Starting phenix.real_space_refine on Fri Sep 19 06:55:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bmy_44715/09_2025/9bmy_44715.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bmy_44715/09_2025/9bmy_44715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bmy_44715/09_2025/9bmy_44715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bmy_44715/09_2025/9bmy_44715.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bmy_44715/09_2025/9bmy_44715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bmy_44715/09_2025/9bmy_44715.map" } resolution = 2.86 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= -0.000 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 2 5.21 5 S 117 5.16 5 C 15068 2.51 5 N 4090 2.21 5 O 4421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s 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: 23707 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 23593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2937, 23593 Classifications: {'peptide': 2937} Link IDs: {'PTRANS': 131, 'TRANS': 2805} Chain breaks: 3 Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 114 Unusual residues: {' MG': 2, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 5.86, per 1000 atoms: 0.25 Number of scatterers: 23707 At special positions: 0 Unit cell: (143.505, 112.258, 208.314, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 117 16.00 P 9 15.00 Mg 2 11.99 O 4421 8.00 N 4090 7.00 C 15068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5588 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 20 sheets defined 64.5% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 1457 through 1471 Processing helix chain 'A' and resid 1489 through 1509 removed outlier: 3.545A pdb=" N LYS A1508 " --> pdb=" O VAL A1504 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A1509 " --> pdb=" O SER A1505 " (cutoff:3.500A) Processing helix chain 'A' and resid 1510 through 1514 removed outlier: 4.152A pdb=" N LYS A1514 " --> pdb=" O PRO A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1554 removed outlier: 3.914A pdb=" N VAL A1536 " --> pdb=" O ALA A1532 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A1546 " --> pdb=" O ARG A1542 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A1554 " --> pdb=" O ILE A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1561 removed outlier: 4.068A pdb=" N HIS A1559 " --> pdb=" O ALA A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1585 Processing helix chain 'A' and resid 1587 through 1593 Processing helix chain 'A' and resid 1596 through 1614 Processing helix chain 'A' and resid 1615 through 1626 removed outlier: 3.954A pdb=" N SER A1624 " --> pdb=" O GLU A1620 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER A1625 " --> pdb=" O ARG A1621 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A1626 " --> pdb=" O GLU A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1632 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1646 through 1652 removed outlier: 3.585A pdb=" N GLN A1651 " --> pdb=" O ALA A1648 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1658 removed outlier: 3.641A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1728 removed outlier: 3.592A pdb=" N TRP A1701 " --> pdb=" O LYS A1697 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE A1727 " --> pdb=" O GLU A1723 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 removed outlier: 3.515A pdb=" N TYR A1745 " --> pdb=" O TRP A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1769 Processing helix chain 'A' and resid 1770 through 1772 No H-bonds generated for 'chain 'A' and resid 1770 through 1772' Processing helix chain 'A' and resid 1777 through 1797 Processing helix chain 'A' and resid 1801 through 1828 Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1852 through 1855 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 Processing helix chain 'A' and resid 1937 through 1952 Processing helix chain 'A' and resid 1960 through 1963 Processing helix chain 'A' and resid 1964 through 1987 removed outlier: 3.894A pdb=" N GLN A1973 " --> pdb=" O SER A1969 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN A1974 " --> pdb=" O ALA A1970 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS A1985 " --> pdb=" O ALA A1981 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A1986 " --> pdb=" O LEU A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2034 Processing helix chain 'A' and resid 2045 through 2058 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix removed outlier: 3.506A pdb=" N GLU A2078 " --> pdb=" O LYS A2074 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2117 removed outlier: 3.679A pdb=" N GLU A2117 " --> pdb=" O ARG A2113 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2130 Processing helix chain 'A' and resid 2132 through 2146 Processing helix chain 'A' and resid 2147 through 2149 No H-bonds generated for 'chain 'A' and resid 2147 through 2149' Processing helix chain 'A' and resid 2150 through 2152 No H-bonds generated for 'chain 'A' and resid 2150 through 2152' Processing helix chain 'A' and resid 2153 through 2165 Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2215 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2255 through 2259 removed outlier: 3.876A pdb=" N ILE A2259 " --> pdb=" O PRO A2256 " (cutoff:3.500A) Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2293 through 2297 removed outlier: 3.520A pdb=" N GLN A2296 " --> pdb=" O GLY A2293 " (cutoff:3.500A) Processing helix chain 'A' and resid 2308 through 2313 Processing helix chain 'A' and resid 2315 through 2320 Processing helix chain 'A' and resid 2352 through 2358 removed outlier: 3.630A pdb=" N ARG A2358 " --> pdb=" O ALA A2354 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2385 Processing helix chain 'A' and resid 2411 through 2424 Processing helix chain 'A' and resid 2425 through 2428 removed outlier: 3.670A pdb=" N THR A2428 " --> pdb=" O PRO A2425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2425 through 2428' Processing helix chain 'A' and resid 2431 through 2443 removed outlier: 3.783A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A2443 " --> pdb=" O HIS A2439 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 Processing helix chain 'A' and resid 2482 through 2504 removed outlier: 3.998A pdb=" N ARG A2492 " --> pdb=" O ARG A2488 " (cutoff:3.500A) Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2549 through 2552 Processing helix chain 'A' and resid 2558 through 2562 removed outlier: 3.950A pdb=" N VAL A2562 " --> pdb=" O THR A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2587 Processing helix chain 'A' and resid 2600 through 2611 removed outlier: 3.812A pdb=" N ALA A2611 " --> pdb=" O SER A2607 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.209A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2689 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2740 through 2756 Processing helix chain 'A' and resid 2757 through 2758 No H-bonds generated for 'chain 'A' and resid 2757 through 2758' Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 5.061A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2784 Processing helix chain 'A' and resid 2795 through 2809 removed outlier: 3.779A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 Processing helix chain 'A' and resid 2839 through 2858 removed outlier: 3.738A pdb=" N ASP A2851 " --> pdb=" O ASP A2847 " (cutoff:3.500A) Processing helix chain 'A' and resid 2862 through 2868 Processing helix chain 'A' and resid 2885 through 2904 removed outlier: 3.575A pdb=" N VAL A2899 " --> pdb=" O ALA A2895 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A2902 " --> pdb=" O LYS A2898 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2927 removed outlier: 3.503A pdb=" N ILE A2925 " --> pdb=" O ARG A2921 " (cutoff:3.500A) Processing helix chain 'A' and resid 2942 through 2954 Processing helix chain 'A' and resid 2968 through 2985 Processing helix chain 'A' and resid 2997 through 2999 No H-bonds generated for 'chain 'A' and resid 2997 through 2999' Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 4.300A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A3006 " --> pdb=" O SER A3002 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A3007 " --> pdb=" O GLY A3003 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A3010 " --> pdb=" O GLU A3006 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A3013 " --> pdb=" O ASN A3009 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3040 removed outlier: 3.536A pdb=" N GLU A3040 " --> pdb=" O GLY A3036 " (cutoff:3.500A) Processing helix chain 'A' and resid 3046 through 3061 Processing helix chain 'A' and resid 3071 through 3082 removed outlier: 4.229A pdb=" N ALA A3080 " --> pdb=" O LYS A3076 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A3081 " --> pdb=" O ASP A3077 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3088 Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3164 removed outlier: 3.562A pdb=" N LEU A3154 " --> pdb=" O VAL A3150 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS A3155 " --> pdb=" O HIS A3151 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 3242 removed outlier: 3.623A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3450 through 3482 Processing helix chain 'A' and resid 3482 through 3495 Processing helix chain 'A' and resid 3495 through 3517 removed outlier: 4.939A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLY