Starting phenix.real_space_refine on Fri Sep 19 09:53:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9blz_44682/09_2025/9blz_44682.cif Found real_map, /net/cci-nas-00/data/ceres_data/9blz_44682/09_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_44682/09_2025/9blz_44682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9blz_44682/09_2025/9blz_44682.map" model { file = "/net/cci-nas-00/data/ceres_data/9blz_44682/09_2025/9blz_44682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9blz_44682/09_2025/9blz_44682.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.85, per 1000 atoms: 0.23 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: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.75 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: 8.67 Time building geometry restraints manager: 2.95 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.740 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: 1.810 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 28.480 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.740 ------------------------------------------------------------------------------- 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 : 9.61 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG A1806 TYR 0.016 0.001 TYR A1546 PHE 0.019 0.002 PHE A1960 TRP 0.074 0.002 TRP A1537 HIS 0.010 0.001 HIS A1500 Details of bonding type rmsd covalent geometry : bond 0.00375 (23837) covalent geometry : angle 0.66348 (32335) hydrogen bonds : bond 0.12541 ( 1374) hydrogen bonds : angle 5.81468 ( 3972) *********************** 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 : 1.123 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: 0.7771 (mt-10) outliers start: 1 outliers final: 1 residues processed: 397 average time/residue: 0.8767 time to fit residues: 389.9231 Evaluate side-chains 328 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 327 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 A2475 ASN A2554 GLN A2577 HIS A2677 GLN A2752 ASN A3092 ASN A3198 GLN A3202 ASN A3523 GLN A3527 ASN ** A3650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3838 ASN A4012 ASN A4137 ASN A4262 GLN A4266 ASN A4295 GLN A4477 GLN A4491 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.165321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.133536 restraints weight = 24094.337| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.30 r_work: 0.3427 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23837 Z= 0.168 Angle : 0.606 8.207 32335 Z= 0.314 Chirality : 0.043 0.185 3632 Planarity : 0.005 0.049 4141 Dihedral : 7.473 155.719 3211 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.87 % Allowed : 6.78 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.16), residues: 2881 helix: 1.90 (0.12), residues: 1675 sheet: -0.04 (0.31), residues: 250 loop : 0.63 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1488 TYR 0.022 0.002 TYR A4196 PHE 0.022 0.002 PHE A1960 TRP 0.019 0.002 TRP A1537 HIS 0.008 0.001 HIS A2689 Details of bonding type rmsd covalent geometry : bond 0.00367 (23837) covalent geometry : angle 0.60569 (32335) hydrogen bonds : bond 0.05263 ( 1374) hydrogen bonds : angle 4.45347 ( 3972) *********************** 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 405 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 357 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 1566 GLN cc_start: 0.6920 (tm-30) cc_final: 0.6282 (tm-30) REVERT: A 1601 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7520 (mm) REVERT: A 1621 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7522 (mtp-110) REVERT: A 2043 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8139 (mptt) REVERT: A 2332 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.6956 (pmm-80) REVERT: A 2484 GLU cc_start: 0.6291 (tm-30) cc_final: 0.5962 (tm-30) REVERT: A 2516 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6834 (pt0) REVERT: A 2561 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7789 (mtpp) REVERT: A 2688 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: A 2763 ARG cc_start: 0.6740 (ttp80) cc_final: 0.5830 (tpm-80) REVERT: A 2865 LYS cc_start: 0.6816 (ttpp) cc_final: 0.6449 (tptp) REVERT: A 3006 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7161 (tp30) REVERT: A 3035 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7052 (pp20) REVERT: A 3620 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7864 (tpp-160) REVERT: A 3721 ARG cc_start: 0.7510 (mmm-85) cc_final: 0.7264 (mmm-85) REVERT: A 4043 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8034 (mtp) REVERT: A 4276 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7219 (mmp-170) REVERT: A 4331 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8172 (tp) outliers start: 48 outliers final: 18 residues processed: 378 average time/residue: 0.9136 time to fit residues: 387.7397 Evaluate side-chains 354 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 325 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1571 ILE Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1601 LEU 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 2332 ARG Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2449 LEU 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 2822 ILE Chi-restraints excluded: chain A residue 2841 GLU 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 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 4043 MET Chi-restraints excluded: chain A residue 4276 ARG 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 75 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 165 optimal weight: 0.0870 chunk 240 optimal weight: 10.0000 chunk 208 optimal weight: 1.9990 chunk 158 optimal weight: 8.9990 chunk 91 optimal weight: 0.2980 chunk 185 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 257 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 overall best weight: 1.