Starting phenix.real_space_refine on Mon Aug 25 00:16:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bmr_44708/08_2025/9bmr_44708.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bmr_44708/08_2025/9bmr_44708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bmr_44708/08_2025/9bmr_44708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bmr_44708/08_2025/9bmr_44708.map" model { file = "/net/cci-nas-00/data/ceres_data/9bmr_44708/08_2025/9bmr_44708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bmr_44708/08_2025/9bmr_44708.cif" } resolution = 2.6 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= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 2 5.21 5 S 117 5.16 5 C 15068 2.51 5 N 4090 2.21 5 O 4421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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: 5.75, per 1000 atoms: 0.24 Number of scatterers: 23707 At special positions: 0 Unit cell: (143, 119.9, 209, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 117 16.00 P 9 15.00 Mg 2 11.99 O 4421 8.00 N 4090 7.00 C 15068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 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: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 1457 through 1471 Processing helix chain 'A' and resid 1489 through 1509 removed outlier: 3.545A pdb=" N LYS A1508 " --> pdb=" O VAL A1504 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU A1509 " --> pdb=" O SER A1505 " (cutoff:3.500A) Processing helix chain 'A' and resid 1510 through 1514 removed outlier: 4.151A pdb=" N LYS A1514 " --> pdb=" O PRO A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1554 removed outlier: 3.915A pdb=" N VAL A1536 " --> pdb=" O ALA A1532 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A1546 " --> pdb=" O ARG A1542 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A1554 " --> pdb=" O ILE A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1561 removed outlier: 4.068A pdb=" N HIS A1559 " --> pdb=" O ALA A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1585 Processing helix chain 'A' and resid 1587 through 1593 Processing helix chain 'A' and resid 1596 through 1614 Processing helix chain 'A' and resid 1615 through 1626 removed outlier: 3.953A pdb=" N SER A1624 " --> pdb=" O GLU A1620 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A1625 " --> pdb=" O ARG A1621 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A1626 " --> pdb=" O GLU A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1632 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1646 through 1652 removed outlier: 3.585A pdb=" N GLN A1651 " --> pdb=" O ALA A1648 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1658 removed outlier: 3.641A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1728 removed outlier: 3.592A pdb=" N TRP A1701 " --> pdb=" O LYS A1697 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE A1727 " --> pdb=" O GLU A1723 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 removed outlier: 3.515A pdb=" N TYR A1745 " --> pdb=" O TRP A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1769 Processing helix chain 'A' and resid 1770 through 1772 No H-bonds generated for 'chain 'A' and resid 1770 through 1772' Processing helix chain 'A' and resid 1777 through 1797 Processing helix chain 'A' and resid 1801 through 1828 Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1852 through 1855 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 Processing helix chain 'A' and resid 1937 through 1952 Processing helix chain 'A' and resid 1960 through 1963 Processing helix chain 'A' and resid 1964 through 1987 removed outlier: 3.894A pdb=" N GLN A1973 " --> pdb=" O SER A1969 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN A1974 " --> pdb=" O ALA A1970 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS A1985 " --> pdb=" O ALA A1981 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A1986 " --> pdb=" O LEU A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2034 Processing helix chain 'A' and resid 2045 through 2058 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix removed outlier: 3.507A pdb=" N GLU A2078 " --> pdb=" O LYS A2074 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2117 removed outlier: 3.679A pdb=" N GLU A2117 " --> pdb=" O ARG A2113 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2130 Processing helix chain 'A' and resid 2132 through 2146 Processing helix chain 'A' and resid 2147 through 2149 No H-bonds generated for 'chain 'A' and resid 2147 through 2149' Processing helix chain 'A' and resid 2150 through 2152 No H-bonds generated for 'chain 'A' and resid 2150 through 2152' Processing helix chain 'A' and resid 2153 through 2165 Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2215 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2255 through 2259 removed outlier: 3.876A pdb=" N ILE A2259 " --> pdb=" O PRO A2256 " (cutoff:3.500A) Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2293 through 2297 removed outlier: 3.520A pdb=" N GLN A2296 " --> pdb=" O GLY A2293 " (cutoff:3.500A) Processing helix chain 'A' and resid 2308 through 2313 Processing helix chain 'A' and resid 2315 through 2320 Processing helix chain 'A' and resid 2352 through 2358 removed outlier: 3.631A pdb=" N ARG A2358 " --> pdb=" O ALA A2354 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2385 Processing helix chain 'A' and resid 2411 through 2424 Processing helix chain 'A' and resid 2425 through 2428 removed outlier: 3.669A pdb=" N THR A2428 " --> pdb=" O PRO A2425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2425 through 2428' Processing helix chain 'A' and resid 2431 through 2443 removed outlier: 3.783A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A2443 " --> pdb=" O HIS A2439 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 Processing helix chain 'A' and resid 2482 through 2504 removed outlier: 3.998A pdb=" N ARG A2492 " --> pdb=" O ARG A2488 " (cutoff:3.500A) Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2549 through 2552 Processing helix chain 'A' and resid 2558 through 2562 removed outlier: 3.949A pdb=" N VAL A2562 " --> pdb=" O THR A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2587 Processing helix chain 'A' and resid 2600 through 2611 removed outlier: 3.812A pdb=" N ALA A2611 " --> pdb=" O SER A2607 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.209A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2689 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2740 through 2756 Processing helix chain 'A' and resid 2757 through 2758 No H-bonds generated for 'chain 'A' and resid 2757 through 2758' Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 5.062A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2784 Processing helix chain 'A' and resid 2795 through 2809 removed outlier: 3.779A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 Processing helix chain 'A' and resid 2839 through 2858 removed outlier: 3.739A pdb=" N ASP A2851 " --> pdb=" O ASP A2847 " (cutoff:3.500A) Processing helix chain 'A' and resid 2862 through 2868 Processing helix chain 'A' and resid 2885 through 2904 removed outlier: 3.575A pdb=" N VAL A2899 " --> pdb=" O ALA A2895 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A2902 " --> pdb=" O LYS A2898 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2927 removed outlier: 3.503A pdb=" N ILE A2925 " --> pdb=" O ARG A2921 " (cutoff:3.500A) Processing helix chain 'A' and resid 2942 through 2954 Processing helix chain 'A' and resid 2968 through 2985 Processing helix chain 'A' and resid 2997 through 2999 No H-bonds generated for 'chain 'A' and resid 2997 through 2999' Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 4.300A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A3006 " --> pdb=" O SER A3002 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A3007 " --> pdb=" O GLY A3003 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A3010 " --> pdb=" O GLU A3006 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A3013 " --> pdb=" O ASN A3009 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3040 removed outlier: 3.537A pdb=" N GLU A3040 " --> pdb=" O GLY A3036 " (cutoff:3.500A) Processing helix chain 'A' and resid 3046 through 3061 Processing helix chain 'A' and resid 3071 through 3082 removed outlier: 4.228A pdb=" N ALA A3080 " --> pdb=" O LYS A3076 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A3081 " --> pdb=" O ASP A3077 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3088 Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3164 removed outlier: 3.561A pdb=" N LEU A3154 " --> pdb=" O VAL A3150 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS A3155 " --> pdb=" O HIS A3151 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 3242 removed outlier: 3.623A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3450 through 3482 Processing helix chain 'A' and resid 3482 through 3495 Processing helix chain 'A' and resid 3495 through 3517 removed outlier: 4.939A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLY A3505 " --> pdb=" O SER A3501 " (cutoff:3.500A) Processing helix chain 'A' and resid 3518 through 3520 No H-bonds generated