A3505 " --> pdb=" O SER A3501 " (cutoff:3.500A) Processing helix chain 'A' and resid 3518 through 3520 No H-bonds generated for 'chain 'A' and resid 3518 through 3520' Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3583 Processing helix chain 'A' and resid 3594 through 3604 Processing helix chain 'A' and resid 3618 through 3630 Processing helix chain 'A' and resid 3637 through 3641 Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3650 Processing helix chain 'A' and resid 3689 through 3695 removed outlier: 3.610A pdb=" N ARG A3695 " --> pdb=" O ASP A3691 " (cutoff:3.500A) Processing helix chain 'A' and resid 3704 through 3721 Processing helix chain 'A' and resid 3721 through 3756 Processing helix chain 'A' and resid 3763 through 3799 removed outlier: 3.605A pdb=" N ILE A3767 " --> pdb=" O ASP A3763 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A3790 " --> pdb=" O GLU A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3801 through 3817 Processing helix chain 'A' and resid 3818 through 3821 Processing helix chain 'A' and resid 3828 through 3842 removed outlier: 3.613A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3847 removed outlier: 3.654A pdb=" N LYS A3847 " --> pdb=" O PRO A3844 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 removed outlier: 3.591A pdb=" N PHE A3864 " --> pdb=" O THR A3860 " (cutoff:3.500A) Processing helix chain 'A' and resid 3874 through 3875 No H-bonds generated for 'chain 'A' and resid 3874 through 3875' Processing helix chain 'A' and resid 3876 through 3878 No H-bonds generated for 'chain 'A' and resid 3876 through 3878' Processing helix chain 'A' and resid 3879 through 3895 Processing helix chain 'A' and resid 3901 through 3909 Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 Processing helix chain 'A' and resid 3965 through 3969 Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4014 Processing helix chain 'A' and resid 4018 through 4023 Processing helix chain 'A' and resid 4026 through 4034 Processing helix chain 'A' and resid 4051 through 4063 Processing helix chain 'A' and resid 4073 through 4088 Processing helix chain 'A' and resid 4098 through 4101 Processing helix chain 'A' and resid 4102 through 4115 removed outlier: 3.632A pdb=" N GLN A4108 " --> pdb=" O GLY A4104 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A4115 " --> pdb=" O LYS A4111 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4142 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.590A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4175 through 4194 removed outlier: 3.769A pdb=" N LEU A4194 " --> pdb=" O ILE A4190 " (cutoff:3.500A) Processing helix chain 'A' and resid 4196 through 4201 removed outlier: 3.880A pdb=" N TRP A4201 " --> pdb=" O ALA A4197 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4227 Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 removed outlier: 3.521A pdb=" N PHE A4305 " --> pdb=" O ARG A4301 " (cutoff:3.500A) Processing helix chain 'A' and resid 4317 through 4322 Processing helix chain 'A' and resid 4324 through 4327 Processing helix chain 'A' and resid 4328 through 4347 Processing helix chain 'A' and resid 4375 through 4391 Processing helix chain 'A' and resid 4401 through 4406 removed outlier: 4.213A pdb=" N LYS A4406 " --> pdb=" O VAL A4402 " (cutoff:3.500A) Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4474 through 4498 removed outlier: 3.580A pdb=" N SER A4480 " --> pdb=" O ILE A4476 " (cutoff:3.500A) Processing helix chain 'A' and resid 4500 through 4505 removed outlier: 3.524A pdb=" N LYS A4505 " --> pdb=" O LYS A4502 " (cutoff:3.500A) Processing helix chain 'A' and resid 4516 through 4532 removed outlier: 3.567A pdb=" N TYR A4520 " --> pdb=" O VAL A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4535 through 4537 No H-bonds generated for 'chain 'A' and resid 4535 through 4537' Processing helix chain 'A' and resid 4631 through 4638 removed outlier: 3.577A pdb=" N PHE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1477 through 1480 removed outlier: 3.884A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1663 through 1666 removed outlier: 7.566A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.382A pdb=" N PHE A1686 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1842 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 removed outlier: 6.536A pdb=" N GLY A1901 " --> pdb=" O ARG A2037 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU A2039 " --> pdb=" O GLY A1901 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER A1903 " --> pdb=" O LEU A2039 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1931 removed outlier: 6.324A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASP A1958 " --> pdb=" O LEU A1928 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE A1930 " --> pdb=" O ASP A1958 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA7, first strand: chain 'A' and resid 2249 through 2254 Processing sheet with id=AA8, first strand: chain 'A' and resid 2266 through 2268 Processing sheet with id=AA9, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AB1, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 6.142A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2644 removed outlier: 4.044A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2873 through 2874 Processing sheet with id=AB5, first strand: chain 'A' and resid 2957 through 2959 removed outlier: 6.291A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A2935 " --> pdb=" O MET A3068 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N HIS A2932 " --> pdb=" O VAL A3090 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ASN A3092 " --> pdb=" O HIS A2932 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A2934 " --> pdb=" O ASN A3092 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE A3094 " --> pdb=" O LEU A2934 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ILE A2936 " --> pdb=" O PHE A3094 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3610 through 3613 Processing sheet with id=AB7, first strand: chain 'A' and resid 3653 through 3656 Processing sheet with id=AB8, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.246A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A4042 " --> pdb=" O PHE A4145 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE A4147 " --> pdb=" O LEU A4042 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N CYS A4044 " --> pdb=" O PHE A4147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4283 through 4285 Processing sheet with id=AC1, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.129A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A4587 " --> pdb=" O THR A4546 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4564 through 4571 removed outlier: 7.191A pdb=" N ILE A4581 " --> pdb=" O GLY A4567 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N THR A4569 " --> pdb=" O ASN A4579 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N ASN A4579 " --> pdb=" O THR A4569 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N ASN A4571 " --> pdb=" O LEU A4577 " (cutoff:3.500A) removed outlier: 10.187A pdb=" N LEU A4577 " --> pdb=" O ASN A4571 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL A4609 " --> pdb=" O ILE A4619 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N THR A4621 " --> pdb=" O LEU A4607 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A4607 " --> pdb=" O THR A4621 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASP A4623 " --> pdb=" O VAL A4605 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL A4605 " --> pdb=" O ASP A4623 " (cutoff:3.500A) 1415 hydrogen bonds defined for protein. 4098 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.61 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7818 1.34 - 1.46: 4905 1.46 - 1.58: 11280 1.58 - 1.69: 14 1.69 - 1.81: 196 Bond restraints: 24213 Sorted by residual: bond pdb=" C4 ADP A4704 " pdb=" C5 ADP A4704 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C4 ADP A4701 " pdb=" C5 ADP A4701 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C4 ADP A4703 " pdb=" C5 ADP A4703 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C5 ADP A4703 " pdb=" C6 ADP A4703 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C5 ADP A4701 " pdb=" C6 ADP A4701 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.70e+01 ... (remaining 24208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 32468 2.45 - 4.91: 325 4.91 - 7.36: 28 7.36 - 9.82: 10 9.82 - 12.27: 7 Bond angle restraints: 32838 Sorted by residual: angle pdb=" PB ATP A4702 " pdb=" O3B ATP A4702 " pdb=" PG ATP A4702 " ideal model delta sigma weight residual 139.87 134.09 5.78 1.00e+00 1.00e+00 3.34e+01 angle pdb=" PA ADP A4704 " pdb=" O3A ADP A4704 " pdb=" PB ADP A4704 " ideal model delta sigma weight residual 120.50 132.77 -12.27 3.00e+00 1.11e-01 1.67e+01 angle pdb=" PA ADP A4703 " pdb=" O3A ADP A4703 " pdb=" PB ADP A4703 " ideal model delta sigma weight residual 120.50 132.68 -12.18 3.00e+00 1.11e-01 1.65e+01 angle pdb=" PA ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PB ADP A4701 " ideal model delta sigma weight residual 120.50 131.51 -11.01 3.00e+00 1.11e-01 1.35e+01 angle pdb=" C1' ADP A4701 " pdb=" C2' ADP A4701 " pdb=" C3' ADP A4701 " ideal model delta sigma weight residual 111.00 100.18 10.82 3.00e+00 1.11e-01 1.30e+01 ... (remaining 32833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.16: 14305 31.16 - 62.31: 316 62.31 - 93.47: 68 93.47 - 124.63: 2 124.63 - 155.78: 2 Dihedral angle restraints: 14693 sinusoidal: 6090 harmonic: 8603 Sorted by residual: dihedral pdb=" O1B ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PB ADP A4701 " pdb=" PA ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 95.78 -155.78 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" C5' ADP A4703 " pdb=" O5' ADP A4703 " pdb=" PA ADP A4703 " pdb=" O2A ADP A4703 " ideal model delta sinusoidal sigma weight residual 300.00 174.37 125.63 1 2.00e+01 2.50e-03 3.80e+01 dihedral pdb=" C5' ADP A4701 " pdb=" O5' ADP A4701 " pdb=" PA ADP A4701 " pdb=" O2A ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 50.60 -110.59 1 2.00e+01 2.50e-03 3.24e+01 ... (remaining 14690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2756 0.042 - 0.083: 709 0.083 - 0.125: 201 0.125 - 0.167: 21 0.167 - 0.208: 5 Chirality restraints: 3692 Sorted by residual: chirality pdb=" CA VAL A2345 " pdb=" N VAL A2345 " pdb=" C VAL A2345 " pdb=" CB VAL A2345 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA LEU A2668 " pdb=" N LEU A2668 " pdb=" C LEU A2668 " pdb=" CB LEU A2668 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.82e-01 chirality pdb=" CA ILE A2016 " pdb=" N ILE A2016 " pdb=" C ILE A2016 " pdb=" CB ILE A2016 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.57e-01 ... (remaining 3689 not shown) Planarity restraints: 4206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A4195 " -0.448 9.50e-02 1.11e+02 2.01e-01 2.47e+01 pdb=" NE ARG A4195 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A4195 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A4195 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A4195 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1537 " -0.012 2.00e-02 2.50e+03 1.35e-02 4.58e+00 pdb=" CG TRP A1537 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A1537 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A1537 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1537 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A1537 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1537 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1537 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1537 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A1537 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A2858 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO A2859 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A2859 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A2859 " -0.026 5.00e-02 4.00e+02 ... (remaining 4203 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.38: 31 2.38 - 3.01: 12566 3.01 - 3.64: 37797 3.64 - 4.27: 58429 4.27 - 4.90: 93734 Nonbonded interactions: 202557 Sorted by model distance: nonbonded pdb=" OE2 GLU A2344 " pdb="MG MG A4706 " model vdw 1.745 2.170 nonbonded pdb=" OG SER A2231 " pdb="MG MG A4706 " model vdw 1.959 2.170 nonbonded pdb=" O2G ATP A4702 " pdb="MG MG A4706 " model vdw 2.072 2.170 nonbonded pdb=" OG1 THR A1913 " pdb="MG MG A4705 " model vdw 2.095 2.170 nonbonded pdb=" O3B ADP A4701 " pdb="MG MG A4705 " model vdw 2.102 2.170 ... (remaining 202552 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.780 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 26.770 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 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:7.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 24213 Z= 0.209 Angle : 0.620 12.271 32838 Z= 0.327 Chirality : 0.041 0.208 3692 Planarity : 0.005 0.201 4206 Dihedral : 14.217 155.782 9105 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.54 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.58 (0.15), residues: 2929 helix: 1.48 (0.12), residues: 1704 sheet: 0.09 (0.34), residues: 235 loop : 0.77 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2492 TYR 0.018 0.002 TYR A2472 PHE 0.017 0.002 PHE A1960 TRP 0.034 0.001 TRP A1537 HIS 0.015 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00384 (24213) covalent geometry : angle 0.61997 (32838) hydrogen bonds : bond 0.20841 ( 1415) hydrogen bonds : angle 6.47155 ( 4098) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 634 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 2222 MET cc_start: 0.8470 (mtm) cc_final: 0.8149 (mtm) REVERT: A 2331 GLU cc_start: 0.7962 (tt0) cc_final: 0.7548 (tt0) REVERT: A 3784 VAL cc_start: 0.7964 (t) cc_final: 0.7626 (m) REVERT: A 3875 MET cc_start: 0.8897 (mtp) cc_final: 0.8669 (mtm) REVERT: A 4095 MET cc_start: 0.8459 (ttp) cc_final: 0.8132 (ttm) outliers start: 0 outliers final: 1 residues processed: 634 average time/residue: 0.8494 time to fit residues: 601.3250 Evaluate side-chains 310 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 309 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1473 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 197 optimal weight: 0.0980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1748 GLN A1784 ASN A1832 ASN A1855 GLN A1931 ASN A2187 GLN A2212 GLN A2430 ASN A2442 GLN A2713 ASN A2849 ASN A2954 ASN A2987 ASN A3087 ASN A3092 ASN A3119 ASN A3523 GLN A3636 GLN A3735 GLN A3751 GLN ** A3754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3906 GLN A4038 ASN A4062 GLN A4079 GLN A4397 HIS A4425 GLN A4444 GLN A4506 ASN A4544 ASN ** A4573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.138489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.110007 restraints weight = 29620.690| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.91 r_work: 0.3195 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24213 Z= 0.154 Angle : 0.578 8.611 32838 Z= 0.295 Chirality : 0.042 0.154 3692 Planarity : 0.004 0.063 4206 Dihedral : 7.254 160.607 3263 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.53 % Allowed : 11.52 % Favored : 85.95 % 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: 2.00 (0.16), residues: 2929 helix: 1.92 (0.12), residues: 1723 sheet: -0.09 (0.34), residues: 234 loop : 0.78 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A3167 TYR 0.020 0.001 TYR A2748 PHE 0.023 0.002 PHE A2682 TRP 0.016 0.001 TRP A2234 HIS 0.013 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00342 (24213) covalent geometry : angle 0.57850 (32838) hydrogen bonds : bond 0.05332 ( 1415) hydrogen bonds : angle 4.56748 ( 4098) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 331 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 1560 LEU cc_start: 0.8020 (tp) cc_final: 0.7599 (mm) REVERT: A 1564 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.5815 (mp0) REVERT: A 1889 TYR cc_start: 0.8655 (m-10) cc_final: 0.8379 (m-10) REVERT: A 1980 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7390 (mt-10) REVERT: A 2018 MET cc_start: 0.9139 (mtm) cc_final: 0.8854 (mtp) REVERT: A 2043 LYS cc_start: 0.8688 (mmtt) cc_final: 0.8353 (mtpp) REVERT: A 2175 MET cc_start: 0.7742 (mtp) cc_final: 0.7263 (mtt) REVERT: A 2187 GLN cc_start: 0.8067 (mt0) cc_final: 0.7816 (tt0) REVERT: A 2222 MET cc_start: 0.8896 (mtm) cc_final: 0.8523 (mtm) REVERT: A 2286 LYS cc_start: 0.8863 (tttm) cc_final: 0.8547 (ttpp) REVERT: A 2331 GLU cc_start: 0.8517 (tt0) cc_final: 0.8033 (tt0) REVERT: A 2573 ASP cc_start: 0.8411 (m-30) cc_final: 0.8165 (m-30) REVERT: A 2763 ARG cc_start: 0.8265 (mmm-85) cc_final: 0.7696 (mmm-85) REVERT: A 2841 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7287 (tm-30) REVERT: A 2855 LEU cc_start: 0.8048 (mt) cc_final: 0.7847 (mm) REVERT: A 3022 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7974 (mt-10) REVERT: A 3199 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7316 (ttp) REVERT: A 3598 GLU cc_start: 0.7742 (tp30) cc_final: 0.7288 (pt0) REVERT: A 3746 GLU cc_start: 0.7610 (tp30) cc_final: 0.7197 (tt0) REVERT: A 3791 MET cc_start: 0.7724 (tpt) cc_final: 0.7497 (mmm) REVERT: A 3937 ARG cc_start: 0.7982 (mtt-85) cc_final: 0.7751 (mtt90) REVERT: A 4108 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7766 (mt0) REVERT: A 4270 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7825 (mm-30) REVERT: A 4338 ASP cc_start: 0.8203 (t0) cc_final: 0.7797 (m-30) REVERT: A 4426 ASP cc_start: 0.7639 (m-30) cc_final: 0.7425 (m-30) REVERT: A 4447 TYR cc_start: 0.8098 (t80) cc_final: 0.7724 (t80) outliers start: 66 outliers final: 19 residues processed: 367 average time/residue: 0.7589 time to fit residues: 314.3049 Evaluate side-chains 302 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 280 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1564 GLU Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 2106 GLU Chi-restraints excluded: chain A residue 2172 ARG Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2804 ARG Chi-restraints excluded: chain A residue 2986 LYS Chi-restraints excluded: chain A residue 3199 MET Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3750 LEU Chi-restraints excluded: chain A residue 3765 THR Chi-restraints excluded: chain A residue 4108 GLN Chi-restraints excluded: chain A residue 4465 SER Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4582 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 44 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 238 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2005 GLN A2827 HIS A3636 GLN ** A3754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4038 ASN A4062 GLN A4079 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.132561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.104041 restraints weight = 30158.887| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.94 