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1646 ASN A1779 HIS A2471 GLN A2475 ASN A2554 GLN A2930 GLN A3188 HIS A3202 ASN ** A3650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4023 GLN A4137 ASN A4295 GLN A4444 GLN A4477 GLN A4491 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.167578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.134390 restraints weight = 24311.510| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.44 r_work: 0.3468 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23837 Z= 0.132 Angle : 0.537 7.441 32335 Z= 0.276 Chirality : 0.041 0.167 3632 Planarity : 0.004 0.044 4141 Dihedral : 7.245 155.974 3211 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.71 % Allowed : 9.27 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.16), residues: 2881 helix: 2.10 (0.12), residues: 1673 sheet: -0.06 (0.31), residues: 250 loop : 0.65 (0.21), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2091 TYR 0.020 0.002 TYR A1546 PHE 0.017 0.002 PHE A2776 TRP 0.016 0.001 TRP A4222 HIS 0.004 0.001 HIS A2689 Details of bonding type rmsd covalent geometry : bond 0.00280 (23837) covalent geometry : angle 0.53743 (32335) hydrogen bonds : bond 0.04703 ( 1374) hydrogen bonds : angle 4.25519 ( 3972) *********************** 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 390 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 346 time to evaluate : 1.066 Fit side-chains REVERT: A 1566 GLN cc_start: 0.6681 (tm-30) cc_final: 0.5982 (tm-30) REVERT: A 1601 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7335 (mm) REVERT: A 1603 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.7019 (ttp-110) REVERT: A 1621 ARG cc_start: 0.7807 (ttp80) cc_final: 0.7203 (mtp-110) REVERT: A 1760 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.6874 (mp0) REVERT: A 1829 LYS cc_start: 0.7834 (mptm) cc_final: 0.7338 (mptt) REVERT: A 2175 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6734 (mtm) REVERT: A 2262 ASP cc_start: 0.8570 (m-30) cc_final: 0.8311 (m-30) REVERT: A 2332 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7248 (pmm-80) REVERT: A 2484 GLU cc_start: 0.6068 (tm-30) cc_final: 0.5612 (tm-30) REVERT: A 2516 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6468 (pt0) REVERT: A 2538 GLU cc_start: 0.7780 (pt0) cc_final: 0.7539 (pt0) REVERT: A 2688 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: A 2763 ARG cc_start: 0.6559 (ttp80) cc_final: 0.5311 (tpm-80) REVERT: A 3035 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6642 (pp20) REVERT: A 3620 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7297 (tpp-160) REVERT: A 3721 ARG cc_start: 0.7195 (mmm-85) cc_final: 0.6958 (mmm-85) REVERT: A 4043 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8116 (mtp) REVERT: A 4276 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.6859 (mmp-170) REVERT: A 4491 ASN cc_start: 0.7774 (m-40) cc_final: 0.7549 (m110) outliers start: 44 outliers final: 19 residues processed: 368 average time/residue: 0.8879 time to fit residues: 367.5947 Evaluate side-chains 351 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 322 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1571 ILE Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1601 LEU Chi-restraints excluded: chain A residue 1603 ARG 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 2064 VAL Chi-restraints excluded: chain A residue 2175 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 2449 LEU 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 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 3035 GLU 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 4043 MET Chi-restraints excluded: chain A residue 4276 ARG Chi-restraints excluded: chain A residue 4468 THR 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 114 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 108 optimal weight: 0.0010 chunk 80 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1779 HIS A1931 ASN A2102 ASN A2554 GLN A2654 GLN A2713 ASN A3202 ASN A3650 ASN A3754 ASN A3826 GLN A4137 ASN A4295 GLN A4444 GLN A4477 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.169512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.138051 restraints weight = 24239.414| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.37 r_work: 0.3511 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23837 Z= 0.109 Angle : 0.500 6.720 32335 Z= 0.256 Chirality : 0.039 0.169 3632 Planarity : 0.004 0.044 4141 Dihedral : 6.953 153.578 3211 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.99 % Allowed : 9.86 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.30 (0.16), residues: 2881 helix: 2.29 (0.12), residues: 1669 sheet: -0.05 (0.32), residues: 250 loop : 0.74 (0.21), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1621 TYR 0.022 0.001 TYR A4527 PHE 0.015 0.001 PHE A2912 TRP 0.016 0.001 TRP A2234 HIS 0.005 0.001 HIS A1985 Details of bonding type rmsd covalent geometry : bond 0.00224 (23837) covalent geometry : angle 0.50049 (32335) hydrogen bonds : bond 0.04149 ( 1374) hydrogen bonds : angle 4.07712 ( 3972) *********************** 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 403 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 352 time to evaluate : 1.101 Fit side-chains REVERT: A 1488 ARG cc_start: 0.8195 (ptt90) cc_final: 0.7824 (ptt-90) REVERT: A 1566 GLN cc_start: 0.6820 (tm-30) cc_final: 0.6137 (tm-30) REVERT: A 1601 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7439 (mm) REVERT: A 1603 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7172 (ttp-110) REVERT: A 1610 LYS cc_start: 0.7953 (mttm) cc_final: 0.7515 (mppt) REVERT: A 1621 ARG cc_start: 0.7827 (ttp80) cc_final: 0.7282 (mtp-110) REVERT: A 1829 LYS cc_start: 0.7790 (mptm) cc_final: 0.7283 (mptt) REVERT: A 2043 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7966 (mptt) REVERT: A 2262 ASP cc_start: 0.8625 (m-30) cc_final: 0.8403 (m-30) REVERT: A 2332 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7302 (pmm-80) REVERT: A 2471 GLN cc_start: 0.7037 (OUTLIER) cc_final: 0.6246 (tm-30) REVERT: A 2484 GLU cc_start: 0.6160 (tm-30) cc_final: 0.5767 (tm-30) REVERT: A 2516 GLU cc_start: 0.7346 (mt-10) cc_final: 0.6690 (pt0) REVERT: A 2538 GLU cc_start: 0.7762 (pt0) cc_final: 0.7539 (pt0) REVERT: A 2661 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8474 (mp) REVERT: A 2688 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: A 2763 ARG cc_start: 0.6698 (ttp80) cc_final: 0.5562 (tpm-80) REVERT: A 2855 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6821 (mp) REVERT: A 2994 MET cc_start: 0.8431 (ttp) cc_final: 0.8140 (ptm) REVERT: A 3006 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7090 (tp30) REVERT: A 3035 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6825 (pp20) REVERT: A 3721 ARG cc_start: 0.7214 (mmm-85) cc_final: 0.7007 (mmm-85) REVERT: A 3906 GLN cc_start: 0.7582 (tp40) cc_final: 0.6999 (tm-30) REVERT: A 4043 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8142 (mtp) REVERT: A 4108 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7196 (mt0) REVERT: A 4279 ASP cc_start: 0.6767 (m-30) cc_final: 0.6421 (m-30) REVERT: A 4491 ASN cc_start: 0.7877 (m-40) cc_final: 0.7636 (m110) outliers start: 51 outliers final: 20 residues processed: 379 average time/residue: 0.9140 time to fit residues: 388.8879 Evaluate side-chains 354 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 323 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1571 ILE Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1601 LEU Chi-restraints excluded: chain A residue 1603 ARG Chi-restraints excluded: chain A residue 1635 GLU Chi-restraints excluded: chain A residue 1697 LYS 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 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 2449 LEU Chi-restraints excluded: chain A residue 2471 GLN Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2661 LEU Chi-restraints excluded: chain A residue 2688 GLU Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2963 VAL 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 3503 ILE 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 4645 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 276 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 95 optimal weight: 0.0980 chunk 6 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1612 GLN A1779 HIS A2554 GLN A3202 ASN A3538 GLN A3799 GLN A4023 GLN A4137 ASN A4295 GLN A4477 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.167452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.134304 restraints weight = 24234.327| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.42 r_work: 0.3468 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1784 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= 0.135 Angle : 0.528 7.039 32335 Z= 0.271 Chirality : 0.040 0.174 3632 Planarity : 0.004 0.045 4141 Dihedral : 7.014 153.109 3211 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.91 % Allowed : 10.63 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.16), residues: 2881 helix: 2.25 (0.12), residues: 1671 sheet: -0.06 (0.31), residues: 250 loop : 0.73 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1621 TYR 0.021 0.002 TYR A1546 PHE 0.018 0.002 PHE A1568 TRP 0.016 0.001 TRP A4222 HIS 0.004 0.001 HIS A2689 Details of bonding type rmsd covalent geometry : bond 0.00290 (23837) covalent geometry : angle 0.52838 (32335) hydrogen bonds : bond 0.04511 ( 1374) hydrogen bonds : angle 4.12141 ( 3972) *********************** 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 388 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 339 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 1488 ARG cc_start: 0.8208 (ptt90) cc_final: 0.7799 (ptt-90) REVERT: A 1566 GLN cc_start: 0.6691 (tm-30) cc_final: 0.5965 (tm-30) REVERT: A 1601 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7380 (mm) REVERT: A 1603 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7064 (ttp-110) REVERT: A 1610 LYS cc_start: 0.7839 (mttm) cc_final: 0.7587 (mmtm) REVERT: A 1621 ARG cc_start: 0.7765 (ttp80) cc_final: 0.7529 (ttp-170) REVERT: A 1829 LYS cc_start: 0.7772 (mptm) cc_final: 0.7179 (mptt) REVERT: A 2043 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7821 (mptt) REVERT: A 2262 ASP cc_start: 0.8586 (m-30) cc_final: 0.8316 (m-30) REVERT: A 2332 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7299 (pmm-80) REVERT: A 2471 GLN cc_start: 0.6985 (OUTLIER) cc_final: 0.6134 (tm-30) REVERT: A 2484 GLU cc_start: 0.6035 (tm-30) cc_final: 0.5594 (tm-30) REVERT: A 2516 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6531 (pt0) REVERT: A 2538 GLU cc_start: 0.7788 (pt0) cc_final: 0.7569 (pt0) REVERT: A 2688 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: A 2763 ARG cc_start: 0.6608 (ttp80) cc_final: 0.5565 (tpm-80) REVERT: A 2855 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6795 (mp) REVERT: A 2994 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8025 (ptm) REVERT: A 3006 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.6997 (tp30) REVERT: A 3035 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6647 (pp20) REVERT: A 3078 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7436 (tpt170) REVERT: A 3611 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7245 (ttm110) REVERT: A 3620 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7587 (tpp-160) REVERT: A 3721 ARG cc_start: 0.7109 (mmm-85) cc_final: 0.6847 (mmm-85) REVERT: A 3906 GLN cc_start: 0.7514 (tp40) cc_final: 0.6853 (tm-30) REVERT: A 4043 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8055 (mtp) REVERT: A 4108 GLN cc_start: 0.7595 (mm-40) cc_final: 0.7078 (mt0) REVERT: A 4276 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7007 (mmp-170) REVERT: A 4279 ASP cc_start: 0.6645 (m-30) cc_final: 0.5836 (m-30) REVERT: A 4491 ASN cc_start: 0.7788 (m-40) cc_final: 0.7560 (m110) outliers start: 49 outliers final: 27 residues processed: 365 average time/residue: 0.9215 time to fit residues: 377.1165 Evaluate side-chains 371 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 329 time to evaluate : 1.441 ------------------------------------------------------------------------------- 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 1603 ARG 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 2012 MET Chi-restraints excluded: chain A residue 2043 LYS 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 2449 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 2561 LYS Chi-restraints excluded: chain A residue 2574 THR 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 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 3078 ARG Chi-restraints excluded: chain A residue 3161 LEU Chi-restraints excluded: chain A residue 3611 ARG 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 4043 MET Chi-restraints excluded: chain A residue 4075 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 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 123 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 146 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 151 optimal weight: 9.9990 chunk 263 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1612 GLN A1779 HIS A2554 GLN A3202 ASN A3799 GLN A4079 GLN 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 = 0.3963 r_free = 0.3963 target = 0.166344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.132919 restraints weight = 24268.146| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.42 r_work: 0.3448 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23837 Z= 0.151 Angle : 0.549 7.209 32335 Z= 0.282 Chirality : 0.041 0.206 3632 Planarity : 0.004 0.046 4141 Dihedral : 7.092 153.551 3211 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.10 % Allowed : 10.79 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.16), residues: 2881 helix: 2.21 (0.12), residues: 1665 sheet: -0.08 (0.31), residues: 250 loop : 0.73 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2729 TYR 0.021 0.002 TYR A4527 PHE 0.020 0.002 PHE A1568 TRP 0.017 0.002 TRP A4222 HIS 0.004 0.001 HIS A2588 Details of bonding type rmsd covalent geometry : bond 0.00330 (23837) covalent geometry : angle 0.54856 (32335) hydrogen bonds : bond 0.04699 ( 1374) hydrogen bonds : angle 4.17144 ( 3972) *********************** 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 393 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 339 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 1488 ARG cc_start: 0.8247 (ptt90) cc_final: 0.7867 (ptt-90) REVERT: A 1566 GLN cc_start: 0.6752 (tm-30) cc_final: 0.6026 (tm-30) REVERT: A 1601 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7410 (mm) REVERT: A 1603 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7116 (ttp-110) REVERT: A 1621 ARG cc_start: 0.7847 (ttp80) cc_final: 0.7605 (ttp-170) REVERT: A 1829 LYS cc_start: 0.7805 (mptm) cc_final: 0.7215 (mptt) REVERT: A 2043 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7917 (mptt) REVERT: A 2332 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7384 (pmm-80) REVERT: A 2471 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6179 (tm-30) REVERT: A 2484 GLU cc_start: 0.6058 (tm-30) cc_final: 0.5560 (tm-30) REVERT: A 2516 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6592 (pt0) REVERT: A 2538 GLU cc_start: 0.7849 (pt0) cc_final: 0.7638 (pt0) REVERT: A 2688 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7854 (tt0) REVERT: A 2763 ARG cc_start: 0.6643 (ttp80) cc_final: 0.5637 (tpm-80) REVERT: A 2855 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6831 (mp) REVERT: A 2994 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8092 (ptm) REVERT: A 3006 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7035 (tp30) REVERT: A 3035 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6763 (pp20) REVERT: A 3078 