for 'chain 'A' and resid 3518 through 3520' Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3583 Processing helix chain 'A' and resid 3594 through 3604 Processing helix chain 'A' and resid 3618 through 3630 Processing helix chain 'A' and resid 3637 through 3641 Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3650 Processing helix chain 'A' and resid 3689 through 3695 removed outlier: 3.609A pdb=" N ARG A3695 " --> pdb=" O ASP A3691 " (cutoff:3.500A) Processing helix chain 'A' and resid 3704 through 3721 Processing helix chain 'A' and resid 3721 through 3756 Processing helix chain 'A' and resid 3763 through 3799 removed outlier: 3.604A pdb=" N ILE A3767 " --> pdb=" O ASP A3763 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A3790 " --> pdb=" O GLU A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3801 through 3817 Processing helix chain 'A' and resid 3818 through 3821 Processing helix chain 'A' and resid 3828 through 3842 removed outlier: 3.612A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3847 removed outlier: 3.654A pdb=" N LYS A3847 " --> pdb=" O PRO A3844 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 removed outlier: 3.591A pdb=" N PHE A3864 " --> pdb=" O THR A3860 " (cutoff:3.500A) Processing helix chain 'A' and resid 3874 through 3875 No H-bonds generated for 'chain 'A' and resid 3874 through 3875' Processing helix chain 'A' and resid 3876 through 3878 No H-bonds generated for 'chain 'A' and resid 3876 through 3878' Processing helix chain 'A' and resid 3879 through 3895 Processing helix chain 'A' and resid 3901 through 3909 Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 Processing helix chain 'A' and resid 3965 through 3969 Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4014 Processing helix chain 'A' and resid 4018 through 4023 Processing helix chain 'A' and resid 4026 through 4034 Processing helix chain 'A' and resid 4051 through 4063 Processing helix chain 'A' and resid 4073 through 4088 Processing helix chain 'A' and resid 4098 through 4101 Processing helix chain 'A' and resid 4102 through 4115 removed outlier: 3.631A pdb=" N GLN A4108 " --> pdb=" O GLY A4104 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A4115 " --> pdb=" O LYS A4111 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4142 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.591A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4175 through 4194 removed outlier: 3.769A pdb=" N LEU A4194 " --> pdb=" O ILE A4190 " (cutoff:3.500A) Processing helix chain 'A' and resid 4196 through 4201 removed outlier: 3.881A pdb=" N TRP A4201 " --> pdb=" O ALA A4197 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4227 Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 removed outlier: 3.521A pdb=" N PHE A4305 " --> pdb=" O ARG A4301 " (cutoff:3.500A) Processing helix chain 'A' and resid 4317 through 4322 Processing helix chain 'A' and resid 4324 through 4327 Processing helix chain 'A' and resid 4328 through 4347 Processing helix chain 'A' and resid 4375 through 4391 Processing helix chain 'A' and resid 4401 through 4406 removed outlier: 4.213A pdb=" N LYS A4406 " --> pdb=" O VAL A4402 " (cutoff:3.500A) Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4474 through 4498 removed outlier: 3.580A pdb=" N SER A4480 " --> pdb=" O ILE A4476 " (cutoff:3.500A) Processing helix chain 'A' and resid 4500 through 4505 removed outlier: 3.524A pdb=" N LYS A4505 " --> pdb=" O LYS A4502 " (cutoff:3.500A) Processing helix chain 'A' and resid 4516 through 4532 removed outlier: 3.568A pdb=" N TYR A4520 " --> pdb=" O VAL A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4535 through 4537 No H-bonds generated for 'chain 'A' and resid 4535 through 4537' Processing helix chain 'A' and resid 4631 through 4638 removed outlier: 3.577A pdb=" N PHE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1477 through 1480 removed outlier: 3.884A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1663 through 1666 removed outlier: 7.566A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.568A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.382A pdb=" N PHE A1686 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1842 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 removed outlier: 6.536A pdb=" N GLY A1901 " --> pdb=" O ARG A2037 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU A2039 " --> pdb=" O GLY A1901 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER A1903 " --> pdb=" O LEU A2039 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1931 removed outlier: 6.323A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASP A1958 " --> pdb=" O LEU A1928 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE A1930 " --> pdb=" O ASP A1958 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA7, first strand: chain 'A' and resid 2249 through 2254 Processing sheet with id=AA8, first strand: chain 'A' and resid 2266 through 2268 Processing sheet with id=AA9, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AB1, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 6.142A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2644 removed outlier: 4.044A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2873 through 2874 Processing sheet with id=AB5, first strand: chain 'A' and resid 2957 through 2959 removed outlier: 6.290A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A2935 " --> pdb=" O MET A3068 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N HIS A2932 " --> pdb=" O VAL A3090 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ASN A3092 " --> pdb=" O HIS A2932 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A2934 " --> pdb=" O ASN A3092 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE A3094 " --> pdb=" O LEU A2934 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE A2936 " --> pdb=" O PHE A3094 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3610 through 3613 Processing sheet with id=AB7, first strand: chain 'A' and resid 3653 through 3656 Processing sheet with id=AB8, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.246A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A4042 " --> pdb=" O PHE A4145 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE A4147 " --> pdb=" O LEU A4042 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N CYS A4044 " --> pdb=" O PHE A4147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4283 through 4285 Processing sheet with id=AC1, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.130A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A4587 " --> pdb=" O THR A4546 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4564 through 4571 removed outlier: 7.190A pdb=" N ILE A4581 " --> pdb=" O GLY A4567 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N THR A4569 " --> pdb=" O ASN A4579 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N ASN A4579 " --> pdb=" O THR A4569 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N ASN A4571 " --> pdb=" O LEU A4577 " (cutoff:3.500A) removed outlier: 10.187A pdb=" N LEU A4577 " --> pdb=" O ASN A4571 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL A4609 " --> pdb=" O ILE A4619 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N THR A4621 " --> pdb=" O LEU A4607 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A4607 " --> pdb=" O THR A4621 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASP A4623 " --> pdb=" O VAL A4605 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A4605 " --> pdb=" O ASP A4623 " (cutoff:3.500A) 1415 hydrogen bonds defined for protein. 4098 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.80 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7817 1.34 - 1.46: 4781 1.46 - 1.58: 11405 1.58 - 1.69: 14 1.69 - 1.81: 196 Bond restraints: 24213 Sorted by residual: bond pdb=" C4 ADP A4704 " pdb=" C5 ADP A4704 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C4 ADP A4701 " pdb=" C5 ADP A4701 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C4 ADP A4703 " pdb=" C5 ADP A4703 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" C5 ADP A4703 " pdb=" C6 ADP A4703 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C5 ADP A4701 " pdb=" C6 ADP A4701 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.72e+01 ... (remaining 24208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 32469 2.45 - 4.91: 324 4.91 - 7.36: 28 7.36 - 9.81: 10 9.81 - 12.27: 7 Bond angle restraints: 32838 Sorted by residual: angle pdb=" PB ATP A4702 " pdb=" O3B ATP A4702 " pdb=" PG ATP A4702 " ideal model delta sigma weight residual 139.87 134.14 5.73 1.00e+00 1.00e+00 3.28e+01 angle pdb=" PA ADP A4704 " pdb=" O3A ADP A4704 " pdb=" PB ADP A4704 " ideal model delta sigma weight residual 120.50 132.77 -12.27 3.00e+00 1.11e-01 1.67e+01 angle pdb=" PA ADP A4703 " pdb=" O3A ADP A4703 " pdb=" PB ADP A4703 " ideal model delta sigma weight residual 120.50 132.68 -12.18 3.00e+00 1.11e-01 1.65e+01 angle pdb=" PA ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PB ADP A4701 " ideal model delta sigma weight residual 120.50 131.52 -11.02 3.00e+00 1.11e-01 1.35e+01 angle pdb=" C1' ADP A4701 " pdb=" C2' ADP A4701 " pdb=" C3' ADP A4701 " ideal model