Starting phenix.real_space_refine on Fri Jun 20 21:52:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bmj_44701/06_2025/9bmj_44701.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bmj_44701/06_2025/9bmj_44701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bmj_44701/06_2025/9bmj_44701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bmj_44701/06_2025/9bmj_44701.map" model { file = "/net/cci-nas-00/data/ceres_data/9bmj_44701/06_2025/9bmj_44701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bmj_44701/06_2025/9bmj_44701.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.067 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 1 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 38 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23706 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: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 113 Unusual residues: {' MG': 1, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 13.95, per 1000 atoms: 0.59 Number of scatterers: 23706 At special positions: 0 Unit cell: (145.824, 119.437, 209.709, 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 1 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: 6.55 Conformation dependent library (CDL) restraints added in 3.2 seconds 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5588 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 20 sheets defined 64.4% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.37 Creating SS restraints... Processing helix chain 'A' and resid 1457 through 1472 Processing helix chain 'A' and resid 1489 through 1510 removed outlier: 3.513A pdb=" N LEU A1493 " --> pdb=" O GLY A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1552 removed outlier: 4.235A pdb=" N PHE A1516 " --> pdb=" O TYR A1512 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU A1518 " --> pdb=" O LYS A1514 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASP A1519 " --> pdb=" O VAL A1515 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE A1538 " --> pdb=" O PHE A1534 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1561 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 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 1650 removed outlier: 3.610A pdb=" N LYS A1649 " --> pdb=" O ASN A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1658 removed outlier: 3.772A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1728 removed outlier: 4.416A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE A1727 " --> pdb=" O GLU A1723 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 removed outlier: 3.505A pdb=" N TYR A1745 " --> pdb=" O TRP A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1770 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 1986 removed outlier: 3.781A pdb=" N GLN A1973 " --> pdb=" O SER A1969 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN A1974 " --> pdb=" O ALA A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2034 Processing helix chain 'A' and resid 2045 through 2057 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix Processing helix chain 'A' and resid 2089 through 2118 removed outlier: 3.611A pdb=" N LEU A2093 " --> pdb=" O GLY A2089 " (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 2152 through 2165 removed outlier: 4.097A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) 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: 3.844A 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 2279 through 2290 Processing helix chain 'A' and resid 2293 through 2297 removed outlier: 3.593A 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 2357 Processing helix chain 'A' and resid 2370 through 2385 Processing helix chain 'A' and resid 2411 through 2424 Processing helix chain 'A' and resid 2431 through 2441 Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.675A pdb=" N CYS A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2503 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 Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.861A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2611 removed outlier: 3.803A pdb=" N ALA A2611 " --> pdb=" O SER A2607 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.382A 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 2764 Proline residue: A2760 - end of helix removed outlier: 4.635A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2784 removed outlier: 3.621A pdb=" N ALA A2771 " --> pdb=" O GLU A2767 " (cutoff:3.500A) Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.737A 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 Processing helix chain 'A' and resid 2862 through 2867 Processing helix chain 'A' and resid 2885 through 2904 removed outlier: 3.713A pdb=" N GLU A2902 " --> pdb=" O LYS A2898 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2927 Processing helix chain 'A' and resid 2942 through 2954 Processing helix chain 'A' and resid 2968 through 2985 Processing helix chain 'A' and resid 2997 through 2999 No H-bonds generated for 'chain 'A' and resid 2997 through 2999' Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 3.888A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 Processing helix chain 'A' and resid 3046 through 3061 Processing helix chain 'A' and resid 3071 through 3082 removed outlier: 3.742A pdb=" N ALA A3080 " --> pdb=" O LYS A3076 " (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 Processing helix chain 'A' and resid 3172 through 3242 removed outlier: 3.705A 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 3517 removed outlier: 4.549A pdb=" N LYS A3497 " --> pdb=" O SER A3493 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ASN A3498 " --> pdb=" O GLU A3494 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLY A3505 " --> pdb=" O SER A3501 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3582 Processing helix chain 'A' and resid 3594 through 3604 Processing helix chain 'A' and resid 3605 through 3608 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 3651 Processing helix chain 'A' and resid 3689 through 3696 Processing helix chain 'A' and resid 3704 through 3721 Processing helix chain 'A' and resid 3721 through 3755 Processing helix chain 'A' and resid 3763 through 3799 removed outlier: 3.832A pdb=" N ILE A3767 " --> pdb=" O ASP A3763 " (cutoff:3.500A) Processing helix chain 'A' and resid 3801 through 3818 Processing helix chain 'A' and resid 3819 through 3821 No H-bonds generated for 'chain 'A' and resid 3819 through 3821' Processing helix chain 'A' and resid 3828 through 3842 removed outlier: 3.559A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3847 removed outlier: 3.618A pdb=" N LYS A3847 " --> pdb=" O PRO A3844 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 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 3894 Processing helix chain 'A' and resid 3901 through 3911 Processing helix chain 'A' and resid 3912 through 3914 No H-bonds generated for 'chain 'A' and resid 3912 through 3914' Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3940 through 3945 removed outlier: 6.118A pdb=" N ALA A3943 " --> pdb=" O CYS A3940 " (cutoff:3.500A) Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 Processing helix chain 'A' and resid 3965 through 3970 removed outlier: 4.146A pdb=" N VAL A3970 " --> pdb=" O GLU A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4014 Processing helix chain 'A' and resid 4015 through 4017 No H-bonds generated for 'chain 'A' and resid 4015 through 4017' Processing helix chain 'A' and resid 4018 through 4023 removed outlier: 3.853A pdb=" N GLU A4022 " --> pdb=" O MET A4018 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN A4023 " --> pdb=" O SER A4019 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4018 through 4023' Processing helix chain 'A' and resid 4026 through 4033 removed outlier: 3.552A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4063 Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 3.952A pdb=" N LYS A4089 " --> pdb=" O ASN A4085 