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7469 (tpt170) REVERT: A 3611 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7339 (ttm110) REVERT: A 3620 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7638 (tpp-160) REVERT: A 3721 ARG cc_start: 0.7177 (mmm-85) cc_final: 0.6892 (mmm-85) REVERT: A 3779 GLU cc_start: 0.7432 (pt0) cc_final: 0.7097 (pp20) REVERT: A 3906 GLN cc_start: 0.7570 (tp40) cc_final: 0.6903 (tm-30) REVERT: A 4043 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.7973 (mtp) REVERT: A 4075 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7086 (pm20) REVERT: A 4108 GLN cc_start: 0.7621 (mm-40) cc_final: 0.7126 (mt0) REVERT: A 4276 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7059 (mmp-170) REVERT: A 4279 ASP cc_start: 0.6683 (m-30) cc_final: 0.5888 (m-30) REVERT: A 4491 ASN cc_start: 0.7805 (m-40) cc_final: 0.7584 (m110) outliers start: 54 outliers final: 27 residues processed: 367 average time/residue: 0.8018 time to fit residues: 330.6854 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 : 1.149 ------------------------------------------------------------------------------- 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 1603 ARG 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 2012 MET Chi-restraints excluded: chain A residue 2043 LYS 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 2561 LYS Chi-restraints excluded: chain A residue 2574 THR 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 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 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 3799 GLN Chi-restraints excluded: chain A residue 3842 GLU Chi-restraints excluded: chain A residue 4043 MET Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4075 GLU Chi-restraints excluded: chain A residue 4276 ARG Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4626 ILE 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 235 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 231 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 192 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 269 optimal weight: 20.0000 chunk 265 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1612 GLN A1779 HIS A2554 GLN A3202 ASN A3799 GLN A4079 GLN 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 = 0.3958 r_free = 0.3958 target = 0.165825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.132472 restraints weight = 24057.739| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.43 r_work: 0.3444 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23837 Z= 0.157 Angle : 0.557 7.286 32335 Z= 0.287 Chirality : 0.041 0.228 3632 Planarity : 0.004 0.048 4141 Dihedral : 7.142 153.779 3211 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.10 % Allowed : 10.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.16), residues: 2881 helix: 2.17 (0.12), residues: 1665 sheet: -0.10 (0.31), residues: 250 loop : 0.71 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1543 TYR 0.021 0.002 TYR A4527 PHE 0.021 0.002 PHE A1568 TRP 0.017 0.002 TRP A4222 HIS 0.005 0.001 HIS A1500 Details of bonding type rmsd covalent geometry : bond 0.00346 (23837) covalent geometry : angle 0.55695 (32335) hydrogen bonds : bond 0.04789 ( 1374) hydrogen bonds : angle 4.20279 ( 3972) *********************** 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 389 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 335 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1488 ARG cc_start: 0.8249 (ptt90) cc_final: 0.7873 (ptt-90) REVERT: A 1566 GLN cc_start: 0.6733 (tm-30) cc_final: 0.6002 (tm-30) REVERT: A 1601 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7400 (mm) REVERT: A 1603 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7084 (ttp-110) REVERT: A 1621 ARG cc_start: 0.7838 (ttp80) cc_final: 0.7631 (ttp-170) REVERT: A 1829 LYS cc_start: 0.7807 (mptm) cc_final: 0.7194 (mptt) REVERT: A 2043 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7909 (mptt) REVERT: A 2332 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7440 (pmm-80) REVERT: A 2471 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.6153 (tm-30) REVERT: A 2484 GLU cc_start: 0.6032 (tm-30) cc_final: 0.5523 (tm-30) REVERT: A 2516 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6554 (pt0) REVERT: A 2538 GLU cc_start: 0.7841 (pt0) cc_final: 0.7625 (pt0) REVERT: A 2688 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: A 2763 ARG cc_start: 0.6616 (ttp80) cc_final: 0.5612 (tpm-80) REVERT: A 2855 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6819 (mp) REVERT: A 2994 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8066 (ptm) REVERT: A 3006 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7010 (tp30) REVERT: A 3035 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6722 (pp20) REVERT: A 3078 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7436 (tpt170) REVERT: A 3611 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7365 (ttm110) REVERT: A 3620 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7625 (tpp-160) REVERT: A 3779 GLU cc_start: 0.7411 (pt0) cc_final: 0.7064 (pp20) REVERT: A 3906 GLN cc_start: 0.7533 (tp40) cc_final: 0.6855 (tm-30) REVERT: A 4075 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7091 (pm20) REVERT: A 4108 GLN cc_start: 0.7592 (mm-40) cc_final: 0.7081 (mt0) REVERT: A 4276 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.6955 (mmp-170) REVERT: A 4491 