delta sigma weight residual 111.00 100.16 10.84 3.00e+00 1.11e-01 1.31e+01 ... (remaining 32833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.15: 14305 31.15 - 62.30: 316 62.30 - 93.45: 68 93.45 - 124.60: 2 124.60 - 155.75: 2 Dihedral angle restraints: 14693 sinusoidal: 6090 harmonic: 8603 Sorted by residual: dihedral pdb=" O1B ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PB ADP A4701 " pdb=" PA ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 95.74 -155.75 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" C5' ADP A4703 " pdb=" O5' ADP A4703 " pdb=" PA ADP A4703 " pdb=" O2A ADP A4703 " ideal model delta sinusoidal sigma weight residual 300.00 174.39 125.61 1 2.00e+01 2.50e-03 3.80e+01 dihedral pdb=" C5' ADP A4701 " pdb=" O5' ADP A4701 " pdb=" PA ADP A4701 " pdb=" O2A ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 50.57 -110.57 1 2.00e+01 2.50e-03 3.24e+01 ... (remaining 14690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2754 0.042 - 0.083: 708 0.083 - 0.124: 204 0.124 - 0.166: 21 0.166 - 0.207: 5 Chirality restraints: 3692 Sorted by residual: chirality pdb=" CA VAL A2345 " pdb=" N VAL A2345 " pdb=" C VAL A2345 " pdb=" CB VAL A2345 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA LEU A2668 " pdb=" N LEU A2668 " pdb=" C LEU A2668 " pdb=" CB LEU A2668 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" CA ILE A2016 " pdb=" N ILE A2016 " pdb=" C ILE A2016 " pdb=" CB ILE A2016 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.85e-01 ... (remaining 3689 not shown) Planarity restraints: 4206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A4195 " 0.449 9.50e-02 1.11e+02 2.01e-01 2.48e+01 pdb=" NE ARG A4195 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A4195 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A4195 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A4195 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1537 " 0.012 2.00e-02 2.50e+03 1.36e-02 4.65e+00 pdb=" CG TRP A1537 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A1537 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A1537 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1537 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A1537 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1537 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1537 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1537 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A1537 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A2858 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO A2859 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A2859 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A2859 " -0.026 5.00e-02 4.00e+02 ... (remaining 4203 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 31 2.38 - 3.01: 12568 3.01 - 3.64: 37801 3.64 - 4.27: 58426 4.27 - 4.90: 93728 Nonbonded interactions: 202554 Sorted by model distance: nonbonded pdb=" OE2 GLU A2344 " pdb="MG MG A4706 " model vdw 1.745 2.170 nonbonded pdb=" OG SER A2231 " pdb="MG MG A4706 " model vdw 1.959 2.170 nonbonded pdb=" O2G ATP A4702 " pdb="MG MG A4706 " model vdw 2.072 2.170 nonbonded pdb=" OG1 THR A1913 " pdb="MG MG A4705 " model vdw 2.095 2.170 nonbonded pdb=" O3B ADP A4701 " pdb="MG MG A4705 " model vdw 2.102 2.170 ... (remaining 202549 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.170 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 27.050 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 24213 Z= 0.211 Angle : 0.621 12.268 32838 Z= 0.328 Chirality : 0.041 0.207 3692 Planarity : 0.005 0.201 4206 Dihedral : 14.217 155.747 9105 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.54 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.08 (0.34), residues: 235 loop : 0.76 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A2492 TYR 0.018 0.002 TYR A2472 PHE 0.017 0.002 PHE A1960 TRP 0.035 0.002 TRP A1537 HIS 0.014 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00386 (24213) covalent geometry : angle 0.62059 (32838) hydrogen bonds : bond 0.20841 ( 1415) hydrogen bonds : angle 6.47179 ( 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 602 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 602 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1531 MET cc_start: 0.8839 (tpp) cc_final: 0.8520 (mmm) REVERT: A 1709 MET cc_start: 0.8726 (ttp) cc_final: 0.8394 (ttp) REVERT: A 1941 MET cc_start: 0.8160 (mmm) cc_final: 0.7754 (mmm) REVERT: A 2273 ARG cc_start: 0.8333 (mmm160) cc_final: 0.8110 (mmm160) REVERT: A 3169 MET cc_start: 0.8553 (mmt) cc_final: 0.8318 (mmp) REVERT: A 3483 SER cc_start: 0.6291 (t) cc_final: 0.6000 (m) REVERT: A 4590 LEU cc_start: 0.8373 (mt) cc_final: 0.8150 (mp) outliers start: 0 outliers final: 1 residues processed: 602 average time/residue: 0.8552 time to fit residues: 575.4473 Evaluate side-chains 342 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 341 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3077 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.0970 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1471 ASN A1643 ASN A1646 ASN A1670 ASN A2713 ASN A3092 ASN A3542 GLN A3602 ASN A3709 GLN A3735 GLN A3985 GLN A4062 GLN A4079 GLN A4108 GLN A4307 GLN A4386 ASN A4393 GLN A4404 ASN A4506 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.143232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.115998 restraints weight = 29438.924| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.63 r_work: 0.3297 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2290 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= 0.145 Angle : 0.551 6.929 32838 Z= 0.283 Chirality : 0.041 0.151 3692 Planarity : 0.004 0.045 4206 Dihedral : 7.364 154.241 3263 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.42 % Allowed : 10.40 % Favored : 87.18 % 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: 1.98 (0.16), residues: 2929 helix: 1.92 (0.12), residues: 1732 sheet: -0.03 (0.32), residues: 253 loop : 0.73 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1621 TYR 0.020 0.001 TYR A4196 PHE 0.021 0.002 PHE A4413 TRP 0.016 0.001 TRP A2234 HIS 0.012 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00315 (24213) covalent geometry : angle 0.55140 (32838) hydrogen bonds : bond 0.05392 ( 1415) hydrogen bonds : angle 4.50093 ( 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 426 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 363 time to evaluate : 0.973 Fit side-chains REVERT: A 1462 PHE cc_start: 0.6895 (OUTLIER) cc_final: 0.6383 (m-10) REVERT: A 1566 GLN cc_start: 0.7325 (mm110) cc_final: 0.7123 (mm-40) REVERT: A 1709 MET cc_start: 0.9018 (ttp) cc_final: 0.8597 (ttp) REVERT: A 1941 MET cc_start: 0.8891 (mmm) cc_final: 0.8459 (mmm) REVERT: A 1980 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7387 (mt-10) REVERT: A 2051 GLN cc_start: 0.7954 (tm130) cc_final: 0.7711 (tt0) REVERT: A 2074 LYS cc_start: 0.8036 (mptt) cc_final: 0.7825 (mptt) REVERT: A 2133 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7357 (mt-10) REVERT: A 2152 GLU cc_start: 0.7643 (pm20) cc_final: 0.7067 (mt-10) REVERT: A 2205 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8102 (mm-30) REVERT: A 2412 MET cc_start: 0.7060 (tpp) cc_final: 0.6705 (tpt) REVERT: A 2603 MET cc_start: 0.8395 (ttp) cc_final: 0.7955 (ttp) REVERT: A 2616 GLU cc_start: 0.7901 (tt0) cc_final: 0.7385 (pt0) REVERT: A 2629 GLU cc_start: 0.7854 (tp30) cc_final: 0.7612 (tp30) REVERT: A 2640 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7953 (pp20) REVERT: A 2643 ARG cc_start: 0.7879 (mtp85) cc_final: 0.7662 (mmt-90) REVERT: A 2953 MET cc_start: 0.8515 (mtp) cc_final: 0.8239 (mtp) REVERT: A 3006 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7845 (tm-30) REVERT: A 3048 GLU cc_start: 0.7243 (pm20) cc_final: 0.7017 (tp30) REVERT: A 3156 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.6588 (mp-120) REVERT: A 3169 MET cc_start: 0.8845 (mmt) cc_final: 0.8349 (mmp) REVERT: A 3191 ARG cc_start: 0.7457 (ttm170) cc_final: 0.7155 (mmm-85) REVERT: A 3211 THR cc_start: 0.6390 (m) cc_final: 0.6185 (p) REVERT: A 3220 ARG cc_start: 0.6137 (tpp-160) cc_final: 0.5860 (mmm-85) REVERT: A 3558 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7424 (tt0) REVERT: A 3595 GLN cc_start: 0.7930 (mp10) cc_final: 0.7231 (pp30) REVERT: A 3842 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8134 (mt-10) REVERT: A 4023 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7077 (mm-40) REVERT: A 4075 GLU cc_start: 0.7777 (tp30) cc_final: 0.7169 (pm20) REVERT: A 4224 ASP cc_start: 0.7928 (m-30) cc_final: 0.7687 (m-30) REVERT: A 4281 GLU cc_start: 0.7472 (mm-30) cc_final: 0.6864 (pp20) REVERT: A 4301 ARG cc_start: 0.7514 (ttm-80) cc_final: 0.6955 (ptt90) REVERT: A 4415 ARG cc_start: 0.7553 (mtp180) cc_final: 0.6716 (ttp-110) REVERT: A 4422 LYS cc_start: 0.7133 (tttt) cc_final: 0.6597 (pttm) REVERT: A 4571 ASN cc_start: 0.7312 (t0) cc_final: 0.7038 (t0) REVERT: A 4572 ASN cc_start: 0.7925 (t0) cc_final: 0.7612 (t0) REVERT: A 4583 THR cc_start: 0.8210 (m) cc_final: 0.7842 (p) REVERT: A 4591 ARG cc_start: 0.7638 (ttt180) cc_final: 0.7118 (ttt90) REVERT: A 4617 