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4101 No H-bonds generated for 'chain 'A' and resid 4099 through 4101' Processing helix chain 'A' and resid 4102 through 4115 removed outlier: 3.765A 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: 3.525A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4175 through 4194 Processing helix chain 'A' and resid 4196 through 4201 Processing helix chain 'A' and resid 4208 through 4227 Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 Processing helix chain 'A' and resid 4317 through 4322 Processing helix chain 'A' and resid 4324 through 4327 Processing helix chain 'A' and resid 4328 through 4346 Processing helix chain 'A' and resid 4375 through 4391 Processing helix chain 'A' and resid 4401 through 4406 removed outlier: 3.723A pdb=" N LYS A4406 " --> pdb=" O VAL A4402 " (cutoff:3.500A) Processing helix chain 'A' and resid 4407 through 4439 removed outlier: 3.961A pdb=" N ARG A4415 " --> pdb=" O ARG A4411 " (cutoff:3.500A) Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4474 through 4498 removed outlier: 3.517A pdb=" N SER A4498 " --> pdb=" O LEU A4494 " (cutoff:3.500A) Processing helix chain 'A' and resid 4500 through 4507 Processing helix chain 'A' and resid 4516 through 4533 Processing helix chain 'A' and resid 4631 through 4638 Processing sheet with id=AA1, first strand: chain 'A' and resid 1476 through 1480 removed outlier: 4.026A pdb=" N ASP A1476 " --> pdb=" O ARG A1488 " (cutoff:3.500A) removed outlier: 3.836A 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: 7.690A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.682A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.723A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.500A pdb=" N PHE A1686 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 removed outlier: 6.564A pdb=" N GLY A1901 " --> pdb=" O ARG A2037 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU A2039 " --> pdb=" O GLY A1901 " (cutoff:3.500A) removed outlier: 6.437A 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 Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA7, first strand: chain 'A' and resid 2249 through 2254 removed outlier: 7.116A pdb=" N GLY A2219 " --> pdb=" O GLY A2360 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N VAL A2362 " --> pdb=" O GLY A2219 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N MET A2221 " --> pdb=" O VAL A2362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2266 through 2268 Processing sheet with id=AA9, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AB1, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 6.244A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2644 removed outlier: 6.862A pdb=" N VAL A2648 " --> pdb=" O LYS A2702 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2873 through 2874 removed outlier: 3.628A pdb=" N ILE A2882 " --> pdb=" O SER A2874 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2957 through 2959 removed outlier: 6.216A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU A2935 " --> pdb=" O MET A3068 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS A2932 " --> pdb=" O VAL A3090 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ASN A3092 " --> pdb=" O HIS A2932 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU A2934 " --> pdb=" O ASN A3092 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.292A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) 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: 6.139A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL A4041 " --> pdb=" O LEU A4126 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N MET A4128 " --> pdb=" O VAL A4041 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N MET A4043 " --> pdb=" O MET A4128 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A4042 " --> pdb=" O PHE A4145 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N PHE A4147 " --> pdb=" O LEU A4042 " (cutoff:3.500A) removed outlier: 6.732A 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 removed outlier: 6.785A pdb=" N ILE A4294 " --> pdb=" O LEU A4284 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 3.558A pdb=" N VAL A4509 " --> pdb=" O GLY A4559 " (cutoff:3.500A) removed outlier: 4.014A 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: 3.685A pdb=" N GLY A4567 " --> pdb=" O ILE A4581 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE A4581 " --> pdb=" O GLY A4567 " (cutoff:3.500A) removed outlier: 9.486A pdb=" N THR A4569 " --> pdb=" O ASN A4579 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N ASN A4579 " --> pdb=" O THR A4569 " (cutoff:3.500A) removed outlier: 10.078A pdb=" N ASN A4571 " --> pdb=" O LEU A4577 " (cutoff:3.500A) removed outlier: 10.176A pdb=" N LEU A4577 " --> pdb=" O ASN A4571 " (cutoff:3.500A) 1440 hydrogen bonds defined for protein. 4203 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: 17.08 Time building geometry restraints manager: 7.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7807 1.34 - 1.46: 4080 1.46 - 1.58: 12116 1.58 - 1.69: 14 1.69 - 1.81: 196 Bond restraints: 24213 Sorted by residual: bond pdb=" C LEU A2668 " pdb=" N PRO A2669 " ideal model delta sigma weight residual 1.331 1.368 -0.037 1.27e-02 6.20e+03 8.27e+00 bond pdb=" C GLU A2767 " pdb=" N PRO A2768 " ideal model delta sigma weight residual 1.336 1.352 -0.016 1.20e-02 6.94e+03 1.68e+00 bond pdb=" C4 ADP A4701 " pdb=" C5 ADP A4701 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.26e+00 bond pdb=" CA VAL A4545 " pdb=" CB VAL A4545 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.19e+00 bond pdb=" C4 ADP A4703 " pdb=" C5 ADP A4703 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.15e+00 ... (remaining 24208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 32056 1.34 - 2.68: 566 2.68 - 4.03: 163 4.03 - 5.37: 41 5.37 - 6.71: 12 Bond angle restraints: 32838 Sorted by residual: angle pdb=" C GLU A4599 " pdb=" CA GLU A4599 " pdb=" CB GLU A4599 " ideal model delta sigma weight residual 116.34 110.54 5.80 1.40e+00 5.10e-01 1.72e+01 angle pdb=" CA GLY A2266 " pdb=" C GLY A2266 " pdb=" O GLY A2266 " ideal model delta sigma weight residual 122.37 120.01 2.36 7.30e-01 1.88e+00 1.04e+01 angle pdb=" CA GLY A2266 " pdb=" C GLY A2266 " pdb=" N THR A2267 " ideal model delta sigma weight residual 114.13 117.62 -3.49 1.11e+00 8.12e-01 9.89e+00 angle pdb=" N GLU A3785 " pdb=" CA GLU A3785 " pdb=" CB GLU A3785 " ideal model delta sigma weight residual 110.16 114.79 -4.63 1.48e+00 4.57e-01 9.78e+00 angle pdb=" CA GLU A4148 " pdb=" C GLU A4148 " pdb=" N PRO A4149 " ideal model delta sigma weight residual 117.68 119.83 -2.15 7.10e-01 1.98e+00 9.20e+00 ... (remaining 32833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.68: 13416 19.68 - 39.36: 1044 39.36 - 59.04: 163 59.04 - 78.72: 61 78.72 - 98.40: 9 Dihedral angle restraints: 14693 sinusoidal: 6090 harmonic: 8603 Sorted by residual: dihedral pdb=" C5' ADP A4703 " pdb=" O5' ADP A4703 " pdb=" PA ADP A4703 " pdb=" O2A ADP A4703 " ideal model delta sinusoidal sigma weight residual -60.00 -158.39 98.40 1 2.00e+01 2.50e-03 2.75e+01 dihedral pdb=" CA ASP A2885 " pdb=" CB ASP A2885 " pdb=" CG ASP A2885 " pdb=" OD1 ASP A2885 " ideal model delta sinusoidal sigma weight residual -30.00 -89.59 59.59 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CB GLU A2814 " pdb=" CG GLU A2814 " pdb=" CD GLU A2814 " pdb=" OE1 GLU A2814 " ideal model delta sinusoidal sigma weight residual 0.00 89.49 -89.49 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 14690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2624 0.035 - 0.071: 767 0.071 - 0.106: 243 0.106 - 0.142: 55 0.142 - 0.177: 3 Chirality restraints: 3692 Sorted by residual: chirality pdb=" CB ILE A1538 " pdb=" CA ILE A1538 " pdb=" CG1 ILE A1538 " pdb=" CG2 ILE A1538 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CB THR A3663 " pdb=" CA THR A3663 " pdb=" OG1 THR A3663 " pdb=" CG2 THR A3663 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA VAL A4469 " pdb=" N VAL A4469 " pdb=" C VAL A4469 " pdb=" CB VAL A4469 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 3689 not shown) Planarity restraints: 4206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A1543 " 0.010 2.00e-02 2.50e+03 2.00e-02 3.98e+00 pdb=" C ARG A1543 " -0.035 2.00e-02 2.50e+03 pdb=" O ARG A1543 " 0.013 2.00e-02 2.50e+03 pdb=" N TRP A1544 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A1542 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.40e+00 pdb=" C ARG A1542 " 0.032 2.00e-02 2.50e+03 pdb=" O ARG A1542 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG A1543 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A2773 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.33e+00 pdb=" C MET A2773 " -0.032 2.00e-02 2.50e+03 pdb=" O MET A2773 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL A2774 " 0.011 2.00e-02 2.50e+03 ... (remaining 4203 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 132 2.56 - 3.15: 19048 3.15 - 3.73: 37948 3.73 - 4.32: 52033 4.32 - 4.90: 89349 Nonbonded interactions: 198510 Sorted by model distance: nonbonded pdb=" OE2 GLU A2344 " pdb="MG MG A4705 " model vdw 1.978 2.170 nonbonded pdb=" OH TYR A2967 " pdb=" OD2 ASP A2975 " model vdw 2.172 3.040 nonbonded pdb=" OG SER A4319 " pdb=" OD1 ASN A4325 " model vdw 2.175 3.040 nonbonded pdb=" O ASP A4631 " pdb=" OG SER A4634 " model vdw 2.230 3.040 nonbonded pdb=" OE1 GLU A2174 " pdb=" OG1 THR A2176 " model vdw 2.235 3.040 ... (remaining 198505 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: 4.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.980 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 64.920 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 : 0.003 0.041 24213 Z= 0.124 Angle : 0.510 6.712 32838 Z= 0.267 Chirality : 0.039 0.177 3692 Planarity : 0.004 0.044 4206 Dihedral : 14.630 98.396 9105 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.16), residues: 2929 helix: 2.26 (0.13), residues: 1709 sheet: -0.55 (0.31), residues: 266 loop : 0.56 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A4592 HIS 0.003 0.001 HIS A2730 PHE 0.014 0.001 PHE A4620 TYR 0.027 0.001 TYR A3836 ARG 0.007 0.000 ARG A2763 Details of bonding type rmsd hydrogen bonds : bond 0.11624 ( 1440) hydrogen bonds : angle 5.12623 ( 4203) covalent geometry : bond 0.00262 (24213) covalent geometry : angle 0.51047 (32838) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 3.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1612 GLN cc_start: 0.7395 (tt0) cc_final: 0.6759 (tt0) REVERT: A 1745 TYR cc_start: 0.7976 (m-80) cc_final: 0.7321 (m-80) REVERT: A 1997 ILE cc_start: 0.8167 (mm) cc_final: 0.7854 (mm) REVERT: A 2799 MET cc_start: 0.8844 (mmm) cc_final: 0.8599 (mmm) REVERT: A 2901 TYR cc_start: 0.8254 (m-10) cc_final: 0.7752 (m-10) REVERT: A 3030 MET cc_start: 0.8474 (mmp) cc_final: 0.8132 (mmp) REVERT: A 3068 MET cc_start: 0.8967 (ptm) cc_final: 0.8765 (ptm) REVERT: A 3088 ARG cc_start: 0.7989 (mmm160) cc_final: 0.7556 (mmt-90) REVERT: A 3451 TYR cc_start: 0.5471 (m-80) cc_final: 0.4672 (p90) REVERT: A 3480 LYS cc_start: 0.8279 (mmmt) cc_final: 0.7999 (mttt) REVERT: A 4049 TYR cc_start: 0.7091 (m-80) cc_final: 0.6859 (m-80) REVERT: A 4332 LEU cc_start: 0.8606 (mt) cc_final: 0.8384 (mt) REVERT: A 4459 ILE cc_start: 0.8817 (mt) cc_final: 0.8584 (mt) REVERT: A 4593 VAL cc_start: 0.6945 (m) cc_final: 0.6659 (p) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.4037 time to fit residues: 270.6669 Evaluate side-chains 301 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 2.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 247 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 123 optimal weight: 0.0970 chunk 75 optimal weight: 0.6980 chunk 149 optimal weight: 0.2980 chunk 118 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 170 optimal weight: 0.5980 chunk 266 optimal weight: 0.0470 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1646 ASN A2752 ASN A3038 GLN A3523 GLN A3754 ASN ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4444 GLN A4506 ASN A4526 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.135790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.106697 restraints weight = 30033.836| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.16 r_work: 0.3113 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24213 Z= 0.118 Angle : 0.496 6.934 32838 Z= 0.250 Chirality : 0.039 0.140 3692 Planarity : 0.004 0.043 4206 Dihedral : 5.707 98.895 3261 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.96 % Allowed : 6.56 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.16), residues: 2929 helix: 2.49 (0.12), residues: 1731 sheet: -0.49 (0.31), residues: 264 loop : 0.52 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A4592 HIS 0.006 0.001 HIS A3200 PHE 0.023 0.001 PHE A3996 TYR 0.022 0.001 TYR A1546 ARG 0.005 0.000 ARG A3585 Details of bonding type rmsd hydrogen bonds : bond 0.04131 ( 1440) hydrogen bonds : angle 4.05220 ( 4203) covalent geometry : bond 0.00248 (24213) covalent geometry : angle 0.49574 (32838) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 315 time to evaluate : 2.871 Fit side-chains revert: symmetry clash REVERT: A 1516 PHE cc_start: 0.7511 (m-80) cc_final: 0.7271 (m-80) REVERT: A 1631 PHE cc_start: 0.8213 (m-80) cc_final: 0.7935 (m-80) REVERT: A 1745 TYR cc_start: 0.8315 (m-80) cc_final: 0.7535 (m-80) REVERT: A 1893 THR cc_start: 0.7987 (p) cc_final: 0.7651 (p) REVERT: A 1997 ILE cc_start: 0.8109 (mm) cc_final: 0.7811 (mm) REVERT: A 2041 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8399 (mtt) REVERT: A 2133 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7686 (mt-10) REVERT: A 2799 MET cc_start: 0.8854 (mmm) cc_final: 0.8558 (mmm) REVERT: A 2901 TYR cc_start: 0.8082 (m-10) cc_final: 0.7586 (m-10) REVERT: A 3030 MET cc_start: 0.8713 (mmp) cc_final: 0.8346 (mmp) REVERT: A 3068 MET cc_start: 0.9253 (ptm) cc_final: 0.9022 (ptm) REVERT: A 3480 LYS cc_start: 0.8469 (mmmt) cc_final: 0.8021 (mttt) REVERT: A 3516 TYR cc_start: 0.9098 (m-80) cc_final: 0.8808 (m-10) REVERT: A 3799 GLN cc_start: 0.8322 (tp40) cc_final: 0.8117 (tp40) REVERT: A 4049 TYR cc_start: 0.7371 (m-80) cc_final: 0.6769 (m-80) REVERT: A 4276 ARG cc_start: 0.8026 (mtm-85) cc_final: 0.7605 (mtm110) REVERT: A 4307 GLN cc_start: 0.7609 (tt0) cc_final: 0.7105 (mt0) REVERT: A 4332 LEU cc_start: 0.8125 (mt) cc_final: 0.7885 (mt) REVERT: A 4339 MET cc_start: 0.7904 (ttt) cc_final: 0.7616 (ttt) REVERT: A 4347 GLN cc_start: 0.7368 (tt0) cc_final: 0.7158 (tt0) REVERT: A 4544 ASN cc_start: 0.7640 (t0) cc_final: 0.7413 (t0) REVERT: A 4571 ASN cc_start: 0.7611 (m-40) cc_final: 0.6922 (p0) outliers start: 25 outliers final: 17 residues processed: 332 average time/residue: 0.3945 time to fit residues: 203.5973 Evaluate side-chains 290 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 272 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1486 LEU Chi-restraints excluded: chain A residue 1491 ASP Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain A residue 2076 CYS Chi-restraints excluded: chain A residue 2528 THR Chi-restraints excluded: chain A residue 2649 VAL Chi-restraints excluded: chain A residue 2860 ASN Chi-restraints excluded: chain A residue 3009 ASN Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3798 SER Chi-restraints excluded: chain A residue 3962 ASP Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4090 SER Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4437 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 281 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 237 optimal weight: 0.0970 chunk 222 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1559 HIS A2067 ASN A2079 GLN A3152 GLN A3537 GLN A3622 ASN ** A4397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4589 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.130073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.100437 restraints weight = 