ASN cc_start: 0.7763 (m-40) cc_final: 0.7545 (m110) outliers start: 54 outliers final: 25 residues processed: 368 average time/residue: 0.8146 time to fit residues: 337.6466 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 : 1.038 ------------------------------------------------------------------------------- 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 1603 ARG 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 2012 MET Chi-restraints excluded: chain A residue 2043 LYS 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 2841 GLU Chi-restraints excluded: chain A residue 2855 LEU 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 3799 GLN Chi-restraints excluded: chain A residue 3842 GLU Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4075 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 250 optimal weight: 1.9990 chunk 202 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 218 optimal weight: 0.0030 chunk 223 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 238 optimal weight: 0.7980 chunk 230 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 overall best weight: 0.8192 ------------------------------------------------------------------------------- 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 A2654 GLN A3202 ASN A3799 GLN A4079 GLN A4137 ASN A4295 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.168730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.135898 restraints weight = 24328.503| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.43 r_work: 0.3489 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 23837 Z= 0.111 Angle : 0.509 6.720 32335 Z= 0.261 Chirality : 0.039 0.239 3632 Planarity : 0.004 0.048 4141 Dihedral : 6.866 152.437 3211 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.71 % Allowed : 11.65 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.16), residues: 2881 helix: 2.33 (0.12), residues: 1661 sheet: -0.10 (0.32), residues: 240 loop : 0.77 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1543 TYR 0.023 0.001 TYR A4527 PHE 0.015 0.001 PHE A2912 TRP 0.019 0.001 TRP A2234 HIS 0.004 0.001 HIS A1500 Details of bonding type rmsd covalent geometry : bond 0.00230 (23837) covalent geometry : angle 0.50948 (32335) hydrogen bonds : bond 0.04102 ( 1374) hydrogen bonds : angle 4.04444 ( 3972) *********************** 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 384 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 340 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1488 ARG cc_start: 0.8212 (ptt90) cc_final: 0.7831 (ptt-90) REVERT: A 1566 GLN cc_start: 0.6707 (tm-30) cc_final: 0.5991 (tm-30) REVERT: A 1601 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7368 (mm) REVERT: A 1603 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7073 (ttp-110) REVERT: A 1621 ARG cc_start: 0.7761 (ttp80) cc_final: 0.7512 (ttp-170) REVERT: A 1829 LYS cc_start: 0.7756 (mptm) cc_final: 0.7143 (mptt) REVERT: A 2043 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7830 (mptt) REVERT: A 2262 ASP cc_start: 0.8584 (m-30) cc_final: 0.8310 (m-30) REVERT: A 2332 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7278 (pmm-80) REVERT: A 2471 GLN cc_start: 0.6970 (OUTLIER) cc_final: 0.6111 (tm-30) REVERT: A 2484 GLU cc_start: 0.6020 (tm-30) cc_final: 0.5583 (tm-30) REVERT: A 2516 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6531 (pt0) REVERT: A 2538 GLU cc_start: 0.7754 (pt0) cc_final: 0.7527 (pt0) REVERT: A 2688 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: A 2704 GLU cc_start: 0.8454 (tt0) cc_final: 0.8013 (tm-30) REVERT: A 2763 ARG cc_start: 0.6599 (ttp80) cc_final: 0.5576 (tpm-80) REVERT: A 2855 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6816 (mp) REVERT: A 2994 MET cc_start: 0.8358 (ttp) cc_final: 0.8113 (ptm) REVERT: A 3006 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.6986 (tp30) REVERT: A 3035 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6658 (pp20) REVERT: A 3078 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7408 (tpt170) REVERT: A 3611 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7292 (ttm110) REVERT: A 3620 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7284 (tpp-160) REVERT: A 3779 GLU cc_start: 0.7365 (pt0) cc_final: 0.7013 (pp20) REVERT: A 3842 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7999 (pm20) REVERT: A 3906 GLN cc_start: 0.7533 (tp40) cc_final: 0.6848 (tm-30) REVERT: A 4075 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.7020 (pm20) REVERT: A 4108 GLN cc_start: 0.7567 (mm-40) cc_final: 0.7059 (mt0) REVERT: A 4279 ASP cc_start: 0.6545 (m-30) cc_final: 0.6324 (m-30) REVERT: A 4491 ASN cc_start: 0.7771 (m-40) cc_final: 0.7556 (m110) outliers start: 44 outliers final: 19 residues processed: 364 average time/residue: 0.8329 time to fit residues: 340.7852 Evaluate side-chains 350 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 317 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1601 LEU Chi-restraints excluded: chain A residue 1603 ARG Chi-restraints excluded: chain A residue 1697 LYS Chi-restraints excluded: chain A residue 1760 GLU 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 2212 GLN Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2332 ARG 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 2561 LYS Chi-restraints excluded: chain A residue 2688 GLU Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 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 