Starting phenix.real_space_refine on Fri May 23 11:56:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bmj_44701/05_2025/9bmj_44701.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bmj_44701/05_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_44701/05_2025/9bmj_44701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bmj_44701/05_2025/9bmj_44701.map" model { file = "/net/cci-nas-00/data/ceres_data/9bmj_44701/05_2025/9bmj_44701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bmj_44701/05_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-5687/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: 12.79, per 1000 atoms: 0.54 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: 5.69 Conformation dependent library (CDL) restraints added in 2.9 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: 4.00 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: 13.42 Time building geometry restraints manager: 6.69 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: 4.490 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: 0.860 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 56.430 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.220 ------------------------------------------------------------------------------- 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 : 2.553 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: 0.3884 time to fit residues: 257.8339 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 : 2.602 ------------------------------------------------------------------------------- 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 = 0.106698 restraints weight = 30033.840| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.16 r_work: 0.3112 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 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 : 2.586 Fit side-chains revert: symmetry clash REVERT: A 1516 PHE cc_start: 0.7493 (m-80) cc_final: 0.7252 (m-80) REVERT: A 1631 PHE cc_start: 0.8211 (m-80) cc_final: 0.7933 (m-80) REVERT: A 1745 TYR cc_start: 0.8314 (m-80) cc_final: 0.7533 (m-80) REVERT: A 1893 THR cc_start: 0.7984 (p) cc_final: 0.7648 (p) REVERT: A 1997 ILE cc_start: 0.8106 (mm) cc_final: 0.7806 (mm) REVERT: A 2041 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8400 (mtt) REVERT: A 2133 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7687 (mt-10) REVERT: A 2799 MET cc_start: 0.8855 (mmm) cc_final: 0.8560 (mmm) REVERT: A 2901 TYR cc_start: 0.8082 (m-10) cc_final: 0.7586 (m-10) REVERT: A 3030 MET cc_start: 0.8712 (mmp) cc_final: 0.8346 (mmp) REVERT: A 3068 MET cc_start: 0.9255 (ptm) cc_final: 0.9025 (ptm) REVERT: A 3480 LYS cc_start: 0.8468 (mmmt) cc_final: 0.8021 (mttt) REVERT: A 3516 TYR cc_start: 0.9100 (m-80) cc_final: 0.8810 (m-10) REVERT: A 3799 GLN cc_start: 0.8312 (tp40) cc_final: 0.8106 (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: 0.7604 (mtm110) REVERT: A 4307 GLN cc_start: 0.7600 (tt0) cc_final: 0.7095 (mt0) REVERT: A 4332 LEU cc_start: 0.8119 (mt) cc_final: 0.7880 (mt) REVERT: A 4339 MET cc_start: 0.7897 (ttt) cc_final: 0.7609 (ttt) REVERT: A 4347 GLN cc_start: 0.7366 (tt0) cc_final: 0.7156 (tt0) REVERT: A 4544 ASN cc_start: 0.7631 (t0) cc_final: 0.7405 (t0) REVERT: A 4571 ASN cc_start: 0.7609 (m-40) cc_final: 0.6916 (p0) outliers start: 25 outliers final: 17 residues processed: 332 average time/residue: 0.3802 time to fit residues: 195.2886 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 : 2.529 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.9980 chunk 222 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1559 HIS A3152 GLN A3499 GLN A3537 GLN A3622 ASN A4381 HIS ** 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 = 0.3514 r_free = 0.3514 target = 0.125584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.098194 restraints weight = 30416.777| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.02 r_work: 0.2996 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 24213 Z= 0.229 Angle : 0.593 7.060 32838 Z= 0.297 Chirality : 0.043 0.158 3692 Planarity : 0.005 0.047 4206 Dihedral : 5.844 90.149 3261 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.80 % Allowed : 8.64 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.16), residues: 2929 helix: 2.19 (0.12), residues: 1717 sheet: -0.74 (0.32), residues: 250 loop : 0.32 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A2234 HIS 0.005 0.001 HIS A2730 PHE 0.019 0.002 PHE A1568 TYR 0.028 0.002 TYR A1546 