30331.764| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.17 r_work: 0.3017 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24213 Z= 0.183 Angle : 0.549 6.874 32838 Z= 0.275 Chirality : 0.041 0.184 3692 Planarity : 0.004 0.052 4206 Dihedral : 5.662 89.061 3261 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.69 % Allowed : 8.37 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.16), residues: 2929 helix: 2.31 (0.12), residues: 1732 sheet: -0.67 (0.32), residues: 257 loop : 0.40 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A2234 HIS 0.005 0.001 HIS A3200 PHE 0.018 0.002 PHE A4620 TYR 0.026 0.002 TYR A1546 ARG 0.010 0.001 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.04558 ( 1440) hydrogen bonds : angle 4.05933 ( 4203) covalent geometry : bond 0.00440 (24213) covalent geometry : angle 0.54933 (32838) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 278 time to evaluate : 2.978 Fit side-chains revert: symmetry clash REVERT: A 1516 PHE cc_start: 0.7575 (m-80) cc_final: 0.7345 (m-80) REVERT: A 1602 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7757 (mt-10) REVERT: A 1997 ILE cc_start: 0.8211 (mm) cc_final: 0.7876 (mm) REVERT: A 2012 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8623 (ttp) REVERT: A 2189 MET cc_start: 0.8353 (ttm) cc_final: 0.7933 (ttm) REVERT: A 2217 ASN cc_start: 0.8466 (m110) cc_final: 0.8231 (m110) REVERT: A 2412 MET cc_start: 0.7738 (tpt) cc_final: 0.7493 (tpt) REVERT: A 2654 GLN cc_start: 0.8241 (tt0) cc_final: 0.7861 (tt0) REVERT: A 2779 MET cc_start: 0.8706 (mtm) cc_final: 0.8493 (mtp) REVERT: A 2782 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7114 (mm-30) REVERT: A 2799 MET cc_start: 0.8952 (mmm) cc_final: 0.8736 (mmm) REVERT: A 3030 MET cc_start: 0.8793 (mmp) cc_final: 0.8245 (mmp) REVERT: A 3068 MET cc_start: 0.9312 (ptm) cc_final: 0.9082 (ptm) REVERT: A 3478 LEU cc_start: 0.6912 (tp) cc_final: 0.6669 (mp) REVERT: A 3480 LYS cc_start: 0.8646 (mmmt) cc_final: 0.8145 (mttt) REVERT: A 3524 MET cc_start: 0.8635 (tpp) cc_final: 0.8340 (tpp) REVERT: A 3663 THR cc_start: 0.8731 (t) cc_final: 0.8421 (p) REVERT: A 4049 TYR cc_start: 0.7620 (m-80) cc_final: 0.6819 (m-80) REVERT: A 4061 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8058 (mt-10) REVERT: A 4276 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7652 (mtm110) REVERT: A 4292 LYS cc_start: 0.7257 (mmtt) cc_final: 0.6878 (mmtm) REVERT: A 4307 GLN cc_start: 0.7753 (tt0) cc_final: 0.7200 (mt0) REVERT: A 4377 MET cc_start: 0.7326 (mtt) cc_final: 0.6847 (mtm) REVERT: A 4386 ASN cc_start: 0.7346 (m-40) cc_final: 0.7029 (m-40) REVERT: A 4416 GLU cc_start: 0.8379 (tp30) cc_final: 0.8130 (tp30) REVERT: A 4425 GLN cc_start: 0.8205 (tp-100) cc_final: 0.7983 (tp-100) REVERT: A 4544 ASN cc_start: 0.7791 (t0) cc_final: 0.7566 (t0) REVERT: A 4571 ASN cc_start: 0.7553 (m-40) cc_final: 0.6907 (p0) REVERT: A 4592 TRP cc_start: 0.6677 (m100) cc_final: 0.6240 (m100) outliers start: 44 outliers final: 35 residues processed: 312 average time/residue: 0.4718 time to fit residues: 235.3444 Evaluate side-chains 293 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 257 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1486 LEU Chi-restraints excluded: chain A residue 1491 ASP Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2076 CYS Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2212 GLN Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2272 THR Chi-restraints excluded: chain A residue 2528 THR Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2649 VAL Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2788 THR Chi-restraints excluded: chain A residue 2860 ASN Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 3009 ASN Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3798 SER Chi-restraints excluded: chain A residue 3948 ILE Chi-restraints excluded: chain A residue 3962 ASP Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4090 SER Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4129 GLU Chi-restraints excluded: chain A residue 4189 ILE Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4469 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4542 GLU Chi-restraints excluded: chain A residue 4589 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 200 optimal weight: 0.0570 chunk 177 optimal weight: 4.9990 chunk 259 optimal weight: 0.2980 chunk 162 optimal weight: 0.4980 chunk 246 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 69 optimal weight: 0.3980 chunk 282 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1465 GLN A1755 GLN A3523 GLN A4397 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.129535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.102087 restraints weight = 30387.427| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.99 r_work: 0.3069 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 24213 Z= 0.106 Angle : 0.472 6.843 32838 Z= 0.236 Chirality : 0.038 0.146 3692 Planarity : 0.004 0.071 4206 Dihedral : 5.474 87.956 3261 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.19 % Allowed : 9.87 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.16), residues: 2929 helix: 2.52 (0.12), residues: 1731 sheet: -0.63 (0.32), residues: 257 loop : 0.48 (0.21), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2234 HIS 0.003 0.001 HIS A3200 PHE 0.025 0.001 PHE A3996 TYR 0.020 0.001 TYR A1546 ARG 0.014 0.000 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 1440) hydrogen bonds : angle 3.86660 ( 4203) covalent geometry : bond 0.00230 (24213) covalent geometry : angle 0.47213 (32838) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 289 time to evaluate : 2.727 Fit side-chains revert: symmetry clash REVERT: A 1460 GLU cc_start: 0.7689 (tp30) cc_final: 0.7444 (tp30) REVERT: A 1546 TYR cc_start: 0.8040 (p90) cc_final: 0.7757 (p90) REVERT: A 2012 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8562 (ttp) REVERT: A 2189 MET cc_start: 0.8174 (ttm) cc_final: 0.7913 (ttm) REVERT: A 2320 ASP cc_start: 0.8021 (m-30) cc_final: 0.7755 (m-30) REVERT: A 2561 LYS cc_start: 0.8311 (mtmt) cc_final: 0.8106 (mtmm) REVERT: A 2654 GLN cc_start: 0.8212 (tt0) cc_final: 0.7775 (tt0) REVERT: A 2779 MET cc_start: 0.8443 (mtm) cc_final: 0.8124 (mtp) REVERT: A 2782 GLU cc_start: 0.7637 (mt-10) cc_final: 0.6861 (mm-30) REVERT: A 3012 LEU cc_start: 0.8174 (mt) cc_final: 0.7972 (mt) REVERT: A 3030 MET cc_start: 0.8537 (mmp) cc_final: 0.8079 (mmp) REVERT: A 3068 MET cc_start: 0.9180 (ptm) cc_final: 0.8933 (ptm) REVERT: A 3480 LYS cc_start: 0.8578 (mmmt) cc_final: 0.8105 (mttt) REVERT: A 3663 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8355 (p) REVERT: A 4049 TYR cc_start: 0.7477 (m-80) cc_final: 0.6615 (m-80) REVERT: A 4276 ARG cc_start: 0.7887 (mtm-85) cc_final: 0.7483 (mtm110) REVERT: A 4292 LYS cc_start: 0.7193 (mmtt) cc_final: 0.6813 (mmtm) REVERT: A 4304 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7392 (mp0) REVERT: A 4307 GLN cc_start: 0.7540 (tt0) cc_final: 0.6870 (mt0) REVERT: A 4377 MET cc_start: 0.7138 (mtt) cc_final: 0.6670 (mtm) REVERT: A 4386 ASN cc_start: 0.7305 (m-40) cc_final: 0.6981 (m-40) REVERT: A 4416 GLU cc_start: 0.8255 (tp30) cc_final: 0.7972 (tp30) REVERT: A 4425 GLN cc_start: 0.8067 (tp-100) cc_final: 0.7732 (tt0) REVERT: A 4481 ASP cc_start: 0.7402 (t0) cc_final: 0.6889 (t0) REVERT: A 4571 ASN cc_start: 0.7465 (m-40) cc_final: 0.6747 (p0) REVERT: A 4592 TRP cc_start: 0.6541 (m100) cc_final: 0.5116 (m100) outliers start: 31 outliers final: 23 residues processed: 309 average time/residue: 0.3952 time to fit residues: 189.3207 Evaluate side-chains 287 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 262 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1486 LEU Chi-restraints excluded: chain A residue 1491 ASP Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1621 ARG Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2076 CYS Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2649 VAL Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 