r_work: 0.3113 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 24213 Z= 0.196 Angle : 0.579 9.568 32838 Z= 0.291 Chirality : 0.043 0.165 3692 Planarity : 0.004 0.052 4206 Dihedral : 7.198 168.234 3261 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.84 % Allowed : 12.71 % Favored : 84.45 % 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: 1.88 (0.15), residues: 2929 helix: 1.87 (0.12), residues: 1724 sheet: -0.18 (0.32), residues: 246 loop : 0.67 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1488 TYR 0.024 0.002 TYR A2748 PHE 0.018 0.002 PHE A2343 TRP 0.016 0.002 TRP A2234 HIS 0.014 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00469 (24213) covalent geometry : angle 0.57878 (32838) hydrogen bonds : bond 0.05052 ( 1415) hydrogen bonds : angle 4.36295 ( 4098) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 315 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 1461 GLU cc_start: 0.7673 (tp30) cc_final: 0.7343 (tp30) REVERT: A 1498 LYS cc_start: 0.7836 (mttm) cc_final: 0.7371 (mmtt) REVERT: A 1560 LEU cc_start: 0.8069 (tp) cc_final: 0.7793 (mm) REVERT: A 1564 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.5951 (mp0) REVERT: A 1573 THR cc_start: 0.8853 (m) cc_final: 0.8531 (p) REVERT: A 1617 GLU cc_start: 0.7490 (mp0) cc_final: 0.7142 (pt0) REVERT: A 1669 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.6911 (t0) REVERT: A 1967 MET cc_start: 0.8851 (mmt) cc_final: 0.8467 (mmt) REVERT: A 1980 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7409 (mt-10) REVERT: A 2000 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8050 (tm-30) REVERT: A 2018 MET cc_start: 0.9142 (mtm) cc_final: 0.8739 (mtp) REVERT: A 2043 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8351 (mtpp) REVERT: A 2175 MET cc_start: 0.7834 (mtp) cc_final: 0.7417 (mtt) REVERT: A 2222 MET cc_start: 0.8956 (mtm) cc_final: 0.8743 (mtm) REVERT: A 2286 LYS cc_start: 0.8856 (tttm) cc_final: 0.8372 (ttpp) REVERT: A 2331 GLU cc_start: 0.8603 (tt0) cc_final: 0.8208 (tt0) REVERT: A 2841 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7320 (tm-30) REVERT: A 2847 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8631 (m-30) REVERT: A 3022 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8102 (mt-10) REVERT: A 3164 ARG cc_start: 0.7703 (ptp-110) cc_final: 0.6883 (tmm160) REVERT: A 3563 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8207 (mp10) REVERT: A 3598 GLU cc_start: 0.7829 (tp30) cc_final: 0.7398 (pt0) REVERT: A 3779 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.7083 (mm-30) REVERT: A 3788 ASP cc_start: 0.7062 (m-30) cc_final: 0.6834 (m-30) REVERT: A 3791 MET cc_start: 0.7794 (tpt) cc_final: 0.7591 (tpt) REVERT: A 4270 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7863 (mm-30) REVERT: A 4338 ASP cc_start: 0.8210 (t0) cc_final: 0.7822 (m-30) REVERT: A 4447 TYR cc_start: 0.8082 (t80) cc_final: 0.7729 (t80) REVERT: A 4591 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8243 (mmm-85) outliers start: 74 outliers final: 26 residues processed: 362 average time/residue: 0.7020 time to fit residues: 288.1238 Evaluate side-chains 311 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 278 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1564 GLU Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1677 SER Chi-restraints excluded: chain A residue 1829 LYS Chi-restraints excluded: chain A residue 2022 TYR Chi-restraints excluded: chain A residue 2172 ARG Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2612 LEU Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2804 ARG Chi-restraints excluded: chain A residue 2847 ASP Chi-restraints excluded: chain A residue 3022 GLU Chi-restraints excluded: chain A residue 3112 LYS Chi-restraints excluded: chain A residue 3211 THR Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3680 SER Chi-restraints excluded: chain A residue 3765 THR Chi-restraints excluded: chain A residue 3779 GLU Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4108 GLN Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4347 GLN Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4465 SER Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4582 SER Chi-restraints excluded: chain A residue 4591 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 252 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 chunk 283 optimal weight: 5.9990 chunk 206 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2430 ASN A3636 GLN ** A3754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4062 GLN A4079 GLN A4573 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.132419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.104024 restraints weight = 30135.143| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.93 r_work: 0.3113 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24213 Z= 0.170 Angle : 0.541 8.161 32838 Z= 0.272 Chirality : 0.041 0.147 3692 Planarity : 0.004 0.044 4206 Dihedral : 7.066 170.801 3261 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.11 % Allowed : 13.28 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.93 (0.16), residues: 2929 helix: 1.96 (0.12), residues: 1726 sheet: -0.32 (0.32), residues: 247 loop : 0.63 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1488 TYR 0.024 0.002 TYR A2748 PHE 0.015 0.002 PHE A1568 TRP 0.016 0.001 TRP A2234 HIS 0.010 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00406 (24213) covalent geometry : angle 0.54079 (32838) hydrogen bonds : bond 0.04546 ( 1415) hydrogen bonds : angle 4.25575 ( 4098) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 292 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 1461 GLU cc_start: 0.7739 (tp30) cc_final: 0.7348 (tp30) REVERT: A 1478 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7909 (m) REVERT: A 1488 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8179 (mtm110) REVERT: A 1498 LYS cc_start: 0.8058 (mttm) cc_final: 0.7575 (mmtt) REVERT: A 1560 LEU cc_start: 0.8038 (tp) cc_final: 0.7734 (mm) REVERT: A 1564 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.5962 (mp0) REVERT: A 1573 THR cc_start: 0.8845 (m) cc_final: 0.8559 (p) REVERT: A 1617 GLU cc_start: 0.7476 (mp0) cc_final: 0.7096 (pt0) REVERT: A 1669 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.6977 (t0) REVERT: A 1745 TYR cc_start: 0.8852 (m-80) cc_final: 0.8482 (m-80) REVERT: A 1829 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.7795 (mmtm) REVERT: A 1980 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7397 (mt-10) REVERT: A 2000 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8014 (tm-30) REVERT: A 2018 MET cc_start: 0.9089 (mtm) cc_final: 0.8781 (mtp) REVERT: A 2043 LYS cc_start: 0.8762 (mmtt) cc_final: 0.8351 (mtpp) REVERT: A 2172 ARG cc_start: 0.6976 (OUTLIER) cc_final: 0.6654 (ttm-80) REVERT: A 2175 MET cc_start: 0.7893 (mtp) cc_final: 0.7467 (mtt) REVERT: A 2222 MET cc_start: 0.8962 (mtm) cc_final: 0.8762 (mtm) REVERT: A 2286 LYS cc_start: 0.8818 (tttm) cc_final: 0.8365 (ttpp) REVERT: A 2331 GLU cc_start: 0.8596 (tt0) cc_final: 0.8328 (tt0) REVERT: A 2418 ASP cc_start: 0.7954 (m-30) cc_final: 0.7702 (m-30) REVERT: A 2554 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7363 (tm-30) REVERT: A 2763 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.7756 (ptt90) REVERT: A 2839 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: A 2841 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7234 (tm-30) REVERT: A 2847 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.8627 (m-30) REVERT: A 2863 ARG cc_start: 0.7839 (ttm110) cc_final: 0.7018 (ttt90) REVERT: A 3022 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8179 (mt-10) REVERT: A 3141 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.7728 (mm-30) REVERT: A 3163 LYS cc_start: 0.7310 (pttp) cc_final: 0.7083 (mttp) REVERT: A 3164 ARG cc_start: 0.7557 (ptp-110) cc_final: 0.6771 (tmm160) REVERT: A 3598 GLU cc_start: 0.7791 (tp30) cc_final: 0.7327 (pt0) REVERT: A 3788 ASP cc_start: 0.7200 (m-30) cc_final: 0.6958 (m-30) REVERT: A 3791 MET cc_start: 0.7768 (tpt) cc_final: 0.7458 (mmm) REVERT: A 4075 GLU cc_start: 0.7832 (mp0) cc_final: 0.7520 (pm20) REVERT: A 4108 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7846 (mt0) REVERT: A 4270 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7934 (mm-30) REVERT: A 4338 ASP cc_start: 0.8217 (t0) cc_final: 0.7833 (m-30) REVERT: A 4447 TYR cc_start: 0.8098 (t80) cc_final: 0.7707 (t80) REVERT: A 4561 THR cc_start: 0.9297 (OUTLIER) cc_final: 0.8961 (p) REVERT: A 4591 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8195 (mmm-85) outliers start: 81 outliers final: 32 residues processed: 345 average time/residue: 0.7740 time to fit residues: 301.7172 Evaluate side-chains 321 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 276 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1478 VAL Chi-restraints excluded: chain A residue 1488 ARG Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1564 GLU Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1677 SER Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1829 LYS Chi-restraints excluded: chain A residue 2022 TYR Chi-restraints excluded: chain A residue 2106 GLU Chi-restraints excluded: chain A residue 2172 ARG Chi-restraints excluded: chain A residue 2413 LEU Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2554 GLN Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2743 SER Chi-restraints excluded: chain A residue 2804 ARG Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 2847 ASP Chi-restraints excluded: chain A residue 3141 GLU Chi-restraints excluded: chain A residue 3211 THR Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3624 GLU Chi-restraints excluded: chain A residue 3680 SER Chi-restraints excluded: chain A residue 3723 ASP Chi-restraints excluded: chain A residue 3765 THR Chi-restraints excluded: chain A residue 3946 ASP Chi-restraints excluded: chain A residue 3959 ILE Chi-restraints excluded: chain A residue 4108 GLN Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4344 LEU Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4465 SER Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4582 SER Chi-restraints excluded: chain A residue 4591 ARG Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 133 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 234 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 167 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2067 ASN A2187 GLN A2430 ASN A3063 HIS A3636 GLN A3735 GLN A4079 GLN A4573 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.133310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.104997 restraints weight = 29873.412| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.00 r_work: 0.3120 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24213 Z= 0.135 Angle : 0.509 7.215 32838 Z= 0.255 Chirality : 0.040 0.142 3692 Planarity : 0.004 0.044 4206 Dihedral : 6.897 171.574 3261 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.96 % Allowed : 14.32 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.05 (0.16), residues: 2929 helix: 2.08 (0.12), residues: 1731 sheet: -0.43 (0.31), residues: 262 loop : 0.68 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A3654 TYR 0.022 0.001 TYR A2748 PHE 0.015 0.001 PHE A1568 TRP 0.017 0.001 TRP A2234 HIS 0.008 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00311 (24213) covalent geometry : angle 0.50927 (32838) hydrogen bonds : bond 0.04213 ( 1415) hydrogen bonds : angle 4.12366 ( 4098) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 302 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1498 LYS cc_start: 0.8076 (mttm) cc_final: 0.7583 (mmtt) REVERT: A 1560 LEU cc_start: 0.8037 (tp) cc_final: 0.7753 (mm) REVERT: A 1564 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.6010 (mp0) REVERT: A 1573 THR cc_start: 0.8800 (m) cc_final: 0.8541 (p) REVERT: A 1617 GLU cc_start: 0.7496 (mp0) cc_final: 0.7084 (pt0) REVERT: A 1669 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.7030 (t0) REVERT: A 1745 TYR cc_start: 0.8811 (m-80) cc_final: 0.8419 (m-80) REVERT: A 1980 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7361 (mt-10) REVERT: A 2000 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8063 (tm-30) REVERT: A 2018 MET cc_start: 0.9052 (mtm) cc_final: 0.8715 (mtp) REVERT: A 2043 LYS cc_start: 0.8764 (mmtt) cc_final: 0.8326 (mtpp) REVERT: A 2172 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.6701 (ttm-80) REVERT: A 2175 MET cc_start: 0.7846 (mtp) cc_final: 0.7415 (mtt) REVERT: A 2222 MET cc_start: 0.8919 (mtm) cc_final: 0.8610 (mtm) REVERT: A 2286 LYS cc_start: 0.8778 (tttm) cc_final: 0.8173 (ttpp) REVERT: A 2331 GLU cc_start: 0.8549 (tt0) cc_final: 0.8259 (tt0) REVERT: A 2616 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8028 (pt0) REVERT: A 2763 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7751 (ptt90) REVERT: A 2839 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: A 2847 ASP cc_start: 0.8829 (OUTLIER) cc_final: 0.8624 (m-30) REVERT: A 2863 ARG cc_start: 0.7849 (ttm110) cc_final: 0.7028 (ttt90) REVERT: A 2879 LYS cc_start: 0.8449 (pmtt) cc_final: 0.7983 (pptt) REVERT: A 2902 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8022 (mp0) REVERT: A 3022 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8213 (mt-10) REVERT: A 3078 ARG cc_start: 0.8086 (tpp-160) cc_final: 0.7715 (mmt90) REVERT: A 3141 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7694 (mm-30) REVERT: A 3164 ARG cc_start: 0.7521 (ptp-110) cc_final: 0.6859 (tmm160) REVERT: A 3598 GLU cc_start: 0.7791 (tp30) cc_final: 0.7369 (pt0) REVERT: A 3755 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7002 (mp0) REVERT: A 3788 ASP cc_start: 0.7163 (m-30) cc_final: 0.6921 (m-30) REVERT: A 3791 MET cc_start: 0.7666 (tpt) cc_final: 0.7333 (mmm) REVERT: A 3952 GLN cc_start: 0.7106 (mm110) cc_final: 0.6500 (mt0) REVERT: A 3972 TYR cc_start: 0.7593 (t80) cc_final: 0.7176 (t80) REVERT: A 4065 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7368 (mt0) REVERT: A 4075 GLU cc_start: 0.7822 (mp0) cc_final: 0.7482 (pm20) REVERT: A 4108 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7837 (mt0) REVERT: A 4270 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7948 (mm-30) REVERT: A 4441 LYS cc_start: 0.8311 (mppt) cc_final: 0.8070 (mppt) REVERT: A 4447 TYR cc_start: 0.8119 (t80) cc_final: 0.7758 (t80) REVERT: A 4484 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: A 4561 THR cc_start: 0.9235 (OUTLIER) cc_final: 0.8902 (m) REVERT: A 4591 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8198 (mmm-85) outliers start: 77 outliers final: 30 residues processed: 349 average time/residue: 0.7658 time to fit residues: 300.6581 Evaluate side-chains 325 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 281 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1564 GLU Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1677 SER Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2022 TYR Chi-restraints excluded: chain A residue 2172 ARG Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2612 LEU Chi-restraints excluded: chain A residue 2616 GLU Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2743 SER Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2804 ARG Chi-restraints excluded: chain A residue 2811 ARG Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 2847 ASP Chi-restraints excluded: chain A residue 2970 GLU Chi-restraints excluded: chain A residue 3022 GLU Chi-restraints excluded: chain A residue 3141 GLU Chi-restraints excluded: chain A residue 3161 LEU Chi-restraints excluded: chain A residue 3211 THR Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3545 THR Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3723 ASP Chi-restraints excluded: chain A residue 3959 ILE Chi-restraints excluded: chain A residue 4018 MET Chi-restraints excluded: chain A residue 4065 GLN Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4108 GLN Chi-restraints excluded: chain A residue 4344 LEU Chi-restraints excluded: chain A residue 4347 GLN Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4465 SER Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4582 SER Chi-restraints excluded: chain A residue 4591 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 100 optimal weight: 3.9990 chunk 258 optimal weight: 0.9990 chunk 229 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 234 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 291 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2187 GLN A2430 ASN A3473 ASN A3602 ASN A3636 GLN A4079 GLN A4573 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.132565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.104007 restraints weight = 30107.512| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.96 r_work: 0.3097 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24213 Z= 0.153 Angle : 0.526 10.977 32838 Z= 0.262 Chirality : 0.041 0.153 3692 Planarity : 0.004 0.046 4206 Dihedral : 6.852 172.099 3261 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.19 % Allowed : 14.78 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.06 (0.16), residues: 2929 helix: 2.10 (0.12), residues: 1729 sheet: -0.49 (0.31), residues: 262 loop : 0.67 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A3654 TYR 0.023 0.001 TYR A2748 PHE 0.017 0.002 PHE A3996 TRP 0.016 0.001 TRP A2234 HIS 0.009 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00364 (24213) covalent geometry : angle 0.52585 (32838) hydrogen bonds : bond 0.04247 ( 1415) hydrogen bonds : angle 4.11474 ( 4098) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 294 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 1498 LYS cc_start: 0.8112 (mttm) cc_final: 0.7607 (mmtt) REVERT: A 1560 LEU cc_start: 0.8047 (tp) cc_final: 0.7645 (mm) REVERT: A 1564 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.5953 (mp0) REVERT: A 1573 THR cc_start: 0.8776 (m) cc_final: 0.8512 (p) REVERT: A 1579 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8359 (mmm) REVERT: A 1745 TYR cc_start: 0.8833 (m-80) cc_final: 0.8454 (m-80) REVERT: A 1829 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.7668 (mmtm) REVERT: A 1831 ASP cc_start: 0.8860 (p0) cc_final: 0.8658 (p0) REVERT: A 1980 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7446 (mt-10) REVERT: A 2000 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8100 (tm-30) REVERT: A 2018 MET cc_start: 0.9068 (mtm) cc_final: 0.8738 (mtp) REVERT: A 2043 LYS cc_start: 0.8769 (mmtt) cc_final: 0.8318 (mtpp) REVERT: A 2172 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6737 (ttm-80) REVERT: A 2175 MET cc_start: 0.7834 (mtp) cc_final: 0.7418 (mtt) REVERT: A 2222 MET cc_start: 0.8942 (mtm) cc_final: 0.8696 (mtm) REVERT: A 2286 LYS cc_start: 0.8823 (tttm) cc_final: 0.8401 (ttpp) REVERT: A 2331 GLU cc_start: 0.8610 (tt0) cc_final: 0.8335 (tt0) REVERT: A 2616 