3732 LEU Chi-restraints excluded: chain A residue 3796 THR Chi-restraints excluded: chain A residue 3799 GLN Chi-restraints excluded: chain A residue 3842 GLU Chi-restraints excluded: chain A residue 4075 GLU Chi-restraints excluded: chain A residue 4276 ARG Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4626 ILE 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 81 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 238 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 267 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 176 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 A3799 GLN A4079 GLN A4137 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.166104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.132629 restraints weight = 24170.589| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.43 r_work: 0.3443 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 9.171 32335 Z= 0.289 Chirality : 0.041 0.243 3632 Planarity : 0.004 0.052 4141 Dihedral : 7.026 152.477 3209 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.75 % Allowed : 11.96 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.16), residues: 2881 helix: 2.23 (0.12), residues: 1662 sheet: -0.14 (0.32), residues: 232 loop : 0.71 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1543 TYR 0.022 0.002 TYR A4527 PHE 0.020 0.002 PHE A1568 TRP 0.016 0.002 TRP A4222 HIS 0.005 0.001 HIS A1500 Details of bonding type rmsd covalent geometry : bond 0.00336 (23837) covalent geometry : angle 0.56424 (32335) hydrogen bonds : bond 0.04700 ( 1374) hydrogen bonds : angle 4.16606 ( 3972) *********************** 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 370 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 325 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1488 ARG cc_start: 0.8249 (ptt90) cc_final: 0.7859 (ptt-90) REVERT: A 1566 GLN cc_start: 0.6782 (tm-30) cc_final: 0.6059 (tm-30) REVERT: A 1601 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7416 (mm) REVERT: A 1603 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7121 (ttp-110) REVERT: A 1621 ARG cc_start: 0.7826 (ttp80) cc_final: 0.7620 (ttp-170) REVERT: A 1829 LYS cc_start: 0.7797 (mptm) cc_final: 0.7169 (mptt) REVERT: A 2043 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7904 (mptt) REVERT: A 2262 ASP cc_start: 0.8608 (m-30) cc_final: 0.8334 (m-30) REVERT: A 2332 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7513 (pmm-80) REVERT: A 2471 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.6189 (tm-30) REVERT: A 2484 GLU cc_start: 0.6067 (tm-30) cc_final: 0.5558 (tm-30) REVERT: A 2516 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6592 (pt0) REVERT: A 2538 GLU cc_start: 0.7874 (pt0) cc_final: 0.7664 (pt0) REVERT: A 2688 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7832 (tt0) REVERT: A 2763 ARG cc_start: 0.6649 (ttp80) cc_final: 0.5667 (tpm-80) REVERT: A 2855 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6860 (mp) REVERT: A 2994 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8132 (ptm) REVERT: A 3006 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7046 (tp30) REVERT: A 3035 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6764 (pp20) REVERT: A 3078 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7445 (tpt170) REVERT: A 3611 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7375 (ttm110) REVERT: A 3620 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7617 (tpp-160) REVERT: A 3779 GLU cc_start: 0.7429 (pt0) cc_final: 0.7073 (pp20) REVERT: A 3906 GLN cc_start: 0.7572 (tp40) cc_final: 0.6902 (tm-30) REVERT: A 4075 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7129 (pm20) REVERT: A 4108 GLN cc_start: 0.7614 (mm-40) cc_final: 0.7119 (mt0) REVERT: A 4276 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7032 (mmp-170) REVERT: A 4406 LYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6784 (mttm) REVERT: A 4491 ASN cc_start: 0.7810 (m-40) cc_final: 0.7593 (m110) outliers start: 45 outliers final: 20 residues processed: 350 average time/residue: 0.8573 time to fit residues: 337.4345 Evaluate side-chains 352 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 316 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1601 LEU Chi-restraints excluded: chain A residue 1603 ARG Chi-restraints excluded: chain A residue 1697 LYS Chi-restraints excluded: chain A residue 1760 GLU 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 2212 GLN Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2332 ARG 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 2855 LEU 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 3611 ARG 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 4071 ILE Chi-restraints excluded: chain A residue 4075 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 158 optimal weight: 8.9990 chunk 210 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 263 optimal weight: 9.9990 chunk 200 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 chunk 286 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 A3202 ASN A3535 HIS 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 = 0.3959 r_free = 0.3959 target = 0.165959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.132538 restraints weight = 24207.027| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.45 r_work: 0.3445 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 23837 Z= 0.180 Angle : 0.731 59.194 32335 