ARG 0.020 0.001 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.04964 ( 1440) hydrogen bonds : angle 4.19897 ( 4203) covalent geometry : bond 0.00556 (24213) covalent geometry : angle 0.59277 (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 323 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 276 time to evaluate : 2.677 Fit side-chains revert: symmetry clash REVERT: A 2012 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8613 (ttp) REVERT: A 2189 MET cc_start: 0.8489 (ttm) cc_final: 0.8134 (ttm) REVERT: A 2654 GLN cc_start: 0.8369 (tt0) cc_final: 0.7993 (tt0) REVERT: A 2779 MET cc_start: 0.8708 (mtm) cc_final: 0.8497 (mtp) REVERT: A 2782 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7111 (mm-30) REVERT: A 3068 MET cc_start: 0.9273 (ptm) cc_final: 0.9067 (ptm) REVERT: A 3478 LEU cc_start: 0.6946 (tp) cc_final: 0.6684 (mp) REVERT: A 3480 LYS cc_start: 0.8623 (mmmt) cc_final: 0.8155 (mttt) REVERT: A 3516 TYR cc_start: 0.9074 (m-80) cc_final: 0.8846 (m-80) REVERT: A 3524 MET cc_start: 0.8641 (tpp) cc_final: 0.8336 (tpp) REVERT: A 3663 THR cc_start: 0.8770 (t) cc_final: 0.8445 (p) REVERT: A 4049 TYR cc_start: 0.7598 (m-80) cc_final: 0.6725 (m-80) REVERT: A 4307 GLN cc_start: 0.7824 (tt0) cc_final: 0.7154 (mt0) REVERT: A 4377 MET cc_start: 0.7333 (mtt) cc_final: 0.6851 (mtm) REVERT: A 4386 ASN cc_start: 0.7374 (m-40) cc_final: 0.7044 (m-40) REVERT: A 4412 PHE cc_start: 0.8005 (t80) cc_final: 0.7475 (t80) REVERT: A 4425 GLN cc_start: 0.8243 (tp-100) cc_final: 0.7863 (tt0) REVERT: A 4544 ASN cc_start: 0.7793 (t0) cc_final: 0.7563 (t0) REVERT: A 4571 ASN cc_start: 0.7592 (m-40) cc_final: 0.6952 (p0) outliers start: 47 outliers final: 35 residues processed: 310 average time/residue: 0.3969 time to fit residues: 189.1392 Evaluate side-chains 280 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 2.580 ------------------------------------------------------------------------------- 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 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 2953 MET Chi-restraints excluded: chain A residue 2968 THR 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 3610 THR 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 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 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: 0.0670 chunk 177 optimal weight: 6.9990 chunk 259 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 282 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1465 GLN A1755 GLN A2079 GLN A3038 GLN A4397 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.128289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.100991 restraints weight = 30362.713| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.97 r_work: 0.3062 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24213 Z= 0.114 Angle : 0.478 6.859 32838 Z= 0.240 Chirality : 0.039 0.152 3692 Planarity : 0.004 0.046 4206 Dihedral : 5.608 90.388 3261 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.31 % Allowed : 10.06 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.26 (0.16), residues: 2929 helix: 2.43 (0.12), residues: 1730 sheet: -0.63 (0.33), residues: 243 loop : 0.43 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2234 HIS 0.003 0.001 HIS A3200 PHE 0.014 0.001 PHE A2912 TYR 0.020 0.001 TYR A1546 ARG 0.008 0.000 ARG A2863 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 1440) hydrogen bonds : angle 3.92737 ( 4203) covalent geometry : bond 0.00252 (24213) covalent geometry : angle 0.47826 (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 314 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 280 time to evaluate : 2.678 Fit side-chains revert: symmetry clash REVERT: A 1460 GLU cc_start: 0.7712 (tp30) cc_final: 0.7290 (tp30) REVERT: A 2012 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8571 (ttp) REVERT: A 2090 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8138 (tp) REVERT: A 2172 ARG cc_start: 0.7592 (tmm-80) cc_final: 0.6971 (tmm-80) REVERT: A 2217 ASN cc_start: 0.8537 (m110) cc_final: 0.8256 (m110) REVERT: A 2471 GLN cc_start: 0.7980 (tm-30) cc_final: 0.7673 (tt0) REVERT: A 2654 GLN cc_start: 0.8330 (tt0) cc_final: 0.7912 (tt0) REVERT: A 2773 MET cc_start: 0.8729 (mtp) cc_final: 0.8322 (mtm) REVERT: A 2779 MET cc_start: 0.8521 (mtm) cc_final: 0.8200 (mtp) REVERT: A 2782 GLU cc_start: 0.7601 (mt-10) cc_final: 0.6870 (mm-30) REVERT: A 3012 LEU cc_start: 0.8517 (mt) cc_final: 0.8291 (mt) REVERT: A 3068 MET cc_start: 0.9192 (ptm) cc_final: 0.8971 (ptm) REVERT: A 3480 LYS cc_start: 0.8627 (mmmt) cc_final: 0.8125 (mttt) REVERT: A 3516 TYR cc_start: 0.8982 (m-80) cc_final: 0.8699 (m-80) REVERT: A 3663 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8378 (p) REVERT: A 4049 TYR cc_start: 0.7467 (m-80) cc_final: 0.7059 (m-80) REVERT: A 4292 LYS cc_start: 0.7116 (mmtt) cc_final: 0.6804 (mmtm) REVERT: A 4377 MET cc_start: 0.7229 (mtt) cc_final: 0.6736 (mtm) REVERT: A 4386 ASN cc_start: 0.7319 (m-40) cc_final: 0.7007 (m-40) REVERT: A 4425 GLN cc_start: 0.8186 (tp-100) cc_final: 0.7914 (tt0) REVERT: A 4571 ASN cc_start: 0.7507 (m-40) cc_final: 0.6892 (p0) REVERT: A 4592 TRP cc_start: 0.6850 (m100) cc_final: 0.5523 (m100) outliers start: 34 outliers final: 23 residues processed: 304 average time/residue: 0.3884 time to fit residues: 181.1779 Evaluate side-chains 283 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 257 time to evaluate : 2.733 ------------------------------------------------------------------------------- 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 1625 SER Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2090 LEU 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 2968 THR 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 3610 THR Chi-restraints excluded: chain A residue 3663 THR Chi-restraints excluded: chain A residue 3962 ASP Chi-restraints excluded: chain A residue 3981 THR 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 4469 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: 2.9990 chunk 169 optimal weight: 0.0980 chunk 182 optimal weight: 2.9990 chunk 114 optimal weight: 0.1980 chunk 54 optimal weight: 0.2980 chunk 275 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 249 optimal weight: 0.6980 chunk 187 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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** A3038 GLN A3104 GLN A4038 ASN A4566 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.129253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.101828 restraints weight = 30245.865| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.99 r_work: 0.3059 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2824 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= 0.104 Angle : 0.461 6.620 32838 Z= 0.230 Chirality : 0.038 0.142 3692 Planarity : 0.004 0.044 4206 Dihedral : 5.416 85.666 3261 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.57 % Allowed : 10.60 % Favored : 87.83 % 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: 1729 sheet: -0.55 (0.33), residues: 242 loop : 0.45 (0.21), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.003 0.001 HIS A3200 PHE 0.018 0.001 PHE A3996 TYR 0.021 0.001 TYR A1546 ARG 0.009 0.000 ARG A2863 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 1440) hydrogen bonds : angle 3.80400 ( 4203) covalent geometry : bond 0.00227 (24213) covalent geometry : angle 0.46098 (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 322 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 281 time to evaluate : 2.649 Fit side-chains revert: symmetry clash REVERT: A 1460 GLU cc_start: 0.7683 (tp30) cc_final: 0.7345 (tp30) REVERT: A 1516 PHE cc_start: 0.7450 (m-80) cc_final: 0.7162 (m-80) REVERT: A 1531 MET cc_start: 0.8128 (tpp) cc_final: 0.7875 (tpp) REVERT: A 2012 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8454 (ttp) REVERT: A 2090 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8142 (tp) REVERT: A 2172 ARG cc_start: 0.7584 (tmm-80) cc_final: 0.6984 (tmm-80) REVERT: A 2180 GLU cc_start: 0.7742 (tp30) cc_final: 0.7432 (tp30) REVERT: A 2189 MET cc_start: 0.8160 (mtp) cc_final: 0.7742 (ttm) REVERT: A 2467 ARG cc_start: 0.8494 (mtt90) cc_final: 0.8197 (mtt90) REVERT: A 2471 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7605 (tt0) REVERT: A 2578 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7597 (mt-10) REVERT: A 2654 GLN cc_start: 0.8300 (tt0) cc_final: 0.7833 (tt0) REVERT: A 2773 MET cc_start: 0.8689 (mtp) cc_final: 0.8294 (mtm) REVERT: A 2779 MET cc_start: 0.8487 (mtm) cc_final: 0.8170 (mtp) REVERT: A 2782 GLU cc_start: 0.7557 (mt-10) cc_final: 0.6819 (mm-30) REVERT: A 2867 MET cc_start: 0.8431 (mmm) cc_final: 0.7944 (mtm) REVERT: A 3012 LEU cc_start: 0.8568 (mt) cc_final: 0.8304 (mt) REVERT: A 3068 MET cc_start: 0.9161 (ptm) cc_final: 0.8937 (ptm) REVERT: A 3478 LEU cc_start: 0.6622 (tp) cc_final: 0.6342 (mp) REVERT: A 3480 