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8060 (pt0) REVERT: A 2763 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7742 (ptt90) REVERT: A 2839 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7743 (mp0) REVERT: A 2863 ARG cc_start: 0.7848 (ttm110) cc_final: 0.7013 (ttt90) REVERT: A 2879 LYS cc_start: 0.8545 (pmtt) cc_final: 0.8127 (pptt) REVERT: A 2902 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8050 (mp0) REVERT: A 3022 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8251 (mt-10) REVERT: A 3078 ARG cc_start: 0.8044 (tpp-160) cc_final: 0.7716 (mmt90) REVERT: A 3141 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7809 (mm-30) REVERT: A 3164 ARG cc_start: 0.7625 (ptp-110) cc_final: 0.6979 (tmm160) REVERT: A 3598 GLU cc_start: 0.7826 (tp30) cc_final: 0.7397 (pt0) REVERT: A 3755 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7049 (mp0) REVERT: A 3788 ASP cc_start: 0.7175 (m-30) cc_final: 0.6955 (m-30) REVERT: A 3972 TYR cc_start: 0.7521 (t80) cc_final: 0.7106 (t80) REVERT: A 4075 GLU cc_start: 0.7889 (mp0) cc_final: 0.7520 (pm20) REVERT: A 4108 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7855 (mt0) REVERT: A 4270 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7990 (mm-30) REVERT: A 4419 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.6798 (ptm) REVERT: A 4447 TYR cc_start: 0.8151 (t80) cc_final: 0.7825 (t80) REVERT: A 4484 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: A 4561 THR cc_start: 0.9237 (OUTLIER) cc_final: 0.8938 (p) REVERT: A 4591 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7457 (ttp-110) outliers start: 83 outliers final: 35 residues processed: 345 average time/residue: 0.7989 time to fit residues: 310.5191 Evaluate side-chains 320 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 271 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1564 GLU Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1677 SER Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1829 LYS Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2022 TYR Chi-restraints excluded: chain A residue 2172 ARG Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2616 GLU Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2743 SER Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2804 ARG Chi-restraints excluded: chain A residue 2811 ARG Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 2970 GLU Chi-restraints excluded: chain A residue 3022 GLU Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3141 GLU Chi-restraints excluded: chain A residue 3161 LEU Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3545 THR Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3624 GLU Chi-restraints excluded: chain A residue 3680 SER Chi-restraints excluded: chain A residue 3723 ASP Chi-restraints excluded: chain A residue 3765 THR Chi-restraints excluded: chain A residue 3946 ASP Chi-restraints excluded: chain A residue 4018 MET Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4108 GLN Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4344 LEU Chi-restraints excluded: chain A residue 4419 MET Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4465 SER Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4582 SER Chi-restraints excluded: chain A residue 4591 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 163 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 291 optimal weight: 3.9990 chunk 292 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 212 optimal weight: 0.7980 chunk 186 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1612 GLN A2187 GLN A2430 ASN A4079 GLN A4573 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.132509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.104093 restraints weight = 29902.941| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.94 r_work: 0.3096 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24213 Z= 0.150 Angle : 0.529 10.039 32838 Z= 0.264 Chirality : 0.040 0.150 3692 Planarity : 0.004 0.050 4206 Dihedral : 6.824 172.125 3261 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.84 % Allowed : 15.51 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.07 (0.16), residues: 2929 helix: 2.13 (0.12), residues: 1729 sheet: -0.50 (0.31), residues: 262 loop : 0.65 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A3654 TYR 0.023 0.001 TYR A2748 PHE 0.016 0.002 PHE A1568 TRP 0.017 0.001 TRP A2234 HIS 0.008 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00355 (24213) covalent geometry : angle 0.52871 (32838) hydrogen bonds : bond 0.04188 ( 1415) hydrogen bonds : angle 4.10508 ( 4098) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 285 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1488 ARG cc_start: 0.8294 (mtm110) cc_final: 0.8037 (mpp80) REVERT: A 1498 LYS cc_start: 0.8122 (mttm) cc_final: 0.7605 (mmtt) REVERT: A 1560 LEU cc_start: 0.8053 (tp) cc_final: 0.7645 (mm) REVERT: A 1564 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.5976 (mp0) REVERT: A 1573 THR cc_start: 0.8790 (m) cc_final: 0.8542 (p) REVERT: A 1745 TYR cc_start: 0.8825 (m-80) cc_final: 0.8451 (m-80) REVERT: A 1829 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.7657 (mmtm) REVERT: A 1980 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7455 (mt-10) REVERT: A 2000 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8137 (tm-30) REVERT: A 2018 MET cc_start: 0.9044 (mtm) cc_final: 0.8713 (mtp) REVERT: A 2043 LYS cc_start: 0.8790 (mmtt) cc_final: 0.8283 (mtpp) REVERT: A 2172 ARG cc_start: 0.7064 (mtp85) cc_final: 0.6786 (ttm-80) REVERT: A 2175 MET cc_start: 0.7939 (mtp) cc_final: 0.7572 (mtt) REVERT: A 2222 MET cc_start: 0.8942 (mtm) cc_final: 0.8687 (mtm) REVERT: A 2286 LYS cc_start: 0.8788 (tttm) cc_final: 0.8188 (ttpp) REVERT: A 2331 GLU cc_start: 0.8596 (tt0) cc_final: 0.8322 (tt0) REVERT: A 2616 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8066 (pt0) REVERT: A 2763 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7750 (ptt90) REVERT: A 2839 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7724 (mp0) REVERT: A 2863 ARG cc_start: 0.7863 (ttm110) cc_final: 0.7056 (ttt90) REVERT: A 2879 LYS cc_start: 0.8555 (pmtt) cc_final: 0.8151 (pptt) REVERT: A 2902 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8025 (mp0) REVERT: A 3006 GLU cc_start: 0.8628 (tp30) cc_final: 0.8353 (mm-30) REVERT: A 3022 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8366 (mt-10) REVERT: A 3078 ARG cc_start: 0.8067 (tpp-160) cc_final: 0.7748 (mmt90) REVERT: A 3141 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.7819 (mm-30) REVERT: A 3598 GLU cc_start: 0.7835 (tp30) cc_final: 0.7398 (pt0) REVERT: A 3726 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6919 (pp20) REVERT: A 3755 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7092 (mp0) REVERT: A 3968 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: A 4075 GLU cc_start: 0.7858 (mp0) cc_final: 0.7559 (pm20) REVERT: A 4108 GLN cc_start: 0.8389 (tt0) cc_final: 0.7861 (mt0) REVERT: A 4270 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7996 (mm-30) REVERT: A 4447 TYR cc_start: 0.8143 (t80) cc_final: 0.7842 (t80) REVERT: A 4561 THR cc_start: 0.9228 (OUTLIER) cc_final: 0.8939 (p) REVERT: A 4591 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8288 (mmm-85) outliers start: 74 outliers final: 43 residues processed: 329 average time/residue: 0.7954 time to fit residues: 294.9375 Evaluate side-chains 327 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 273 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1499 GLU Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1564 GLU Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1603 ARG Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1677 SER Chi-restraints excluded: chain A residue 1679 ARG Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1829 LYS Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2022 TYR Chi-restraints excluded: chain A residue 2509 LYS Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2616 GLU Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2743 SER Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2804 ARG Chi-restraints excluded: chain A residue 2811 ARG Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 2970 GLU Chi-restraints excluded: chain A residue 3022 GLU Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3141 GLU Chi-restraints excluded: chain A residue 3161 LEU Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3545 THR Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3680 SER Chi-restraints excluded: chain A residue 3723 ASP Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 3750 LEU Chi-restraints excluded: chain A residue 3765 THR Chi-restraints excluded: chain A residue 3946 ASP Chi-restraints excluded: chain A residue 3968 GLN Chi-restraints excluded: chain A residue 4018 MET Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4344 LEU Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4465 SER Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4582 SER Chi-restraints excluded: chain A residue 4591 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 117 optimal weight: 0.3980 chunk 83 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 245 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 289 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN A1922 GLN A1985 HIS A2187 GLN A2430 ASN ** A3214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3584 ASN A4079 GLN A4573 