3009 ASN Chi-restraints excluded: chain A residue 3043 MET Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3663 THR Chi-restraints excluded: chain A residue 3798 SER Chi-restraints excluded: chain A residue 3962 ASP Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4090 SER Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4542 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 159 optimal weight: 8.9990 chunk 169 optimal weight: 0.3980 chunk 182 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 54 optimal weight: 0.0010 chunk 275 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 249 optimal weight: 0.9980 chunk 187 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1559 HIS ** A1810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3104 GLN A4038 ASN A4063 ASN A4381 HIS A4566 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.129720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.102018 restraints weight = 30199.484| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.04 r_work: 0.3059 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24213 Z= 0.113 Angle : 0.470 8.333 32838 Z= 0.232 Chirality : 0.038 0.144 3692 Planarity : 0.004 0.052 4206 Dihedral : 5.344 84.351 3261 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.57 % Allowed : 10.29 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.16), residues: 2929 helix: 2.57 (0.12), residues: 1731 sheet: -0.61 (0.32), residues: 248 loop : 0.47 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.003 0.001 HIS A3200 PHE 0.016 0.001 PHE A4620 TYR 0.021 0.001 TYR A1546 ARG 0.011 0.000 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 1440) hydrogen bonds : angle 3.79274 ( 4203) covalent geometry : bond 0.00255 (24213) covalent geometry : angle 0.46957 (32838) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 280 time to evaluate : 2.664 Fit side-chains revert: symmetry clash REVERT: A 1464 LYS cc_start: 0.8270 (mmtt) cc_final: 0.8057 (mmmt) REVERT: A 1516 PHE cc_start: 0.7579 (m-80) cc_final: 0.7351 (m-80) REVERT: A 2012 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8590 (ttp) REVERT: A 2172 ARG cc_start: 0.7652 (tmm-80) cc_final: 0.7071 (tmm-80) REVERT: A 2180 GLU cc_start: 0.7875 (tp30) cc_final: 0.7579 (tp30) REVERT: A 2435 LYS cc_start: 0.8588 (mtpt) cc_final: 0.8378 (mtpt) REVERT: A 2471 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7828 (tt0) REVERT: A 2561 LYS cc_start: 0.8413 (mtmt) cc_final: 0.8205 (mtmm) REVERT: A 2578 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7735 (mt-10) REVERT: A 2654 GLN cc_start: 0.8300 (tt0) cc_final: 0.7954 (tt0) REVERT: A 2773 MET cc_start: 0.8777 (mtp) cc_final: 0.8336 (mtm) REVERT: A 2779 MET cc_start: 0.8697 (mtm) cc_final: 0.8380 (mtp) REVERT: A 2782 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7086 (mm-30) REVERT: A 3012 LEU cc_start: 0.8576 (mt) cc_final: 0.8363 (mt) REVERT: A 3030 MET cc_start: 0.8695 (mmp) cc_final: 0.8210 (mmp) REVERT: A 3068 MET cc_start: 0.9259 (ptm) cc_final: 0.9054 (ptm) REVERT: A 3478 LEU cc_start: 0.6871 (tp) cc_final: 0.6553 (mp) REVERT: A 3480 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8124 (mttt) REVERT: A 3663 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8371 (p) REVERT: A 4029 HIS cc_start: 0.7469 (t70) cc_final: 0.7161 (t70) REVERT: A 4049 TYR cc_start: 0.7490 (m-80) cc_final: 0.7166 (m-80) REVERT: A 4061 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8058 (mt-10) REVERT: A 4075 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7125 (tp30) REVERT: A 4276 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.7628 (mtm110) REVERT: A 4292 LYS cc_start: 0.7384 (mmtt) cc_final: 0.7013 (mmtm) REVERT: A 4307 GLN cc_start: 0.7755 (tt0) cc_final: 0.7106 (mt0) REVERT: A 4377 MET cc_start: 0.7340 (mtt) cc_final: 0.6828 (mtm) REVERT: A 4386 ASN cc_start: 0.7350 (m-40) cc_final: 0.7055 (m-40) REVERT: A 4412 PHE cc_start: 0.7945 (t80) cc_final: 0.7689 (t80) REVERT: A 4425 GLN cc_start: 0.8204 (tp-100) cc_final: 0.7919 (tt0) REVERT: A 4571 ASN cc_start: 0.7537 (m-40) cc_final: 0.6963 (p0) REVERT: A 4592 TRP cc_start: 0.6751 (m100) cc_final: 0.5885 (m100) REVERT: A 4619 ILE cc_start: 0.8888 (mm) cc_final: 0.8540 (mm) outliers start: 41 outliers final: 33 residues processed: 308 average time/residue: 0.3944 time to fit residues: 188.2500 Evaluate side-chains 301 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 265 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1486 LEU Chi-restraints excluded: chain A residue 1491 ASP Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2076 CYS Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2212 GLN Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2272 THR Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2649 VAL Chi-restraints excluded: chain A residue 2788 THR Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 3009 ASN Chi-restraints excluded: chain A residue 3043 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3663 THR Chi-restraints excluded: chain A residue 3798 SER Chi-restraints excluded: chain A residue 3962 ASP Chi-restraints excluded: chain A residue 3978 THR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4075 GLU Chi-restraints excluded: chain A residue 4090 SER Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4542 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 183 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 226 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.1980 chunk 275 optimal weight: 0.3980 chunk 249 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1559 HIS A1598 GLN ** A1810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2215 GLN A4038 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.131996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.102297 restraints weight = 30217.502| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.18 r_work: 0.3048 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24213 Z= 0.107 Angle : 0.459 7.309 32838 Z= 0.229 Chirality : 0.038 0.145 3692 Planarity : 0.003 0.046 4206 Dihedral : 5.275 85.603 3261 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.69 % Allowed : 10.71 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.16), residues: 2929 helix: 2.64 (0.12), residues: 1732 sheet: -0.60 (0.32), residues: 243 loop : 0.52 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.004 0.001 HIS A1559 PHE 0.014 0.001 PHE A4620 TYR 0.023 0.001 TYR A1546 ARG 0.008 0.000 ARG A2863 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 1440) hydrogen bonds : angle 3.76476 ( 4203) covalent geometry : bond 0.00241 (24213) covalent geometry : angle 0.45854 (32838) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 281 time to evaluate : 2.670 Fit side-chains revert: symmetry clash REVERT: A 1516 PHE cc_start: 0.7553 (m-80) cc_final: 0.7295 (m-80) REVERT: A 1621 ARG cc_start: 0.7681 (ttp-110) cc_final: 0.7450 (ttp-110) REVERT: A 2012 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8596 (ttp) REVERT: A 2172 ARG cc_start: 0.7664 (tmm-80) cc_final: 0.7055 (tmm-80) REVERT: A 2180 GLU cc_start: 0.7866 (tp30) cc_final: 0.7512 (tp30) REVERT: A 2435 LYS cc_start: 0.8584 (mtpt) cc_final: 0.8365 (mtpt) REVERT: A 2471 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7719 (tt0) REVERT: A 2654 GLN cc_start: 0.8328 (tt0) cc_final: 0.7856 (tt0) REVERT: A 2773 MET cc_start: 0.8773 (mtp) cc_final: 0.8370 (mtm) REVERT: A 2782 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7084 (mm-30) REVERT: A 2867 MET cc_start: 0.8492 (mmm) cc_final: 0.8076 (mtm) REVERT: A 3012 LEU cc_start: 0.8678 (mt) cc_final: 0.8452 (mt) REVERT: A 3030 MET cc_start: 0.8601 (mmp) cc_final: 0.8121 (mmp) REVERT: A 3068 MET cc_start: 0.9264 (ptm) cc_final: 0.9058 (ptm) REVERT: A 3478 LEU cc_start: 0.6891 (tp) cc_final: 0.6609 (mp) REVERT: A 3480 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8132 (mttt) REVERT: A 3663 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8397 (p) REVERT: A 4049 TYR