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7461 (p0) outliers start: 63 outliers final: 18 residues processed: 401 average time/residue: 0.8721 time to fit residues: 393.1678 Evaluate side-chains 333 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 309 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1462 PHE Chi-restraints excluded: chain A residue 1465 GLN Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1799 GLU Chi-restraints excluded: chain A residue 2110 LYS Chi-restraints excluded: chain A residue 2133 GLU Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2746 GLN Chi-restraints excluded: chain A residue 2764 THR Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2847 ASP Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3156 GLN Chi-restraints excluded: chain A residue 3680 SER Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3928 THR Chi-restraints excluded: chain A residue 4073 SER Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4204 LYS Chi-restraints excluded: chain A residue 4311 LEU Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 44 optimal weight: 0.0970 chunk 154 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 238 optimal weight: 0.7980 chunk 188 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1832 ASN A2781 GLN A3063 HIS A3542 GLN A3754 ASN A4108 GLN A4232 ASN A4307 GLN A4393 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.140863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.113789 restraints weight = 29573.965| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.60 r_work: 0.3263 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24213 Z= 0.153 Angle : 0.526 7.135 32838 Z= 0.267 Chirality : 0.041 0.151 3692 Planarity : 0.004 0.043 4206 Dihedral : 6.987 145.420 3261 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.53 % Allowed : 12.09 % Favored : 85.37 % 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: 2.02 (0.16), residues: 2929 helix: 1.99 (0.12), residues: 1730 sheet: -0.17 (0.33), residues: 246 loop : 0.71 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2863 TYR 0.016 0.001 TYR A1546 PHE 0.018 0.002 PHE A2912 TRP 0.018 0.001 TRP A2234 HIS 0.009 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00351 (24213) covalent geometry : angle 0.52567 (32838) hydrogen bonds : bond 0.04836 ( 1415) hydrogen bonds : angle 4.27219 ( 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 403 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 337 time to evaluate : 0.926 Fit side-chains REVERT: A 1462 PHE cc_start: 0.6971 (OUTLIER) cc_final: 0.6391 (m-10) REVERT: A 1564 GLU cc_start: 0.7613 (mp0) cc_final: 0.7392 (mp0) REVERT: A 1566 GLN cc_start: 0.7192 (mm110) cc_final: 0.6971 (mm-40) REVERT: A 1583 SER cc_start: 0.7781 (t) cc_final: 0.7429 (p) REVERT: A 1617 GLU cc_start: 0.7673 (mp0) cc_final: 0.7416 (tm-30) REVERT: A 1709 MET cc_start: 0.8981 (ttp) cc_final: 0.8580 (ttp) REVERT: A 1941 MET cc_start: 0.8928 (mmm) cc_final: 0.8447 (mmm) REVERT: A 2051 GLN cc_start: 0.7994 (tm130) cc_final: 0.7745 (tt0) REVERT: A 2133 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7409 (mm-30) REVERT: A 2152 GLU cc_start: 0.7722 (pm20) cc_final: 0.7177 (mt-10) REVERT: A 2310 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8285 (mt-10) REVERT: A 2412 MET cc_start: 0.7115 (tpp) cc_final: 0.6900 (tpt) REVERT: A 2603 MET cc_start: 0.8562 (ttp) cc_final: 0.8098 (ttp) REVERT: A 2616 GLU cc_start: 0.7952 (tt0) cc_final: 0.7460 (pt0) REVERT: A 2629 GLU cc_start: 0.8001 (tp30) cc_final: 0.7696 (tp30) REVERT: A 2640 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7974 (pp20) REVERT: A 2764 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8363 (p) REVERT: A 2804 ARG cc_start: 0.8482 (tpt170) cc_final: 0.8191 (tpt170) REVERT: A 2953 MET cc_start: 0.8567 (mtp) cc_final: 0.8285 (mtp) REVERT: A 3048 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7073 (tp30) REVERT: A 3156 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.6777 (mp-120) REVERT: A 3160 ARG cc_start: 0.7122 (mtp180) cc_final: 0.6828 (mtp-110) REVERT: A 3169 MET cc_start: 0.8852 (mmt) cc_final: 0.8449 (mmp) REVERT: A 3178 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8035 (m-30) REVERT: A 3188 HIS cc_start: 0.7741 (t70) cc_final: 0.6995 (m-70) REVERT: A 3191 ARG cc_start: 0.7442 (ttm170) cc_final: 0.7139 (mmm-85) REVERT: A 3595 GLN cc_start: 0.8002 (mp10) cc_final: 0.7251 (pp30) REVERT: A 3747 LYS cc_start: 0.7516 (ttpt) cc_final: 0.7264 (tttt) REVERT: A 3904 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: A 3906 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7476 (tm-30) REVERT: A 4023 GLN cc_start: 0.7491 (mm-40) cc_final: 0.7047 (mm-40) REVERT: A 4075 GLU cc_start: 0.7810 (tp30) cc_final: 0.7117 (pm20) REVERT: A 4128 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8684 (pmm) REVERT: A 4224 ASP cc_start: 0.8104 (m-30) cc_final: 0.7800 (m-30) REVERT: A 4281 GLU cc_start: 0.7505 (mm-30) cc_final: 0.6824 (pp20) REVERT: A 4422 LYS cc_start: 0.7168 (tttt) cc_final: 0.6647 (pttm) REVERT: A 4456 VAL cc_start: 0.8083 (t) cc_final: 0.7594 (m) REVERT: A 4546 THR cc_start: 0.6664 (m) cc_final: 0.6419 (p) REVERT: A 4572 ASN cc_start: 0.7783 (t0) cc_final: 0.7472 (t0) REVERT: A 4583 THR cc_start: 0.8225 (m) cc_final: 0.7635 (p) REVERT: A 4591 ARG cc_start: 0.7644 (ttt180) cc_final: 0.7153 (ttt90) outliers start: 66 outliers final: 24 residues processed: 378 average time/residue: 0.8404 time to fit residues: 357.1948 Evaluate side-chains 341 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 307 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1462 PHE Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1556 ASP Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1878 LYS Chi-restraints excluded: chain A residue 2133 GLU Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2746 GLN Chi-restraints excluded: chain A residue 2764 THR Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2847 ASP Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3048 GLU Chi-restraints excluded: chain A residue 3087 ASN Chi-restraints excluded: chain A residue 3156 GLN Chi-restraints excluded: chain A residue 3178 ASP Chi-restraints excluded: chain A residue 3718 LYS Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3904 GLU Chi-restraints excluded: chain A residue 3906 GLN Chi-restraints excluded: chain A residue 3928 THR Chi-restraints excluded: chain A residue 3959 ILE Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4204 LYS Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4311 LEU Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4540 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 252 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1810 HIS A2296 GLN A3499 GLN A3542 GLN A4108 GLN A4232 ASN A4307 GLN A4397 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.137019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109908 restraints weight = 29706.592| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.62 r_work: 0.3216 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 24213 Z= 0.261 Angle : 0.612 7.424 32838 Z= 0.311 Chirality : 0.046 0.183 3692 Planarity : 0.005 0.052 4206 Dihedral : 7.045 117.082 3261 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.15 % Allowed : 12.74 % Favored : 84.11 % 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: 1.68 (0.15), residues: 2929 helix: 1.71 (0.12), residues: 1729 sheet: -0.19 (0.31), residues: 253 loop : 0.56 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A2243 TYR 0.021 0.002 TYR A1546 PHE 0.019 0.002 PHE A2343 TRP 0.018 0.002 TRP A2234 HIS 0.012 0.001 HIS A1810 Details of bonding type rmsd covalent geometry : bond 0.00630 (24213) covalent geometry : angle 0.61245 (32838) hydrogen bonds : bond 0.05233 ( 1415) hydrogen bonds : angle 4.37320 ( 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 404 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 322 time to evaluate : 1.039 Fit side-chains REVERT: A 1462 PHE cc_start: 0.7030 (OUTLIER) cc_final: 0.6503 (m-10) REVERT: A 1464 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7344 (mtpt) REVERT: A 1564 GLU cc_start: 0.7750 (mp0) cc_final: 0.7549 (mp0) REVERT: A 1583 SER cc_start: 0.8026 (t) cc_final: 0.7571 (p) REVERT: A 1584 LYS cc_start: 0.7629 (mmtp) cc_final: 0.7301 (ptpt) REVERT: A 1617 GLU cc_start: 0.7668 (mp0) cc_final: 0.7389 (tm-30) REVERT: A 1709 MET cc_start: 0.9093 (ttp) cc_final: 0.8694 (ttp) REVERT: A 2051 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: A 2310 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8401 (mt-10) REVERT: A 2412 MET cc_start: 0.7356 (tpp) cc_final: 0.7148 (tpt) REVERT: A 2603 MET cc_start: 0.8599 (ttp) cc_final: 0.8197 (ttp) REVERT: A 2629 GLU cc_start: 0.8114 (tp30) cc_final: 0.7849 (tp30) REVERT: A 2640 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7967 (pp20) REVERT: A 2953 MET cc_start: 0.8606 (mtp) cc_final: 0.8236 (mtp) REVERT: A 3038 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7480 (tm-30) REVERT: A 3048 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7029 (tp30) REVERT: A 3156 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.6445 (mp-120) REVERT: A 3164 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7000 (ttp-110) REVERT: A 3169 MET cc_start: 0.8894 (mmt) cc_final: 0.8525 (mmp) REVERT: A 3178 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8007 (m-30) REVERT: A 3191 ARG cc_start: 0.7569 (ttm170) cc_final: 0.7123 (mmm-85) REVERT: A 3542 GLN cc_start: 0.8431 (mm-40) cc_final: 0.7853 (mt0) REVERT: A 3595 GLN cc_start: 0.7986 (mp10) cc_final: 0.7229 (pp30) REVERT: A 3775 ARG cc_start: 0.7630 (ptp-110) cc_final: 0.7393 (ptp-110) REVERT: A 3893 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7283 (pttp) REVERT: A 3906 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7559 (tm-30) REVERT: A 4004 MET cc_start: 0.8462 (tpt) cc_final: 0.7834 (tpt) REVERT: A 4023 GLN cc_start: 0.7470 (mm-40) cc_final: 0.7136 (mm-40) REVERT: A 4075 GLU cc_start: 0.7883 (tp30) cc_final: 0.7149 (pm20) REVERT: A 4209 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7419 (tp30) REVERT: A 4281 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6841 (pp20) REVERT: A 4422 LYS cc_start: 0.7204 (tttt) cc_final: 0.6879 (tppt) REVERT: A 4583 THR cc_start: 0.8342 (m) cc_final: 0.7951 (t) outliers start: 82 outliers final: 32 residues processed: 370 average time/residue: 0.8267 time to fit residues: 345.8321 Evaluate side-chains 347 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 304 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1462 PHE Chi-restraints excluded: chain A residue 1464 LYS Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1878 LYS Chi-restraints excluded: chain A residue 2051 GLN Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2429 SER Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2746 GLN Chi-restraints excluded: chain A residue 2764 THR Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2847 ASP Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3038 GLN Chi-restraints excluded: chain A residue 3048 GLU Chi-restraints excluded: chain A residue 3087 ASN Chi-restraints excluded: chain A residue 3156 GLN Chi-restraints excluded: chain A residue 3164 ARG Chi-restraints excluded: chain A residue 3178 ASP Chi-restraints excluded: chain A residue 3482 LEU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3729 SER Chi-restraints excluded: chain A residue 3755 GLU Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3850 THR Chi-restraints excluded: chain A residue 3893 LYS Chi-restraints excluded: chain A residue 3906 GLN Chi-restraints excluded: chain A residue 3928 THR Chi-restraints excluded: chain A residue 3959 ILE Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4204 LYS Chi-restraints excluded: chain A residue 4311 LEU Chi-restraints excluded: chain A residue 4377 MET Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4604 VAL 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: 1.9990 chunk 222 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 234 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3826 GLN A3854 GLN A4012 ASN A4054 HIS A4108 GLN A4232 ASN A4307 GLN A4466 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.139843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112734 restraints weight = 29348.970| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.58 r_work: 0.3252 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3264 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= 0.130 Angle : 0.507 6.352 32838 Z= 0.257 Chirality : 0.040 0.150 3692 Planarity : 0.004 0.047 4206 Dihedral : 6.767 115.871 3261 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.53 % Allowed : 14.01 % Favored : 83.45 % 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: 1.97 (0.16), residues: 2929 helix: 2.00 (0.12), residues: 1725 sheet: -0.18 (0.32), residues: 256 loop : 0.61 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1621 TYR 0.017 0.001 TYR A2748 PHE 0.017 0.001 PHE A2912 TRP 0.019 0.001 TRP A2234 HIS 0.005 0.001 HIS A3837 Details of bonding type rmsd covalent geometry : bond 0.00293 (24213) covalent geometry : angle 0.50660 (32838) hydrogen bonds : bond 0.04318 ( 1415) hydrogen bonds : angle 4.13429 ( 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 391 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 325 time to evaluate : 1.009 Fit side-chains REVERT: A 1462 PHE cc_start: 0.7033 (OUTLIER) cc_final: 0.6538 (m-10) REVERT: A 1464 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7309 (mtpt) REVERT: A 1583 SER cc_start: 0.7977 (t) cc_final: 0.7509 (p) REVERT: A 1584 LYS cc_start: 0.7486 (mmtp) cc_final: 0.7206 (ptpt) REVERT: A 1709 MET cc_start: 0.8987 (ttp) cc_final: 0.8631 (ttp) REVERT: A 2051 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7687 (tt0) REVERT: A 2310 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8395 (mt-10) REVERT: A 2412 MET cc_start: 0.7294 (tpp) cc_final: 0.7071 (tpt) REVERT: A 2629 GLU cc_start: 0.8081 (tp30) cc_final: 0.7836 (tp30) REVERT: A 2759 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7831 (mm) REVERT: A 2848 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7965 (pt0) REVERT: A 2953 MET cc_start: 0.8636 (mtp) cc_final: 0.8304 (mtp) REVERT: A 3048 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6901 (tp30) REVERT: A 3156 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.6728 (mp-120) REVERT: A 3164 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6979 (ttp-110) REVERT: A 3169 MET cc_start: 0.8890 (mmt) cc_final: 0.8558 (mmp) REVERT: A 3191 ARG cc_start: 0.7461 (ttm170) cc_final: 0.7121 (mmm-85) REVERT: A 3480 LYS cc_start: 0.7725 (tptp) cc_final: 0.7517 (tppt) REVERT: A 3595 GLN cc_start: 0.8001 (mp10) cc_final: 0.7281 (pp30) REVERT: A 3715 GLU cc_start: 0.8301 (tp30) cc_final: 0.7907 (tp30) REVERT: A 3775 ARG cc_start: 0.7534 (ptp-110) cc_final: 0.7329 (ptp-110) REVERT: A 3906 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: A 4023 GLN cc_start: 0.7457 (mm-40) cc_final: 0.7111 (mm-40) REVERT: A 4075 GLU cc_start: 0.7734 (tp30) cc_final: 0.6865 (pm20) REVERT: A 4224 ASP cc_start: 0.8159 (m-30) cc_final: 0.7828 (m-30) REVERT: A 4415 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7362 (mtp180) REVERT: A 4422 LYS cc_start: 0.7226 (tttt) cc_final: 0.6877 (tppt) REVERT: A 4456 VAL cc_start: 0.8136 (t) cc_final: 0.7747 (m) REVERT: A 4490 GLN cc_start: 0.7120 (mt0) cc_final: 0.6814 (mt0) REVERT: A 4583 THR cc_start: 0.8208 (m) cc_final: 0.7550 (p) outliers start: 66 outliers final: 28 residues processed: 366 average time/residue: 0.8481 time to fit residues: 348.9622 Evaluate side-chains 343 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 306 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1462 PHE Chi-restraints excluded: chain A residue 1464 LYS Chi-restraints excluded: chain A residue 1556 ASP Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2051 GLN Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2746 GLN Chi-restraints excluded: chain A residue 2759 ILE Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3048 GLU Chi-restraints excluded: chain A residue 3087 ASN Chi-restraints excluded: chain A residue 3156 GLN Chi-restraints excluded: chain A residue 3164 ARG Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3668 ASP Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3906 GLN Chi-restraints excluded: chain A residue 3928 THR Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4311 LEU Chi-restraints excluded: chain A residue 4415 ARG Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 100 optimal weight: 7.9990 chunk 258 optimal weight: 0.9990 chunk 229 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 234 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 291 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1559 HIS A3542 GLN A3709 GLN A3854 GLN A4054 HIS A4108 GLN A4232 ASN A4307 GLN A4466 HIS A4572 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.137730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.110560 restraints weight = 29659.169| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.62 r_work: 0.3229 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24213 Z= 0.202 Angle : 0.564 6.939 32838 Z= 0.285 Chirality : 0.043 0.169 3692 Planarity : 0.005 0.060 4206 Dihedral : 6.848 108.303 3261 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.76 % Allowed : 14.32 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.84 (0.15), residues: 2929 helix: 1.87 (0.12), residues: 1730 sheet: -0.30 (0.31), residues: 256 loop : 0.59 (0.21), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1621 TYR 0.018 0.002 TYR A1546 PHE 0.020 0.002 PHE A1568 TRP 0.018 0.002 TRP A2234 HIS 0.005 0.001 HIS A3837 Details of bonding type rmsd covalent geometry : bond 0.00484 (24213) covalent geometry : angle 0.56385 (32838) hydrogen bonds : bond 0.04696 ( 1415) hydrogen bonds : angle 4.20860 ( 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 387 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 315 time to evaluate : 0.980 Fit side-chains REVERT: A 1462 PHE cc_start: 0.7041 (OUTLIER) cc_final: 0.6602 (m-80) REVERT: A 1464 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7355 (mtpt) REVERT: A 1564 GLU cc_start: 0.7687 (mp0) cc_final: 0.7478 (mp0) REVERT: A 1583 SER cc_start: 0.8075 (t) cc_final: 0.7586 (p) REVERT: A 1584 LYS cc_start: 0.7493 (mmtp) cc_final: 0.7230 (ptpt) REVERT: A 1650 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8468 (mp) REVERT: A 1709 MET cc_start: 0.9046 (ttp) cc_final: 0.8693 (ttp) REVERT: A 2051 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7694 (tt0) REVERT: A 2078 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7280 (mm-30) REVERT: A 2310 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8422 (mt-10) REVERT: A 2412 MET cc_start: 0.7312 (tpp) cc_final: 0.7107 (tpt) REVERT: A 2640 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7891 (pp20) REVERT: A 2763 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7493 (mtp85) REVERT: A 2848 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7953 (pt0) REVERT: A 2953 MET cc_start: 0.8615 (mtp) cc_final: 0.8235 (mtp) REVERT: A 3048 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6920 (tp30) REVERT: A 3156 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.6567 (mp-120) REVERT: A 3163 LYS cc_start: 0.7675 (ttmm) cc_final: 0.7337 (mtmm) REVERT: A 3164 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6908 (ttp-110) REVERT: A 3169 MET cc_start: 0.8866 (mmt) cc_final: 0.8550 (mmp) REVERT: A 3191 ARG cc_start: 0.7500 (ttm170) cc_final: 0.7285 (mmt-90) REVERT: A 3480 LYS cc_start: 0.7756 (tptp) cc_final: 0.7526 (tppt) REVERT: A 3595 GLN cc_start: 0.8041 (mp10) cc_final: 0.7283 (pp30) REVERT: A 3715 GLU cc_start: 0.8305 (tp30) cc_final: 0.7896 (tp30) REVERT: A 3729 SER cc_start: 0.8008 (m) cc_final: 0.7450 (p) REVERT: A 3775 ARG cc_start: 0.7533 (ptp-110) cc_final: 0.7306 (ptp-110) REVERT: A 3795 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6947 (mm-30) REVERT: A 3906 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7592 (tm-30) REVERT: A 4004 MET cc_start: 0.8412 (tpt) cc_final: 0.7807 (tpt) REVERT: A 4023 GLN cc_start: 0.7414 (mm-40) cc_final: 0.7139 (mm-40) REVERT: A 4075 GLU cc_start: 0.7806 (tp30) cc_final: 0.7065 (pm20) REVERT: A 4209 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7424 (tp30) REVERT: A 4224 ASP cc_start: 0.8199 (m-30) cc_final: 0.7860 (m-30) REVERT: A 4281 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6874 (pp20) REVERT: A 4415 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.6902 (ttp-110) REVERT: A 4419 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6987 (ptt) REVERT: A 4422 LYS cc_start: 0.7297 (tttt) cc_final: 0.7003 (tppt) REVERT: A 4456 VAL cc_start: 0.8171 (t) cc_final: 0.7766 (m) REVERT: A 4490 GLN cc_start: 0.7193 (mt0) cc_final: 0.6910 (mt0) REVERT: A 4572 ASN cc_start: 0.7592 (t0) cc_final: 0.7301 (t0) REVERT: A 4583 THR cc_start: 0.8305 (m) cc_final: 0.7936 (t) outliers start: 72 outliers final: 34 residues processed: 360 average time/residue: 0.8444 time to fit residues: 342.0214 Evaluate side-chains 352 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 305 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1462 PHE Chi-restraints excluded: chain A residue 1464 LYS Chi-restraints excluded: chain A residue 1543 ARG Chi-restraints excluded: chain A residue 1556 ASP Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1878 LYS Chi-restraints excluded: chain A residue 2051 GLN Chi-restraints excluded: chain A residue 2063 GLU Chi-restraints excluded: chain A residue 2078 GLU Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2555 ILE Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2746 GLN Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2847 ASP Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3048 GLU Chi-restraints excluded: chain A residue 3087 ASN Chi-restraints excluded: chain A residue 3156 GLN Chi-restraints excluded: chain A residue 3164 ARG Chi-restraints excluded: chain A residue 3482 LEU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3906 GLN Chi-restraints excluded: chain A residue 3928 THR Chi-restraints excluded: chain A residue 3959 ILE Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4311 LEU Chi-restraints excluded: chain A residue 4377 MET Chi-restraints excluded: chain A residue 4415 ARG Chi-restraints excluded: chain A residue 4419 MET Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 163 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 291 optimal weight: 0.9990 chunk 292 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 212 optimal weight: 0.7980 chunk 186 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1559 HIS A3542 GLN A4054 HIS A4079 GLN A4108 GLN A4232 ASN A4307 GLN A4466 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.139766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112671 restraints weight = 29347.428| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.62 r_work: 0.3258 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3446 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= 0.131 Angle : 0.508 6.362 32838 Z= 0.257 Chirality : 0.040 0.153 3692 Planarity : 0.004 0.052 4206 Dihedral : 6.692 110.768 3261 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.26 % Allowed : 15.09 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.08 (0.16), residues: 2929 helix: 2.09 (0.12), residues: 1733 sheet: -0.22 (0.32), residues: 256 loop : 0.65 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A1621 TYR 0.017 0.001 TYR A2748 PHE 0.016 0.001 PHE A2912 TRP 0.019 0.001 TRP A2234 HIS 0.005 0.001 HIS A3837 Details of bonding type rmsd covalent geometry : bond 0.00297 (24213) covalent geometry : angle 0.50810 (32838) hydrogen bonds : bond 0.04135 ( 1415) hydrogen bonds : angle 4.06729 ( 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 378 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 319 time to evaluate : 0.910 Fit side-chains REVERT: A 1462 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6583 (m-80) REVERT: A 1569 GLN cc_start: 0.7596 (tp40) cc_final: 0.6909 (tm-30) REVERT: A 1583 SER cc_start: 0.8028 (t) cc_final: 0.7538 (p) REVERT: A 1584 LYS cc_start: 0.7315 (mmtp) cc_final: 0.7012 (ptpt) REVERT: A 1650 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8436 (mp) REVERT: A 1709 MET cc_start: 0.8954 (ttp) cc_final: 0.8590 (ttp) REVERT: A 1750 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8126 (m) REVERT: A 2051 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7687 (tt0) REVERT: A 2310 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8407 (mt-10) REVERT: A 2412 MET cc_start: 0.7226 (tpp) cc_final: 0.7020 (tpt) REVERT: A 2616 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7542 (tt0) REVERT: A 2759 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7820 (mm) REVERT: A 2763 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7524 (mtp85) REVERT: A 2804 ARG cc_start: 0.8487 (tpt170) cc_final: 0.8191 (tpt170) REVERT: A 2848 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7977 (pt0) REVERT: A 2953 MET cc_start: 0.8643 (mtp) cc_final: 0.8225 (mtp) REVERT: A 3048 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6828 (tp30) REVERT: A 3156 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.6735 (mp-120) REVERT: A 3163 LYS cc_start: 0.7679 (ttmm) cc_final: 0.7340 (mtmm) REVERT: A 3164 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.6850 (ttp-110) REVERT: A 3169 MET cc_start: 0.8888 (mmt) cc_final: 0.8560 (mmp) REVERT: A 3191 ARG cc_start: 0.7406 (ttm170) cc_final: 0.7035 (mmm-85) REVERT: A 3595 GLN cc_start: 0.7968 (mp10) cc_final: 0.7307 (pp30) REVERT: A 3715 GLU cc_start: 0.8270 (tp30) cc_final: 0.7882 (tp30) REVERT: A 3729 SER cc_start: 0.8119 (m) cc_final: 0.7663 (p) REVERT: A 3795 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6683 (mm-30) REVERT: A 4023 GLN cc_start: 0.7339 (mm-40) cc_final: 0.7051 (mm-40) REVERT: A 4075 GLU cc_start: 0.7733 (tp30) cc_final: 0.6853 (pm20) REVERT: A 4209 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7430 (tp30) REVERT: A 4224 ASP cc_start: 0.8177 (m-30) cc_final: 0.7844 (m-30) REVERT: A 4281 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6871 (pp20) REVERT: A 4415 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.6871 (ttp-110) REVERT: A 4419 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.6956 (ptt) REVERT: A 4422 LYS cc_start: 0.7066 (tttt) cc_final: 0.6785 (tppt) REVERT: A 4456 VAL cc_start: 0.8131 (t) cc_final: 0.7731 (m) REVERT: A 4460 LEU cc_start: 0.8375 (tp) cc_final: 0.8071 (tm) REVERT: A 4490 GLN cc_start: 0.7238 (mt0) cc_final: 0.6950 (mt0) REVERT: A 4572 ASN cc_start: 0.7691 (t0) cc_final: 0.7323 (t0) REVERT: A 4583 THR cc_start: 0.8195 (m) cc_final: 0.7881 (t) outliers start: 59 outliers final: 31 residues processed: 357 average time/residue: 0.7106 time to fit residues: 287.0912 Evaluate side-chains 347 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 304 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1462 PHE Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1878 LYS Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2051 GLN Chi-restraints excluded: chain A residue 2063 GLU Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2616 GLU Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2759 ILE Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2847 