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.133313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104767 restraints weight = 29883.935| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.90 r_work: 0.3124 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24213 Z= 0.127 Angle : 0.520 9.951 32838 Z= 0.259 Chirality : 0.040 0.145 3692 Planarity : 0.004 0.057 4206 Dihedral : 6.748 172.100 3261 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.53 % Allowed : 16.16 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.14 (0.16), residues: 2929 helix: 2.19 (0.12), residues: 1732 sheet: -0.52 (0.31), residues: 257 loop : 0.67 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A3654 TYR 0.021 0.001 TYR A2748 PHE 0.015 0.001 PHE A1568 TRP 0.017 0.001 TRP A2234 HIS 0.006 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00291 (24213) covalent geometry : angle 0.52037 (32838) hydrogen bonds : bond 0.04018 ( 1415) hydrogen bonds : angle 4.05083 ( 4098) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 286 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1498 LYS cc_start: 0.8107 (mttm) cc_final: 0.7616 (mmtt) REVERT: A 1564 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.5910 (mp0) REVERT: A 1573 THR cc_start: 0.8762 (m) cc_final: 0.8518 (p) REVERT: A 1688 THR cc_start: 0.8581 (m) cc_final: 0.8116 (p) REVERT: A 1745 TYR cc_start: 0.8775 (m-80) cc_final: 0.8443 (m-80) REVERT: A 1980 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7414 (mt-10) REVERT: A 2000 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8025 (tm-30) REVERT: A 2018 MET cc_start: 0.9007 (mtm) cc_final: 0.8666 (mtp) REVERT: A 2043 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8254 (mtpp) REVERT: A 2172 ARG cc_start: 0.6939 (mtp85) cc_final: 0.6712 (ttm-80) REVERT: A 2175 MET cc_start: 0.7797 (mtp) cc_final: 0.7431 (mtt) REVERT: A 2222 MET cc_start: 0.8926 (mtm) cc_final: 0.8602 (mtm) REVERT: A 2286 LYS cc_start: 0.8756 (tttm) cc_final: 0.8487 (ttpp) REVERT: A 2331 GLU cc_start: 0.8560 (tt0) cc_final: 0.8327 (tt0) REVERT: A 2616 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8055 (pt0) REVERT: A 2763 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7744 (ptt90) REVERT: A 2839 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: A 2863 ARG cc_start: 0.7855 (ttm110) cc_final: 0.7008 (ttt90) REVERT: A 2879 LYS cc_start: 0.8530 (pmtt) cc_final: 0.8117 (pptt) REVERT: A 2902 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7987 (mp0) REVERT: A 3006 GLU cc_start: 0.8599 (tp30) cc_final: 0.8343 (mm-30) REVERT: A 3022 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8304 (mt-10) REVERT: A 3078 ARG cc_start: 0.8033 (tpp-160) cc_final: 0.7714 (mmt90) REVERT: A 3141 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.7705 (mm-30) REVERT: A 3491 LYS cc_start: 0.7554 (mttm) cc_final: 0.7345 (mttm) REVERT: A 3598 GLU cc_start: 0.7794 (tp30) cc_final: 0.7389 (pt0) REVERT: A 3755 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7092 (mp0) REVERT: A 3788 ASP cc_start: 0.7154 (m-30) cc_final: 0.6940 (m-30) REVERT: A 4075 GLU cc_start: 0.7799 (mp0) cc_final: 0.7510 (pm20) REVERT: A 4108 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7797 (mt0) REVERT: A 4270 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7957 (mm-30) REVERT: A 4419 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.6723 (ptm) REVERT: A 4447 TYR cc_start: 0.8137 (t80) cc_final: 0.7872 (t80) REVERT: A 4484 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: A 4561 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.8942 (p) REVERT: A 4591 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8232 (mmm-85) outliers start: 66 outliers final: 32 residues processed: 324 average time/residue: 0.7958 time to fit residues: 290.4302 Evaluate side-chains 318 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 275 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1499 GLU Chi-restraints excluded: chain A residue 1564 GLU Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1679 ARG Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 2022 TYR Chi-restraints excluded: chain A residue 2509 LYS Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2612 LEU Chi-restraints excluded: chain A residue 2616 GLU Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2743 SER Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2804 ARG Chi-restraints excluded: chain A residue 2811 ARG Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 2970 GLU Chi-restraints excluded: chain A residue 3022 GLU Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3141 GLU Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3680 SER Chi-restraints excluded: chain A residue 3723 ASP Chi-restraints excluded: chain A residue 3750 LEU Chi-restraints excluded: chain A residue 3765 THR Chi-restraints excluded: chain A residue 4018 MET Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4108 GLN Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4419 MET Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4465 SER Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4582 SER Chi-restraints excluded: chain A residue 4591 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 156 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 279 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 290 optimal weight: 0.9990 chunk 175 optimal weight: 5.9990 chunk 284 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 285 optimal weight: 0.6980 chunk 240 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1670 ASN A2187 GLN A2430 ASN ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3584 ASN A4079 GLN A4453 ASN A4573 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.133160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.104123 restraints weight = 30144.462| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.94 r_work: 0.3115 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24213 Z= 0.139 Angle : 0.530 10.551 32838 Z= 0.264 Chirality : 0.040 0.149 3692 Planarity : 0.004 0.062 4206 Dihedral : 6.692 171.994 3261 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.30 % Allowed : 16.35 % Favored : 81.34 % 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: 2929 helix: 2.15 (0.12), residues: 1738 sheet: -0.52 (0.31), residues: 257 loop : 0.62 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A3654 TYR 0.022 0.001 TYR A2748 PHE 0.015 0.001 PHE A1568 TRP 0.017 0.001 TRP A2234 HIS 0.007 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00326 (24213) covalent geometry : angle 0.53046 (32838) hydrogen bonds : bond 0.04052 ( 1415) hydrogen bonds : angle 4.05223 ( 4098) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 284 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1498 LYS cc_start: 0.8136 (mttm) cc_final: 0.7647 (mmtt) REVERT: A 1564 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.5961 (mp0) REVERT: A 1573 THR cc_start: 0.8776 (m) cc_final: 0.8545 (p) REVERT: A 1688 THR cc_start: 0.8565 (m) cc_final: 0.8126 (p) REVERT: A 1745 TYR cc_start: 0.8797 (m-80) cc_final: 0.8469 (m-80) REVERT: A 1769 MET cc_start: 0.7816 (mtp) cc_final: 0.7558 (mtp) REVERT: A 1980 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7466 (mt-10) REVERT: A 2000 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8051 (tm-30) REVERT: A 2018 MET cc_start: 0.9014 (mtm) cc_final: 0.8678 (mtp) REVERT: A 2043 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8266 (mtpp) REVERT: A 2172 ARG cc_start: 0.6976 (mtp85) cc_final: 0.6754 (ttm-80) REVERT: A 2175 MET cc_start: 0.7762 (mtp) cc_final: 0.7442 (mtt) REVERT: A 2222 MET cc_start: 0.8939 (mtm) cc_final: 0.8596 (mtm) REVERT: A 2286 LYS cc_start: 0.8782 (tttm) cc_final: 0.8517 (ttpp) REVERT: A 2331 GLU cc_start: 0.8574 (tt0) cc_final: 0.8344 (tt0) REVERT: A 2763 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7752 (ptt90) REVERT: A 2839 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: A 2863 ARG cc_start: 0.7882 (ttm110) cc_final: 0.7026 (ttt90) REVERT: A 2879 LYS cc_start: 0.8426 (pmtt) cc_final: 0.8092 (pptt) REVERT: A 2902 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8032 (mp0) REVERT: A 3006 GLU cc_start: 0.8617 (tp30) cc_final: 0.8369 (mm-30) REVERT: A 3022 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8399 (mt-10) REVERT: A 3078 ARG cc_start: 0.8045 (tpp-160) cc_final: 0.7753 (mmt90) REVERT: A 3141 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.7778 (mm-30) REVERT: A 3491 LYS cc_start: 0.7582 (mttm) cc_final: 0.7370 (mttm) REVERT: A 3598 GLU cc_start: 0.7814 (tp30) cc_final: 0.7416 (pt0) REVERT: A 3606 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8267 (p0) REVERT: A 3726 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6920 (pp20) REVERT: A 3755 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7120 (mp0) REVERT: A 4075 GLU cc_start: 0.7821 (mp0) cc_final: 0.7528 (pm20) REVERT: A 4108 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7824 (mt0) REVERT: A 4270 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7980 (mm-30) REVERT: A 4447 TYR cc_start: 0.8145 (t80) cc_final: 0.7892 (t80) REVERT: A 4484 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: A 4561 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8958 (p) REVERT: A 4591 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7463 (ttp-110) outliers start: 60 outliers final: 35 residues processed: 323 average time/residue: 0.7952 time to fit residues: 289.8383 