cc_start: 0.7494 (m-80) cc_final: 0.7147 (m-80) REVERT: A 4061 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7994 (mt-10) REVERT: A 4075 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7042 (tp30) REVERT: A 4276 ARG cc_start: 0.8029 (mtm-85) cc_final: 0.7640 (mtm110) REVERT: A 4292 LYS cc_start: 0.7410 (mmtt) cc_final: 0.7039 (mmtm) REVERT: A 4307 GLN cc_start: 0.7763 (tt0) cc_final: 0.7085 (mt0) REVERT: A 4377 MET cc_start: 0.7336 (mtt) cc_final: 0.6838 (mtm) REVERT: A 4386 ASN cc_start: 0.7375 (m-40) cc_final: 0.7108 (m-40) REVERT: A 4412 PHE cc_start: 0.7902 (t80) cc_final: 0.7612 (t80) REVERT: A 4425 GLN cc_start: 0.8225 (tp-100) cc_final: 0.7945 (tt0) REVERT: A 4426 ASP cc_start: 0.8234 (t70) cc_final: 0.8017 (m-30) REVERT: A 4477 GLN cc_start: 0.8621 (mt0) cc_final: 0.7607 (pt0) REVERT: A 4571 ASN cc_start: 0.7556 (m-40) cc_final: 0.6962 (p0) REVERT: A 4592 TRP cc_start: 0.6801 (m100) cc_final: 0.5973 (m100) outliers start: 44 outliers final: 35 residues processed: 313 average time/residue: 0.3963 time to fit residues: 191.6258 Evaluate side-chains 307 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 269 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1486 LEU Chi-restraints excluded: chain A residue 1491 ASP Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2076 CYS Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2238 LEU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2649 VAL Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2788 THR Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 3009 ASN Chi-restraints excluded: chain A residue 3043 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3663 THR Chi-restraints excluded: chain A residue 3798 SER Chi-restraints excluded: chain A residue 3948 ILE Chi-restraints excluded: chain A residue 3962 ASP Chi-restraints excluded: chain A residue 3978 THR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4075 GLU Chi-restraints excluded: chain A residue 4090 SER Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4542 GLU Chi-restraints excluded: chain A residue 4576 SER Chi-restraints excluded: chain A residue 4605 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 65 optimal weight: 0.0050 chunk 42 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 222 optimal weight: 3.9990 chunk 291 optimal weight: 0.3980 chunk 283 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN ** A1810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4029 HIS A4038 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.131664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.102053 restraints weight = 30358.097| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.17 r_work: 0.3049 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24213 Z= 0.110 Angle : 0.463 7.485 32838 Z= 0.230 Chirality : 0.038 0.145 3692 Planarity : 0.003 0.047 4206 Dihedral : 5.252 88.775 3261 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.65 % Allowed : 10.94 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.16), residues: 2929 helix: 2.63 (0.12), residues: 1735 sheet: -0.63 (0.32), residues: 243 loop : 0.55 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.008 0.001 HIS A4029 PHE 0.014 0.001 PHE A4620 TYR 0.023 0.001 TYR A1546 ARG 0.007 0.000 ARG A2863 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 1440) hydrogen bonds : angle 3.76439 ( 4203) covalent geometry : bond 0.00248 (24213) covalent geometry : angle 0.46280 (32838) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 279 time to evaluate : 3.991 Fit side-chains revert: symmetry clash REVERT: A 1464 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7999 (mmmt) REVERT: A 1516 PHE cc_start: 0.7588 (m-80) cc_final: 0.7370 (m-80) REVERT: A 2012 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8635 (ttp) REVERT: A 2172 ARG cc_start: 0.7669 (tmm-80) cc_final: 0.7055 (tmm-80) REVERT: A 2180 GLU cc_start: 0.7855 (tp30) cc_final: 0.7383 (tp30) REVERT: A 2435 LYS cc_start: 0.8639 (mtpt) cc_final: 0.8423 (mtpt) REVERT: A 2471 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7730 (tt0) REVERT: A 2654 GLN cc_start: 0.8373 (tt0) cc_final: 0.7869 (tt0) REVERT: A 2773 MET cc_start: 0.8777 (mtp) cc_final: 0.8369 (mtm) REVERT: A 2782 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7055 (mm-30) REVERT: A 2867 MET cc_start: 0.8538 (mmm) cc_final: 0.8192 (mtm) REVERT: A 2869 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6736 (tpm170) REVERT: A 3012 LEU cc_start: 0.8586 (mt) cc_final: 0.8327 (mt) REVERT: A 3030 MET cc_start: 0.8610 (mmp) cc_final: 0.8122 (mmp) REVERT: A 3068 MET cc_start: 0.9276 (ptm) cc_final: 0.9071 (ptm) REVERT: A 3478 LEU cc_start: 0.6907 (tp) cc_final: 0.6643 (mp) REVERT: A 3480 LYS cc_start: 0.8705 (mmmt) cc_final: 0.8186 (mttt) REVERT: A 3542 GLN cc_start: 0.8348 (mm110) cc_final: 0.8025 (mm-40) REVERT: A 3663 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8413 (p) REVERT: A 4049 TYR cc_start: 0.7525 (m-80) cc_final: 0.7155 (m-80) REVERT: A 4061 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7956 (mt-10) REVERT: A 4075 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7055 (tp30) REVERT: A 4157 MET cc_start: 0.8640 (mtp) cc_final: 0.7801 (mtp) REVERT: A 4192 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8060 (mm-30) REVERT: A 4276 ARG cc_start: 0.8210 (mtm-85) cc_final: 0.7778 (mtm110) REVERT: A 4292 LYS cc_start: 0.7509 (mmtt) cc_final: 0.7158 (mmtm) REVERT: A 4307 GLN cc_start: 0.7826 (tt0) cc_final: 0.7174 (mt0) REVERT: A 4377 MET cc_start: 0.7337 (mtt) cc_final: 0.6824 (mtm) REVERT: A 4386 ASN cc_start: 0.7388 (m-40) cc_final: 0.7119 (m-40) REVERT: A 4412 PHE cc_start: 0.7958 (t80) cc_final: 0.7723 (t80) REVERT: A 4425 GLN cc_start: 0.8286 (tp-100) cc_final: 0.8035 (tt0) REVERT: A 4426 ASP cc_start: 0.8243 (t70) cc_final: 0.8007 (m-30) REVERT: A 4477 GLN cc_start: 0.8649 (mt0) cc_final: 0.7701 (pt0) REVERT: A 4571 ASN cc_start: 0.7530 (m-40) cc_final: 0.6975 (p0) REVERT: A 4592 TRP cc_start: 0.6802 (m100) cc_final: 0.6210 (m100) REVERT: A 4594 LYS cc_start: 0.6673 (mmmt) cc_final: 0.6418 (mmmt) outliers start: 43 outliers final: 37 residues processed: 310 average time/residue: 0.8337 time to fit residues: 413.7456 Evaluate side-chains 311 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 270 time to evaluate : 4.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1486 LEU Chi-restraints excluded: chain A residue 1491 ASP Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2215 GLN Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2238 LEU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2649 VAL Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2788 THR Chi-restraints excluded: chain A residue 2869 ARG Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 3009 ASN Chi-restraints excluded: chain A residue 3043 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3663 THR Chi-restraints excluded: chain A residue 3798 SER Chi-restraints excluded: chain A residue 3962 ASP Chi-restraints excluded: chain A residue 3978 THR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4068 SER Chi-restraints excluded: chain A residue 4075 GLU Chi-restraints excluded: chain A residue 4090 SER Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4522 THR Chi-restraints excluded: chain A residue 4542 GLU Chi-restraints excluded: chain A residue 4576 SER Chi-restraints excluded: chain A residue 4605 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 78 optimal weight: 0.7980 chunk 246 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 229 optimal weight: 0.0770 chunk 19 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 286 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1559 HIS A1755 GLN ** A1810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4038 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.129349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.101934 restraints weight = 30169.353| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.01 