS Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2688 GLU Chi-restraints excluded: chain A residue 2788 THR Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2979 VAL Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3035 GLU Chi-restraints excluded: chain A residue 3078 ARG Chi-restraints excluded: chain A residue 3161 LEU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3597 THR Chi-restraints excluded: chain A residue 3611 ARG Chi-restraints excluded: chain A residue 3620 ARG Chi-restraints excluded: chain A residue 3691 ASP Chi-restraints excluded: chain A residue 3732 LEU Chi-restraints excluded: chain A residue 3796 THR Chi-restraints excluded: chain A residue 3842 GLU Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4276 ARG Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4406 LYS Chi-restraints excluded: chain A residue 4645 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 285 optimal weight: 5.9990 chunk 34 optimal weight: 0.0870 chunk 160 optimal weight: 4.9990 chunk 219 optimal weight: 8.9990 chunk 212 optimal weight: 6.9990 chunk 185 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1612 GLN A1779 HIS A2187 GLN A2442 GLN A3202 ASN A4023 GLN A4079 GLN A4137 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.163418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.131198 restraints weight = 24104.222| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.26 r_work: 0.3410 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23837 Z= 0.183 Angle : 0.605 12.835 32335 Z= 0.312 Chirality : 0.043 0.237 3632 Planarity : 0.005 0.050 4141 Dihedral : 7.275 154.882 3209 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.56 % Allowed : 12.27 % Favored : 86.17 % 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: 1.90 (0.15), residues: 2881 helix: 1.97 (0.12), residues: 1663 sheet: -0.29 (0.31), residues: 239 loop : 0.59 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A4222 HIS 0.005 0.001 HIS A2588 PHE 0.022 0.002 PHE A1568 TYR 0.022 0.002 TYR A4527 ARG 0.006 0.001 ARG A1543 Details of bonding type rmsd hydrogen bonds : bond 0.05166 ( 1374) hydrogen bonds : angle 4.33528 ( 3972) covalent geometry : bond 0.00408 (23837) covalent geometry : angle 0.60547 (32335) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 323 time to evaluate : 2.631 Fit side-chains revert: symmetry clash REVERT: A 1488 ARG cc_start: 0.8434 (ptt-90) cc_final: 0.8142 (ptt-90) REVERT: A 1566 GLN cc_start: 0.7011 (tm-30) cc_final: 0.6283 (tm-30) REVERT: A 1601 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7580 (mm) REVERT: A 1829 LYS cc_start: 0.7924 (mptm) cc_final: 0.7380 (mptt) REVERT: A 1980 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7433 (mm-30) REVERT: A 2332 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7343 (pmm-80) REVERT: A 2471 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6354 (tm-30) REVERT: A 2484 GLU cc_start: 0.6208 (tm-30) cc_final: 0.5757 (tm-30) REVERT: A 2516 GLU cc_start: 0.7483 (mt-10) cc_final: 0.6849 (pt0) REVERT: A 2688 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: A 2763 ARG cc_start: 0.6785 (ttp80) cc_final: 0.5891 (tpm-80) REVERT: A 2855 LEU cc_start: 0.7234 (mm) cc_final: 0.6980 (mp) REVERT: A 3006 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7160 (tp30) REVERT: A 3035 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7065 (pp20) REVERT: A 3078 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7598 (tpt170) REVERT: A 3611 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7547 (ttm110) REVERT: A 3620 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7814 (tpp-160) REVERT: A 3779 GLU cc_start: 0.7610 (pt0) cc_final: 0.7312 (pp20) REVERT: A 3906 GLN cc_start: 0.7692 (tp40) cc_final: 0.7117 (tm-30) REVERT: A 4108 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7326 (mt0) REVERT: A 4276 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7461 (mmp-170) REVERT: A 4279 ASP cc_start: 0.6877 (m-30) cc_final: 0.6159 (m-30) REVERT: A 4406 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.7003 (mttm) REVERT: A 4491 ASN cc_start: 0.7931 (m-40) cc_final: 0.7706 (m110) outliers start: 40 outliers final: 23 residues processed: 349 average time/residue: 1.7506 time to fit residues: 693.4017 Evaluate side-chains 352 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 318 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1601 LEU Chi-restraints excluded: chain A residue 1635 GLU Chi-restraints excluded: chain A residue 1697 LYS Chi-restraints excluded: chain A residue 1760 GLU Chi-restraints excluded: chain A residue 1835 SER Chi-restraints excluded: chain A residue 2064 VAL Chi-restraints excluded: chain A residue 2212 GLN Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2332 ARG Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2561 LYS Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2688 GLU Chi-restraints excluded: chain A residue 2788 THR Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2979 VAL Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3035 GLU Chi-restraints excluded: chain A residue 3078 ARG Chi-restraints excluded: chain A residue 3161 LEU Chi-restraints excluded: chain A residue 3597 THR Chi-restraints excluded: chain A residue 3611 ARG Chi-restraints excluded: chain A residue 3620 ARG Chi-restraints excluded: chain A residue 3791 MET Chi-restraints excluded: chain A residue 3796 THR Chi-restraints excluded: chain A residue 3842 GLU Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4276 ARG Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4406 LYS Chi-restraints excluded: chain A residue 4645 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 88 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 254 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1612 GLN A1779 HIS A2187 GLN A2442 GLN ** A3202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4079 GLN A4137 ASN A4477 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.164818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.132505 restraints weight = 24045.927| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.41 r_work: 0.3432 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23837 Z= 0.147 Angle : 0.566 12.859 32335 Z= 0.290 Chirality : 0.041 0.235 3632 Planarity : 0.004 0.044 4141 Dihedral : 7.214 153.116 3209 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.52 % Allowed : 12.27 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.16), residues: 2881 helix: 2.09 (0.12), residues: 1662 sheet: -0.23 (0.32), residues: 232 loop : 0.61 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A4222 HIS 0.005 0.001 HIS A1985 PHE 0.019 0.002 PHE A1568 TYR 0.022 0.002 TYR A4527 ARG 0.008 0.000 ARG A1543 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 1374) hydrogen bonds : angle 4.23105 ( 3972) covalent geometry : bond 0.00322 (23837) covalent geometry : angle 0.56577 (32335) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29978.41 seconds wall clock time: 516 minutes 58.91 seconds (31018.91 seconds total)