Evaluate side-chains 321 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 275 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1499 GLU Chi-restraints excluded: chain A residue 1564 GLU Chi-restraints excluded: chain A residue 1677 SER Chi-restraints excluded: chain A residue 1679 ARG Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2022 TYR Chi-restraints excluded: chain A residue 2509 LYS Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2612 LEU Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2743 SER Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2804 ARG Chi-restraints excluded: chain A residue 2811 ARG Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 2970 GLU Chi-restraints excluded: chain A residue 3022 GLU Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3141 GLU Chi-restraints excluded: chain A residue 3161 LEU Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3545 THR Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3606 ASP Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3680 SER Chi-restraints excluded: chain A residue 3723 ASP Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 3750 LEU Chi-restraints excluded: chain A residue 3765 THR Chi-restraints excluded: chain A residue 4018 MET Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4108 GLN Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4465 SER Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4582 SER Chi-restraints excluded: chain A residue 4591 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 184 optimal weight: 2.9990 chunk 216 optimal weight: 0.5980 chunk 137 optimal weight: 0.7980 chunk 278 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 269 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2187 GLN A2430 ASN ** A3200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3584 ASN A4079 GLN A4573 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.133401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.104316 restraints weight = 30026.637| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.95 r_work: 0.3120 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24213 Z= 0.133 Angle : 0.535 10.431 32838 Z= 0.266 Chirality : 0.040 0.157 3692 Planarity : 0.004 0.054 4206 Dihedral : 6.627 171.950 3261 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.00 % Allowed : 16.89 % Favored : 81.11 % 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: 2.14 (0.16), residues: 2929 helix: 2.18 (0.12), residues: 1732 sheet: -0.51 (0.31), residues: 257 loop : 0.68 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A3654 TYR 0.021 0.001 TYR A2748 PHE 0.015 0.001 PHE A1568 TRP 0.017 0.001 TRP A2234 HIS 0.006 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00311 (24213) covalent geometry : angle 0.53546 (32838) hydrogen bonds : bond 0.03999 ( 1415) hydrogen bonds : angle 4.03371 ( 4098) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 282 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1498 LYS cc_start: 0.8099 (mttm) cc_final: 0.7592 (mmtt) REVERT: A 1560 LEU cc_start: 0.8029 (tp) cc_final: 0.7674 (mm) REVERT: A 1564 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.5936 (mp0) REVERT: A 1573 THR cc_start: 0.8735 (m) cc_final: 0.8506 (p) REVERT: A 1688 THR cc_start: 0.8565 (m) cc_final: 0.8132 (p) REVERT: A 1745 TYR cc_start: 0.8774 (m-80) cc_final: 0.8438 (m-80) REVERT: A 1769 MET cc_start: 0.7810 (mtp) cc_final: 0.7545 (mtp) REVERT: A 1980 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7449 (mt-10) REVERT: A 2000 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8046 (tm-30) REVERT: A 2018 MET cc_start: 0.9013 (mtm) cc_final: 0.8676 (mtp) REVERT: A 2043 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8267 (mtpp) REVERT: A 2172 ARG cc_start: 0.6960 (mtp85) cc_final: 0.6752 (ttm-80) REVERT: A 2175 MET cc_start: 0.7744 (mtp) cc_final: 0.7419 (mtt) REVERT: A 2222 MET cc_start: 0.8932 (mtm) cc_final: 0.8590 (mtm) REVERT: A 2286 LYS cc_start: 0.8773 (tttm) cc_final: 0.8511 (ttpp) REVERT: A 2331 GLU cc_start: 0.8588 (tt0) cc_final: 0.8361 (tt0) REVERT: A 2461 MET cc_start: 0.8992 (mtp) cc_final: 0.8753 (mtm) REVERT: A 2509 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8031 (tmmt) REVERT: A 2510 MET cc_start: 0.8211 (mmm) cc_final: 0.7972 (mmt) REVERT: A 2763 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7746 (ptt90) REVERT: A 2839 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: A 2863 ARG cc_start: 0.7896 (ttm110) cc_final: 0.7048 (ttt90) REVERT: A 2879 LYS cc_start: 0.8415 (pmtt) cc_final: 0.8086 (pptt) REVERT: A 2902 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8042 (mp0) REVERT: A 3006 GLU cc_start: 0.8612 (tp30) cc_final: 0.8375 (mm-30) REVERT: A 3022 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8457 (mt-10) REVERT: A 3078 ARG cc_start: 0.8034 (tpp-160) cc_final: 0.7745 (mmt90) REVERT: A 3141 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.7788 (mm-30) REVERT: A 3491 LYS cc_start: 0.7609 (mttm) cc_final: 0.7398 (mttm) REVERT: A 3598 GLU cc_start: 0.7826 (tp30) cc_final: 0.7406 (pt0) REVERT: A 3606 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8277 (p0) REVERT: A 3652 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7596 (mt-10) REVERT: A 3726 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6879 (pp20) REVERT: A 3755 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7104 (mp0) REVERT: A 4075 GLU cc_start: 0.7826 (mp0) cc_final: 0.7539 (pm20) REVERT: A 4108 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7802 (mt0) REVERT: A 4270 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7990 (mm-30) REVERT: A 4399 LYS cc_start: 0.6891 (tmtt) cc_final: 0.6435 (ttpp) REVERT: A 4419 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.6680 (ptm) REVERT: A 4447 TYR cc_start: 0.8131 (t80) cc_final: 0.7883 (t80) REVERT: A 4484 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: A 4561 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8941 (p) REVERT: A 4591 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7433 (ttp-110) outliers start: 52 outliers final: 33 residues processed: 314 average time/residue: 0.7683 time to fit residues: 272.8900 Evaluate side-chains 324 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 278 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1499 GLU Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1564 GLU Chi-restraints excluded: chain A residue 1677 SER Chi-restraints excluded: chain A residue 1679 ARG Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2022 TYR Chi-restraints excluded: chain A residue 2509 LYS Chi-restraints excluded: chain A residue 2523 THR Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2612 LEU Chi-restraints excluded: chain A residue 2673 LYS Chi-restraints excluded: chain A residue 2743 SER Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2804 ARG Chi-restraints excluded: chain A residue 2811 ARG Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 2970 GLU Chi-restraints excluded: chain A residue 3022 GLU Chi-restraints excluded: chain A residue 3129 VAL Chi-restraints excluded: chain A residue 3141 GLU Chi-restraints excluded: chain A residue 3161 LEU Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3606 ASP Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3680 SER Chi-restraints excluded: chain A residue 3723 ASP Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 3750 LEU Chi-restraints excluded: chain A residue 3765 THR Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4108 GLN Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4419 MET Chi-restraints excluded: chain A residue 4459 ILE Chi-restraints excluded: chain A residue 4465 SER Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4518 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4582 SER Chi-restraints excluded: chain A residue 4591 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 205 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 226 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 240 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 275 optimal weight: 2.9990 chunk 88 optimal weight: 0.0770 chunk 102 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1670 ASN A2187 GLN A2430 ASN A3584 ASN ** A3754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4079 GLN A4573 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.134250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.105288 restraints weight = 29799.191| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.94 r_work: 0.3131 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24213 Z= 0.119 Angle : 0.523 11.536 32838 Z= 0.261 Chirality : 0.040 0.155 3692 Planarity : 0.004 0.053 4206 Dihedral : 6.486 171.071 3261 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.23 % Allowed : 16.81 % Favored : 80.96 % 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: 2.21 (0.16), residues: 2929 helix: 2.24 (0.12), residues: 1731 sheet: -0.50 (0.31), residues: 257 loop : 0.71 (0.21), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A3654 TYR 0.020 0.001 TYR A2748 PHE 0.013 0.001 PHE A1568 TRP 0.017 0.001 TRP A2234 HIS 0.005 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00270 (24213) covalent geometry : angle 0.52345 (32838) hydrogen bonds : bond 0.03829 ( 1415) hydrogen bonds : angle 3.98512 ( 4098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9373.39 seconds wall clock time: 160 minutes 18.91 seconds (9618.91 seconds total)