r_work: 0.3072 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24213 Z= 0.114 Angle : 0.468 8.064 32838 Z= 0.233 Chirality : 0.038 0.142 3692 Planarity : 0.003 0.047 4206 Dihedral : 5.226 86.440 3261 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.73 % Allowed : 11.36 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.16), residues: 2929 helix: 2.65 (0.12), residues: 1734 sheet: -0.65 (0.32), residues: 243 loop : 0.57 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.004 0.001 HIS A1559 PHE 0.015 0.001 PHE A4620 TYR 0.023 0.001 TYR A1546 ARG 0.008 0.000 ARG A2863 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 1440) hydrogen bonds : angle 3.76288 ( 4203) covalent geometry : bond 0.00261 (24213) covalent geometry : angle 0.46834 (32838) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 282 time to evaluate : 2.753 Fit side-chains revert: symmetry clash REVERT: A 1464 LYS cc_start: 0.8256 (mmtt) cc_final: 0.8020 (mmmt) REVERT: A 1516 PHE cc_start: 0.7635 (m-80) cc_final: 0.7414 (m-80) REVERT: A 1621 ARG cc_start: 0.7977 (ttm110) cc_final: 0.7776 (ttp-110) REVERT: A 2012 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8626 (ttp) REVERT: A 2172 ARG cc_start: 0.7687 (tmm-80) cc_final: 0.7100 (tmm-80) REVERT: A 2180 GLU cc_start: 0.7828 (tp30) cc_final: 0.7357 (tp30) REVERT: A 2435 LYS cc_start: 0.8686 (mtpt) cc_final: 0.8453 (mtpt) REVERT: A 2467 ARG cc_start: 0.8704 (mtt90) cc_final: 0.8472 (mtt90) REVERT: A 2471 GLN cc_start: 0.8107 (tm-30) cc_final: 0.7748 (tt0) REVERT: A 2654 GLN cc_start: 0.8398 (tt0) cc_final: 0.7897 (tt0) REVERT: A 2773 MET cc_start: 0.8835 (mtp) cc_final: 0.8423 (mtm) REVERT: A 2782 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7030 (mm-30) REVERT: A 2867 MET cc_start: 0.8517 (mmm) cc_final: 0.8221 (mtm) REVERT: A 2869 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6679 (tpm170) REVERT: A 3012 LEU cc_start: 0.8739 (mt) cc_final: 0.8469 (mt) REVERT: A 3030 MET cc_start: 0.8628 (mmp) cc_final: 0.8120 (mmp) REVERT: A 3478 LEU cc_start: 0.6977 (tp) cc_final: 0.6717 (mp) REVERT: A 3480 LYS cc_start: 0.8733 (mmmt) cc_final: 0.8208 (mttt) REVERT: A 3542 GLN cc_start: 0.8350 (mm110) cc_final: 0.8050 (mm-40) REVERT: A 3663 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8417 (p) REVERT: A 4049 TYR cc_start: 0.7479 (m-80) cc_final: 0.7179 (m-80) REVERT: A 4075 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7244 (tp30) REVERT: A 4276 ARG cc_start: 0.8230 (mtm-85) cc_final: 0.7798 (mtm110) REVERT: A 4292 LYS cc_start: 0.7546 (mmtt) cc_final: 0.7200 (mmtm) REVERT: A 4377 MET cc_start: 0.7374 (mtt) cc_final: 0.6839 (mtm) REVERT: A 4386 ASN cc_start: 0.7371 (m-40) cc_final: 0.7095 (m-40) REVERT: A 4412 PHE cc_start: 0.8015 (t80) cc_final: 0.7778 (t80) REVERT: A 4425 GLN cc_start: 0.8313 (tp-100) cc_final: 0.8084 (tt0) REVERT: A 4426 ASP cc_start: 0.8287 (t70) cc_final: 0.8028 (m-30) REVERT: A 4477 GLN cc_start: 0.8689 (mt0) cc_final: 0.7715 (pt0) REVERT: A 4566 GLN cc_start: 0.8369 (mm110) cc_final: 0.7860 (mm-40) REVERT: A 4571 ASN cc_start: 0.7646 (m-40) cc_final: 0.7050 (p0) REVERT: A 4592 TRP cc_start: 0.6781 (m100) cc_final: 0.6512 (m100) outliers start: 45 outliers final: 38 residues processed: 312 average time/residue: 0.3946 time to fit residues: 190.3586 Evaluate side-chains 307 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 265 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1486 LEU Chi-restraints excluded: chain A residue 1491 ASP Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2215 GLN Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2238 LEU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2649 VAL Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2788 THR Chi-restraints excluded: chain A residue 2869 ARG Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 3009 ASN Chi-restraints excluded: chain A residue 3043 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3663 THR Chi-restraints excluded: chain A residue 3798 SER Chi-restraints excluded: chain A residue 3962 ASP Chi-restraints excluded: chain A residue 3978 THR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4068 SER Chi-restraints excluded: chain A residue 4075 GLU Chi-restraints excluded: chain A residue 4090 SER Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4522 THR Chi-restraints excluded: chain A residue 4576 SER Chi-restraints excluded: chain A residue 4605 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 285 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 273 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 169 optimal weight: 4.9990 chunk 235 optimal weight: 0.0970 chunk 258 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4038 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.132032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.102205 restraints weight = 30189.799| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.17 r_work: 0.3045 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24213 Z= 0.113 Angle : 0.473 7.623 32838 Z= 0.235 Chirality : 0.038 0.143 3692 Planarity : 0.004 0.047 4206 Dihedral : 5.186 82.348 3261 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.65 % Allowed : 11.67 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.16), residues: 2929 helix: 2.66 (0.12), residues: 1734 sheet: -0.66 (0.32), residues: 243 loop : 0.57 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.003 0.001 HIS A3200 PHE 0.018 0.001 PHE A4620 TYR 0.023 0.001 TYR A1546 ARG 0.008 0.000 ARG A2863 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 1440) hydrogen bonds : angle 3.76540 ( 4203) covalent geometry : bond 0.00260 (24213) covalent geometry : angle 0.47317 (32838) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 275 time to evaluate : 2.875 Fit side-chains revert: symmetry clash REVERT: A 1464 LYS cc_start: 0.8254 (mmtt) cc_final: 0.8019 (mmmt) REVERT: A 1516 PHE cc_start: 0.7628 (m-80) cc_final: 0.7413 (m-80) REVERT: A 1873 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8866 (mt) REVERT: A 2012 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8576 (ttp) REVERT: A 2180 GLU cc_start: 0.7586 (tp30) cc_final: 0.7121 (tp30) REVERT: A 2435 LYS cc_start: 0.8656 (mtpt) cc_final: 0.8438 (mtpt) REVERT: A 2471 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7736 (tt0) REVERT: A 2654 GLN cc_start: 0.8427 (tt0) cc_final: 0.7933 (tt0) REVERT: A 2773 MET cc_start: 0.8817 (mtp) cc_final: 0.8403 (mtm) REVERT: A 2782 GLU cc_start: 0.7629 (mt-10) cc_final: 0.6973 (mm-30) REVERT: A 2867 MET cc_start: 0.8544 (mmm) cc_final: 0.8271 (mtm) REVERT: A 2869 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6585 (tpm170) REVERT: A 3012 LEU cc_start: 0.8594 (mt) cc_final: 0.8319 (mt) REVERT: A 3030 MET cc_start: 0.8628 (mmp) cc_final: 0.8108 (mmp) REVERT: A 3478 LEU cc_start: 0.6929 (tp) cc_final: 0.6672 (mp) REVERT: A 3480 LYS cc_start: 0.8742 (mmmt) cc_final: 0.8224 (mttt) REVERT: A 3542 GLN cc_start: 0.8341 (mm110) cc_final: 0.8035 (mm-40) REVERT: A 3663 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8443 (p) REVERT: A 4049 TYR cc_start: 0.7467 (m-80) cc_final: 0.7110 (m-80) REVERT: A 4075 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7183 (tp30) REVERT: A 4292 LYS cc_start: 0.7612 (mmtt) cc_final: 0.7257 (mmtm) REVERT: A 4377 MET cc_start: 0.7343 (mtt) cc_final: 0.6817 (mtm) REVERT: A 4386 ASN cc_start: 0.7492 (m-40) cc_final: 0.7267 (m-40) REVERT: A 4412 PHE cc_start: 0.8034 (t80) cc_final: 0.7780 (t80) REVERT: A 4425 GLN cc_start: 0.8316 (tp-100) cc_final: 0.8104 (tt0) REVERT: A 4426 ASP cc_start: 0.8328 (t70) cc_final: 0.8020 (m-30) REVERT: A 4477 GLN cc_start: 0.8669 (mt0) cc_final: 0.7683 (pt0) REVERT: A 4566 GLN cc_start: 0.8317 (mm110) cc_final: 0.7853 (mm-40) REVERT: A 4571 ASN cc_start: 0.7643 (m-40) cc_final: 0.7029 (p0) REVERT: A 4594 LYS cc_start: 0.5709 (mmmt) cc_final: 0.5263 (mmtt) outliers start: 43 outliers final: 37 residues processed: 304 average time/residue: 0.4144 time to