ASP Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 3048 GLU Chi-restraints excluded: chain A residue 3087 ASN Chi-restraints excluded: chain A residue 3156 GLN Chi-restraints excluded: chain A residue 3164 ARG Chi-restraints excluded: chain A residue 3224 ILE Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3928 THR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4311 LEU Chi-restraints excluded: chain A residue 4377 MET Chi-restraints excluded: chain A residue 4415 ARG Chi-restraints excluded: chain A residue 4419 MET Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 117 optimal weight: 0.0020 chunk 83 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 245 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 147 optimal weight: 0.2980 chunk 289 optimal weight: 0.1980 chunk 225 optimal weight: 4.9990 chunk 240 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2476 HIS A2849 ASN A3542 GLN A4054 HIS A4232 ASN A4307 GLN A4466 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.141483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.115000 restraints weight = 29326.660| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.55 r_work: 0.3274 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24213 Z= 0.107 Angle : 0.488 6.180 32838 Z= 0.246 Chirality : 0.039 0.146 3692 Planarity : 0.004 0.051 4206 Dihedral : 6.469 112.218 3261 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.96 % Allowed : 15.82 % Favored : 82.23 % 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: 2.25 (0.16), residues: 2929 helix: 2.25 (0.12), residues: 1733 sheet: -0.22 (0.32), residues: 256 loop : 0.69 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1621 TYR 0.018 0.001 TYR A2748 PHE 0.016 0.001 PHE A2912 TRP 0.018 0.001 TRP A2234 HIS 0.004 0.001 HIS A3837 Details of bonding type rmsd covalent geometry : bond 0.00233 (24213) covalent geometry : angle 0.48818 (32838) hydrogen bonds : bond 0.03784 ( 1415) hydrogen bonds : angle 3.95070 ( 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 376 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 325 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 1461 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7560 (tp30) REVERT: A 1462 PHE cc_start: 0.7022 (OUTLIER) cc_final: 0.6662 (m-80) REVERT: A 1569 GLN cc_start: 0.7649 (tp40) cc_final: 0.7009 (tm-30) REVERT: A 1583 SER cc_start: 0.7763 (t) cc_final: 0.7263 (p) REVERT: A 1584 LYS cc_start: 0.7325 (mmtp) cc_final: 0.7018 (ptpt) REVERT: A 1709 MET cc_start: 0.8935 (ttp) cc_final: 0.8573 (ttp) REVERT: A 2051 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: A 2310 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8421 (mt-10) REVERT: A 2412 MET cc_start: 0.7405 (tpp) cc_final: 0.7186 (tpt) REVERT: A 2759 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7852 (mm) REVERT: A 2763 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7501 (mtp85) REVERT: A 2848 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8015 (pt0) REVERT: A 2953 MET cc_start: 0.8660 (mtp) cc_final: 0.8291 (mtp) REVERT: A 3048 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6819 (tp30) REVERT: A 3114 ASP cc_start: 0.8563 (t70) cc_final: 0.8174 (t0) REVERT: A 3163 LYS cc_start: 0.7699 (ttmm) cc_final: 0.7362 (mtmm) REVERT: A 3169 MET cc_start: 0.8918 (mmt) cc_final: 0.8600 (mmp) REVERT: A 3188 HIS cc_start: 0.8047 (t70) cc_final: 0.7143 (m-70) REVERT: A 3191 ARG cc_start: 0.7432 (ttm170) cc_final: 0.7039 (mmm-85) REVERT: A 3595 GLN cc_start: 0.7856 (mp10) cc_final: 0.7199 (pp30) REVERT: A 3715 GLU cc_start: 0.8303 (tp30) cc_final: 0.7955 (tp30) REVERT: A 3729 SER cc_start: 0.8155 (m) cc_final: 0.7769 (p) REVERT: A 3795 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6664 (mm-30) REVERT: A 4022 GLU cc_start: 0.7702 (pt0) cc_final: 0.7353 (pp20) REVERT: A 4075 GLU cc_start: 0.7745 (tp30) cc_final: 0.6860 (pm20) REVERT: A 4128 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8564 (pmm) REVERT: A 4209 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7443 (tp30) REVERT: A 4224 ASP cc_start: 0.8161 (m-30) cc_final: 0.7879 (m-30) REVERT: A 4415 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7520 (ttp80) REVERT: A 4419 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.7014 (ptt) REVERT: A 4422 LYS cc_start: 0.7137 (tttt) cc_final: 0.6868 (tppt) REVERT: A 4456 VAL cc_start: 0.8124 (t) cc_final: 0.7724 (m) REVERT: A 4460 LEU cc_start: 0.8435 (tp) cc_final: 0.8150 (tm) REVERT: A 4490 GLN cc_start: 0.7221 (mt0) cc_final: 0.6925 (mt0) REVERT: A 4572 ASN cc_start: 0.7701 (t0) cc_final: 0.7356 (t0) REVERT: A 4583 THR cc_start: 0.8247 (m) cc_final: 0.7644 (p) REVERT: A 4617 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7609 (p0) outliers start: 51 outliers final: 22 residues processed: 356 average time/residue: 0.6748 time to fit residues: 271.4643 Evaluate side-chains 343 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 312 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1462 PHE Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 2051 GLN Chi-restraints excluded: chain A residue 2063 GLU Chi-restraints excluded: chain A residue 2221 MET Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2759 ILE Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2847 ASP Chi-restraints excluded: chain A residue 3048 GLU Chi-restraints excluded: chain A residue 3087 ASN Chi-restraints excluded: chain A residue 3164 ARG Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3928 THR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4311 LEU Chi-restraints excluded: chain A residue 4415 ARG Chi-restraints excluded: chain A residue 4419 MET Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 156 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 279 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 290 optimal weight: 0.0670 chunk 175 optimal weight: 6.9990 chunk 284 optimal weight: 0.0980 chunk 259 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 285 optimal weight: 1.9990 chunk 240 optimal weight: 0.9980 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1612 GLN A1867 ASN A2476 HIS A3542 GLN A4054 HIS A4232 ASN A4307 GLN A4506 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.141275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.114743 restraints weight = 29560.792| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.55 r_work: 0.3270 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24213 Z= 0.115 Angle : 0.500 7.181 32838 Z= 0.251 Chirality : 0.040 0.152 3692 Planarity : 0.004 0.061 4206 Dihedral : 6.417 111.521 3261 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.73 % Allowed : 16.28 % Favored : 82.00 % 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: 2.27 (0.16), residues: 2929 helix: 2.26 (0.12), residues: 1729 sheet: -0.19 (0.32), residues: 256 loop : 0.70 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A1621 TYR 0.017 0.001 TYR A2748 PHE 0.016 0.001 PHE A2912 TRP 0.017 0.001 TRP A2234 HIS 0.005 0.001 HIS A4466 Details of bonding type rmsd covalent geometry : bond 0.00259 (24213) covalent geometry : angle 0.49955 (32838) hydrogen bonds : bond 0.03818 ( 1415) hydrogen bonds : angle 3.94704 ( 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 363 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 318 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: A 1461 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7567 (tp30) REVERT: A 1462 PHE cc_start: 0.7098 (OUTLIER) cc_final: 0.6710 (m-80) REVERT: A 1569 GLN cc_start: 0.7642 (tp40) cc_final: 0.7017 (tm-30) REVERT: A 1583 SER cc_start: 0.7995 (t) cc_final: 0.7516 (p) REVERT: A 1584 LYS cc_start: 0.7332 (mmtp) cc_final: 0.7009 (ptpt) REVERT: A 1612 GLN cc_start: 0.8371 (tt0) cc_final: 0.8053 (tt0) REVERT: A 1709 MET cc_start: 0.8920 (ttp) cc_final: 0.8548 (ttp) REVERT: A 2051 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: A 2310 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8405 (mt-10) REVERT: A 2412 MET cc_start: 0.7347 (tpp) cc_final: 0.7143 (tpt) REVERT: A 2614 ASP cc_start: 0.7544 (m-30) cc_final: 0.7049 (t0) REVERT: A 2759 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7839 (mm) REVERT: A 2763 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7517 (mtp85) REVERT: A 2848 GLU cc_start: 0.8276 (mt-10) cc_final: 0.8012 (pt0) REVERT: A 2953 MET cc_start: 0.8664 (mtp) cc_final: 0.8283 (mtp) REVERT: A 3048 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6838 (tp30) REVERT: A 3163 LYS cc_start: 0.7702 (ttmm) cc_final: 0.7366 (mtmm) REVERT: A 3169 MET cc_start: 0.8922 (mmt) cc_final: 0.8602 (mmp) REVERT: A 3188 HIS cc_start: 0.8076 (t70) cc_final: 0.7195 (m-70) REVERT: A 3191 ARG cc_start: 0.7430 (ttm170) cc_final: 0.7126 (mmm-85) REVERT: A 3595 GLN cc_start: 0.7851 (mp10) cc_final: 0.7210 (pp30) REVERT: A 3715 GLU cc_start: 0.8297 (tp30) cc_final: 0.7942 (tp30) REVERT: A 3729 SER cc_start: 0.8143 (m) cc_final: 0.7817 (p) REVERT: A 3795 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6665 (mm-30) REVERT: A 4022 GLU cc_start: 0.7743 (pt0) cc_final: 0.7377 (pp20) REVERT: A 4075 GLU cc_start: 0.7761 (tp30) cc_final: 0.6986 (pm20) REVERT: A 4128 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8523 (pmm) REVERT: A 4209 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7446 (tp30) REVERT: A 4224 ASP cc_start: 0.8117 (m-30) cc_final: 0.7828 (m-30) REVERT: A 4281 GLU cc_start: 0.7421 (mm-30) cc_final: 0.6890 (pp20) REVERT: A 4301 ARG cc_start: 0.7595 (ttm-80) cc_final: 0.7109 (mtm-85) REVERT: A 4415 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7523 (ttp80) REVERT: A 4419 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.7046 (ptt) REVERT: A 4456 VAL cc_start: 0.8126 (t) cc_final: 0.7720 (m) REVERT: A 4460 LEU cc_start: 0.8466 (tp) cc_final: 0.8195 (tm) REVERT: A 4490 GLN cc_start: 0.7202 (mt0) cc_final: 0.6891 (mt0) REVERT: A 4572 ASN cc_start: 0.7763 (t0) cc_final: 0.7432 (t0) REVERT: A 4583 THR cc_start: 0.8260 (m) cc_final: 0.7642 (p) REVERT: A 4617 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7637 (p0) outliers start: 45 outliers final: 28 residues processed: 345 average time/residue: 0.7182 time to fit residues: 280.1331 Evaluate side-chains 348 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 311 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1462 PHE Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 2051 GLN Chi-restraints excluded: chain A residue 2063 GLU Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2759 ILE Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2847 ASP Chi-restraints excluded: chain A residue 3048 GLU Chi-restraints excluded: chain A residue 3087 ASN Chi-restraints excluded: chain A residue 3164 ARG Chi-restraints excluded: chain A residue 3224 ILE Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3928 THR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4311 LEU Chi-restraints excluded: chain A residue 4415 ARG Chi-restraints excluded: chain A residue 4419 MET Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4604 VAL Chi-restraints excluded: chain A residue 4617 ASP Chi-restraints excluded: chain A residue 4623 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 184 optimal weight: 0.8980 chunk 216 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 278 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 269 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1566 GLN A2476 HIS A2730 HIS A3542 GLN A4054 HIS A4232 ASN A4307 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.140650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113598 restraints weight = 29482.262| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.62 r_work: 0.3269 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24213 Z= 0.134 Angle : 0.515 6.738 32838 Z= 0.259 Chirality : 0.040 0.157 3692 Planarity : 0.004 0.065 4206 Dihedral : 6.442 110.036 3261 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.65 % Allowed : 16.62 % Favored : 81.73 % 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: 2.22 (0.16), residues: 2929 helix: 2.21 (0.12), residues: 1729 sheet: -0.19 (0.32), residues: 256 loop : 0.70 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A1621 TYR 0.017 0.001 TYR A2748 PHE 0.017 0.001 PHE A1568 TRP 0.017 0.001 TRP A2234 HIS 0.004 0.001 HIS A3837 Details of bonding type rmsd covalent geometry : bond 0.00311 (24213) covalent geometry : angle 0.51509 (32838) hydrogen bonds : bond 0.03958 ( 1415) hydrogen bonds : angle 3.97943 ( 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 361 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 318 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1461 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7610 (tp30) REVERT: A 1462 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6713 (m-80) REVERT: A 1569 GLN cc_start: 0.7585 (tp40) cc_final: 0.6949 (tm-30) REVERT: A 1583 SER cc_start: 0.8035 (t) cc_final: 0.7551 (p) REVERT: A 1584 LYS cc_start: 0.7329 (mmtp) cc_final: 0.7005 (ptpt) REVERT: A 1709 MET cc_start: 0.8912 (ttp) cc_final: 0.8591 (ttp) REVERT: A 2051 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7657 (tt0) REVERT: A 2310 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8367 (mt-10) REVERT: A 2412 MET cc_start: 0.7373 (tpp) cc_final: 0.7169 (tpt) REVERT: A 2614 ASP cc_start: 0.7513 (m-30) cc_final: 0.7052 (t0) REVERT: A 2759 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7833 (mm) REVERT: A 2763 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7518 (mtp85) REVERT: A 2848 GLU cc_start: 0.8239 (mt-10) cc_final: 0.8003 (pt0) REVERT: A 2953 MET cc_start: 0.8655 (mtp) cc_final: 0.8263 (mtp) REVERT: A 3048 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6868 (tp30) REVERT: A 3163 LYS cc_start: 0.7702 (ttmm) cc_final: 0.7365 (mtmm) REVERT: A 3169 MET cc_start: 0.8856 (mmt) cc_final: 0.8570 (mmp) REVERT: A 3191 ARG cc_start: 0.7370 (ttm170) cc_final: 0.7044 (mmm-85) REVERT: A 3595 GLN cc_start: 0.7822 (mp10) cc_final: 0.7184 (pp30) REVERT: A 3715 GLU cc_start: 0.8271 (tp30) cc_final: 0.7909 (tp30) REVERT: A 3729 SER cc_start: 0.8143 (m) cc_final: 0.7785 (p) REVERT: A 3795 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6635 (mm-30) REVERT: A 3906 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: A 4022 GLU cc_start: 0.7791 (pt0) cc_final: 0.7455 (pp20) REVERT: A 4075 GLU cc_start: 0.7742 (tp30) cc_final: 0.6964 (pm20) REVERT: A 4128 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8542 (pmm) REVERT: A 4209 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7437 (tp30) REVERT: A 4224 ASP cc_start: 0.8117 (m-30) cc_final: 0.7825 (m-30) REVERT: A 4281 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6889 (pp20) REVERT: A 4301 ARG cc_start: 0.7553 (ttm-80) cc_final: 0.7070 (mtm-85) REVERT: A 4414 GLU cc_start: 0.7469 (pt0) cc_final: 0.7101 (pp20) REVERT: A 4415 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7514 (ttp80) REVERT: A 4419 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.7050 (ptt) REVERT: A 4423 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7622 (tt) REVERT: A 4456 VAL cc_start: 0.8093 (t) cc_final: 0.7674 (m) REVERT: A 4460 LEU cc_start: 0.8446 (tp) cc_final: 0.8183 (tm) REVERT: A 4490 GLN cc_start: 0.7232 (mt0) cc_final: 0.6940 (mt0) REVERT: A 4572 ASN cc_start: 0.7702 (t0) cc_final: 0.7404 (t0) REVERT: A 4583 THR cc_start: 0.8228 (m) cc_final: 0.7912 (t) outliers start: 43 outliers final: 28 residues processed: 343 average time/residue: 0.6757 time to fit residues: 261.6119 Evaluate side-chains 346 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 308 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1462 PHE Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 2051 GLN Chi-restraints excluded: chain A residue 2063 GLU Chi-restraints excluded: chain A residue 2592 VAL Chi-restraints excluded: chain A residue 2615 MET Chi-restraints excluded: chain A residue 2640 GLU Chi-restraints excluded: chain A residue 2759 ILE Chi-restraints excluded: chain A residue 2763 ARG Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2847 ASP Chi-restraints excluded: chain A residue 3006 GLU Chi-restraints excluded: chain A residue 3048 GLU Chi-restraints excluded: chain A residue 3087 ASN Chi-restraints excluded: chain A residue 3164 ARG Chi-restraints excluded: chain A residue 3224 ILE Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3794 VAL Chi-restraints excluded: chain A residue 3906 GLN Chi-restraints excluded: chain A residue 3928 THR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4251 ILE Chi-restraints excluded: chain A residue 4311 LEU Chi-restraints excluded: chain A residue 4415 ARG Chi-restraints excluded: chain A residue 4419 MET Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4604 VAL Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 205 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 226 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 240 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 275 optimal weight: 0.7980 chunk 88 optimal weight: 0.3980 chunk 102 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2476 HIS A3542 GLN A4054 HIS A4232 ASN A4307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.136560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.106893 restraints weight = 27213.140| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.74 r_work: 0.3083 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24213 Z= 0.119 Angle : 0.506 6.955 32838 Z= 0.254 Chirality : 0.040 0.154 3692 Planarity : 0.004 0.064 4206 Dihedral : 6.402 110.941 3261 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.77 % Allowed : 16.81 % Favored : 81.42 % 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: 2.27 (0.16), residues: 2929 helix: 2.28 (0.12), residues: 1721 sheet: -0.20 (0.32), residues: 256 loop : 0.69 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A1621 TYR 0.017 0.001 TYR A2748 PHE 0.015 0.001 PHE A1568 TRP 0.017 0.001 TRP A2234 HIS 0.004 0.001 HIS A3837 Details of bonding type rmsd covalent geometry : bond 0.00270 (24213) covalent geometry : angle 0.50587 (32838) hydrogen bonds : bond 0.03824 ( 1415) hydrogen bonds : angle 3.94927 ( 4098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10227.59 seconds wall clock time: 174 minutes 47.09 seconds (10487.09 seconds total)