Z= 0.402 Chirality : 0.042 0.284 3632 Planarity : 0.004 0.054 4141 Dihedral : 7.034 152.520 3209 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.44 % Allowed : 12.43 % Favored : 86.13 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.16), residues: 2881 helix: 2.20 (0.12), residues: 1665 sheet: -0.14 (0.32), residues: 232 loop : 0.71 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1543 TYR 0.021 0.002 TYR A4527 PHE 0.020 0.002 PHE A1568 TRP 0.016 0.002 TRP A4222 HIS 0.004 0.001 HIS A1500 Details of bonding type rmsd covalent geometry : bond 0.00396 (23837) covalent geometry : angle 0.73078 (32335) hydrogen bonds : bond 0.04741 ( 1374) hydrogen bonds : angle 4.16771 ( 3972) ********************** 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 355 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 318 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1488 ARG cc_start: 0.8245 (ptt90) cc_final: 0.7845 (ptt-90) REVERT: A 1566 GLN cc_start: 0.6750 (tm-30) cc_final: 0.6022 (tm-30) REVERT: A 1601 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7390 (mm) REVERT: A 1603 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7079 (ttp-110) REVERT: A 1621 ARG cc_start: 0.7815 (ttp80) cc_final: 0.7600 (ttp-170) REVERT: A 1829 LYS cc_start: 0.7789 (mptm) cc_final: 0.7144 (mptt) REVERT: A 2043 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7881 (mptt) REVERT: A 2262 ASP cc_start: 0.8598 (m-30) cc_final: 0.8316 (m-30) REVERT: A 2332 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7504 (pmm-80) REVERT: A 2471 GLN cc_start: 0.7018 (OUTLIER) cc_final: 0.6152 (tm-30) REVERT: A 2484 GLU cc_start: 0.6035 (tm-30) cc_final: 0.5518 (tm-30) REVERT: A 2516 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6548 (pt0) REVERT: A 2538 GLU cc_start: 0.7858 (pt0) cc_final: 0.7641 (pt0) REVERT: A 2688 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: A 2763 ARG cc_start: 0.6619 (ttp80) cc_final: 0.5621 (tpm-80) REVERT: A 2855 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6844 (mp) REVERT: A 2994 MET cc_start: 0.8397 (ttp) cc_final: 0.8108 (ptm) REVERT: A 3006 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7021 (tp30) REVERT: A 3035 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6724 (pp20) REVERT: A 3078 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7420 (tpt170) REVERT: A 3611 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7352 (ttm110) REVERT: A 3620 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7588 (tpp-160) REVERT: A 3779 GLU cc_start: 0.7408 (pt0) cc_final: 0.7046 (pp20) REVERT: A 3906 GLN cc_start: 0.7545 (tp40) cc_final: 0.6860 (tm-30) REVERT: A 4075 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7107 (pm20) REVERT: A 4108 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7068 (mt0) REVERT: A 4276 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.6987 (mmp-170) REVERT: A 4406 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6764 (mttm) REVERT: A 4491 ASN cc_start: 0.7770 (m-40) cc_final: 0.7561 (m110) outliers start: 37 outliers final: 19 residues processed: 340 average time/residue: 0.9211 time to fit residues: 351.2375 Evaluate side-chains 350 residues out of total 2567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 316 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1601 LEU Chi-restraints excluded: chain A residue 1603 ARG Chi-restraints excluded: chain A residue 1697 LYS Chi-restraints excluded: chain A residue 1760 GLU 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 2212 GLN Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2332 ARG 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 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 2855 LEU 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 3611 ARG 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 4071 ILE Chi-restraints excluded: chain A residue 4075 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 280 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 238 optimal weight: 8.9990 chunk 271 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 263 optimal weight: 7.9990 chunk 163 optimal weight: 9.9990 chunk 229 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- 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 A3202 ASN A4137 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.165957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132580 restraints weight = 24112.716| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.44 r_work: 0.3445 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 23837 Z= 0.180 Angle : 0.731 59.194 32335 Z= 0.402 Chirality : 0.042 0.284 3632 Planarity : 0.004 0.055 4141 Dihedral : 7.034 152.520 3209 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.32 % Allowed : 12.58 % Favored : 86.09 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.16), residues: 2881 helix: 2.20 (0.12), residues: 1665 sheet: -0.14 (0.32), residues: 232 loop : 0.71 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1543 TYR 0.021 0.002 TYR A4527 PHE 0.020 0.002 PHE A1568 TRP 0.016 0.002 TRP A4222 HIS 0.004 0.001 HIS A1500 Details of bonding type rmsd covalent geometry : bond 0.00396 (23837) covalent geometry : angle 0.73076 (32335) hydrogen bonds : bond 0.04741 ( 1374) hydrogen bonds : angle 4.16771 ( 3972) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15815.61 seconds wall clock time: 268 minutes 34.83 seconds (16114.83 seconds total)