fit residues: 197.1614 Evaluate side-chains 306 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 264 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1486 LEU Chi-restraints excluded: chain A residue 1491 ASP Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2215 GLN Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2238 LEU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2649 VAL Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2788 THR Chi-restraints excluded: chain A residue 2869 ARG Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 3009 ASN Chi-restraints excluded: chain A residue 3043 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3663 THR Chi-restraints excluded: chain A residue 3798 SER Chi-restraints excluded: chain A residue 3962 ASP Chi-restraints excluded: chain A residue 3978 THR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4068 SER Chi-restraints excluded: chain A residue 4075 GLU Chi-restraints excluded: chain A residue 4090 SER Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4522 THR Chi-restraints excluded: chain A residue 4605 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 148 optimal weight: 1.9990 chunk 253 optimal weight: 0.6980 chunk 161 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 chunk 131 optimal weight: 0.0570 chunk 186 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 287 optimal weight: 0.1980 chunk 95 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN ** A1810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4038 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.132244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.102358 restraints weight = 30296.773| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.20 r_work: 0.3046 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24213 Z= 0.109 Angle : 0.476 8.767 32838 Z= 0.237 Chirality : 0.038 0.320 3692 Planarity : 0.004 0.047 4206 Dihedral : 5.150 82.825 3261 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.69 % Allowed : 11.98 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.16), residues: 2929 helix: 2.65 (0.12), residues: 1734 sheet: -0.63 (0.32), residues: 242 loop : 0.58 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A4592 HIS 0.003 0.001 HIS A1559 PHE 0.016 0.001 PHE A4008 TYR 0.023 0.001 TYR A1546 ARG 0.008 0.000 ARG A2863 Details of bonding type rmsd hydrogen bonds : bond 0.03608 ( 1440) hydrogen bonds : angle 3.76439 ( 4203) covalent geometry : bond 0.00246 (24213) covalent geometry : angle 0.47620 (32838) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 281 time to evaluate : 2.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1464 LYS cc_start: 0.8253 (mmtt) cc_final: 0.7997 (mmmt) REVERT: A 1516 PHE cc_start: 0.7635 (m-80) cc_final: 0.7421 (m-80) REVERT: A 1873 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8892 (mt) REVERT: A 2012 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8569 (ttp) REVERT: A 2180 GLU cc_start: 0.7697 (tp30) cc_final: 0.7190 (tp30) REVERT: A 2435 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8456 (mtpt) REVERT: A 2471 GLN cc_start: 0.8067 (tm-30) cc_final: 0.7746 (tt0) REVERT: A 2654 GLN cc_start: 0.8435 (tt0) cc_final: 0.7936 (tt0) REVERT: A 2773 MET cc_start: 0.8834 (mtp) cc_final: 0.8414 (mtm) REVERT: A 2782 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7133 (mm-30) REVERT: A 2867 MET cc_start: 0.8473 (mmm) cc_final: 0.8273 (mtm) REVERT: A 2869 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6566 (tpm170) REVERT: A 2885 ASP cc_start: 0.8100 (t70) cc_final: 0.7545 (t0) REVERT: A 3012 LEU cc_start: 0.8713 (mt) cc_final: 0.8431 (mt) REVERT: A 3030 MET cc_start: 0.8627 (mmp) cc_final: 0.8108 (mmp) REVERT: A 3478 LEU cc_start: 0.6936 (tp) cc_final: 0.6681 (mp) REVERT: A 3480 LYS cc_start: 0.8767 (mmmt) cc_final: 0.8257 (mttt) REVERT: A 3542 GLN cc_start: 0.8349 (mm110) cc_final: 0.8045 (mm-40) REVERT: A 3663 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8411 (p) REVERT: A 4049 TYR cc_start: 0.7459 (m-80) cc_final: 0.7102 (m-80) REVERT: A 4075 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7162 (tp30) REVERT: A 4274 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8806 (p) REVERT: A 4276 ARG cc_start: 0.8104 (mtm110) cc_final: 0.7888 (mtm110) REVERT: A 4292 LYS cc_start: 0.7621 (mmtt) cc_final: 0.7281 (mmtm) REVERT: A 4298 ASP cc_start: 0.8306 (t0) cc_final: 0.7532 (t0) REVERT: A 4377 MET cc_start: 0.7345 (mtt) cc_final: 0.6822 (mtm) REVERT: A 4386 ASN cc_start: 0.7492 (m-40) cc_final: 0.7273 (m-40) REVERT: A 4412 PHE cc_start: 0.8091 (t80) cc_final: 0.7884 (t80) REVERT: A 4426 ASP cc_start: 0.8338 (t70) cc_final: 0.8027 (m-30) REVERT: A 4477 GLN cc_start: 0.8619 (mt0) cc_final: 0.7677 (pt0) REVERT: A 4566 GLN cc_start: 0.8320 (mm110) cc_final: 0.7833 (mm-40) REVERT: A 4571 ASN cc_start: 0.7638 (m-40) cc_final: 0.7029 (p0) REVERT: A 4594 LYS cc_start: 0.5791 (mmmt) cc_final: 0.5243 (mmtt) outliers start: 44 outliers final: 38 residues processed: 311 average time/residue: 0.4197 time to fit residues: 202.9638 Evaluate side-chains 312 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 268 time to evaluate : 2.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1486 LEU Chi-restraints excluded: chain A residue 1491 ASP Chi-restraints excluded: chain A residue 1507 MET Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1561 LEU Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2215 GLN Chi-restraints excluded: chain A residue 2231 SER Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2238 LEU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2627 THR Chi-restraints excluded: chain A residue 2649 VAL Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2788 THR Chi-restraints excluded: chain A residue 2869 ARG Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 3009 ASN Chi-restraints excluded: chain A residue 3043 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3663 THR Chi-restraints excluded: chain A residue 3798 SER Chi-restraints excluded: chain A residue 3962 ASP Chi-restraints excluded: chain A residue 3978 THR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4068 SER Chi-restraints excluded: chain A residue 4075 GLU Chi-restraints excluded: chain A residue 4090 SER Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4341 SER Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4522 THR Chi-restraints excluded: chain A residue 4542 GLU Chi-restraints excluded: chain A residue 4605 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 20 optimal weight: 0.0170 chunk 107 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 9 optimal weight: 0.0970 chunk 13 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 291 optimal weight: 0.8980 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN ** A1810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4038 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.130574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.103519 restraints weight = 29944.840| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.96 r_work: 0.3101 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24213 Z= 0.101 Angle : 0.475 8.148 32838 Z= 0.237 Chirality : 0.038 0.215 3692 Planarity : 0.004 0.046 4206 Dihedral : 5.086 85.935 3261 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.50 % Allowed : 12.36 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.16), residues: 2929 helix: 2.70 (0.12), residues: 1734 sheet: -0.60 (0.32), residues: 242 loop : 0.58 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A4592 HIS 0.002 0.000 HIS A3200 PHE 0.017 0.001 PHE A4620 TYR 0.023 0.001 TYR A1546 ARG 0.008 0.000 ARG A2863 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 1440) hydrogen bonds : angle 3.71701 ( 4203) covalent geometry : bond 0.00219 (24213) covalent geometry : angle 0.47489 (32838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13972.40 seconds wall clock time: 242 minutes 55.94 seconds (14575.94 seconds total)