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8103 (mttt) REVERT: A 3516 TYR cc_start: 0.8933 (m-80) cc_final: 0.8673 (m-80) REVERT: A 3663 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8386 (p) REVERT: A 4049 TYR cc_start: 0.7502 (m-80) cc_final: 0.7125 (m-80) REVERT: A 4075 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6831 (tp30) REVERT: A 4292 LYS cc_start: 0.7480 (mmtt) cc_final: 0.7052 (mmtm) REVERT: A 4377 MET cc_start: 0.7202 (mtt) cc_final: 0.6718 (mtm) REVERT: A 4386 ASN cc_start: 0.7333 (m-40) cc_final: 0.7033 (m-40) REVERT: A 4412 PHE cc_start: 0.7870 (t80) cc_final: 0.7562 (t80) REVERT: A 4425 GLN cc_start: 0.8162 (tp-100) cc_final: 0.7900 (tt0) REVERT: A 4426 ASP cc_start: 0.8120 (t70) cc_final: 0.7877 (m-30) REVERT: A 4571 ASN cc_start: 0.7473 (m-40) cc_final: 0.6855 (p0) REVERT: A 4592 TRP cc_start: 0.6832 (m100) cc_final: 0.5984 (m100) outliers start: 41 outliers final: 31 residues processed: 310 average time/residue: 0.3900 time to fit residues: 186.1563 Evaluate side-chains 299 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 2.644 ------------------------------------------------------------------------------- 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 1625 SER Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2090 LEU Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2212 GLN Chi-restraints excluded: chain A residue 2238 LEU 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 3981 THR Chi-restraints excluded: chain A residue 4075 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 183 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 275 optimal weight: 0.9990 chunk 249 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 288 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3104 GLN A4038 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.128245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.099282 restraints weight = 30215.991| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.10 r_work: 0.3025 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24213 Z= 0.141 Angle : 0.479 6.703 32838 Z= 0.239 Chirality : 0.039 0.148 3692 Planarity : 0.004 0.047 4206 Dihedral : 5.442 84.746 3261 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.65 % Allowed : 10.71 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.53 (0.12), residues: 1729 sheet: -0.64 (0.33), residues: 243 loop : 0.45 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2234 HIS 0.003 0.001 HIS A3200 PHE 0.015 0.001 PHE A1568 TYR 0.024 0.001 TYR A1546 ARG 0.007 0.000 ARG A2863 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 1440) hydrogen bonds : angle 3.85570 ( 4203) covalent geometry : bond 0.00335 (24213) covalent geometry : angle 0.47924 (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 317 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 274 time to evaluate : 2.528 Fit side-chains revert: symmetry clash REVERT: A 1933 ASP cc_start: 0.8532 (p0) cc_final: 0.8322 (p0) REVERT: A 2012 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8576 (ttp) REVERT: A 2090 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8020 (tp) REVERT: A 2172 ARG cc_start: 0.7571 (tmm-80) cc_final: 0.6943 (tmm-80) REVERT: A 2180 GLU cc_start: 0.7726 (tp30) cc_final: 0.7354 (tp30) REVERT: A 2189 MET cc_start: 0.8260 (mtp) cc_final: 0.7808 (ttm) REVERT: A 2471 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7659 (tt0) REVERT: A 2558 GLU cc_start: 0.6770 (mp0) cc_final: 0.6550 (mp0) REVERT: A 2654 GLN cc_start: 0.8360 (tt0) cc_final: 0.7852 (tt0) REVERT: A 2782 GLU cc_start: 0.7610 (mt-10) cc_final: 0.6839 (mm-30) REVERT: A 2869 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6793 (tpm170) REVERT: A 3008 MET cc_start: 0.8391 (mmm) cc_final: 0.8177 (mmp) REVERT: A 3012 LEU cc_start: 0.8614 (mt) cc_final: 0.8329 (mt) REVERT: A 3068 MET cc_start: 0.9164 (ptm) cc_final: 0.8939 (ptm) REVERT: A 3478 LEU cc_start: 0.6636 (tp) cc_final: 0.6349 (mp) REVERT: A 3480 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8121 (mttt) REVERT: A 3663 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8426 (p) REVERT: A 4049 TYR cc_start: 0.7436 (m-80) cc_final: 0.6989 (m-80) REVERT: A 4075 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.6921 (tp30) REVERT: A 4274 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8717 (p) REVERT: A 4276 ARG cc_start: 0.7942 (mtm110) cc_final: 0.7671 (mtm110) REVERT: A 4377 MET cc_start: 0.7192 (mtt) cc_final: 0.6688 (mtm) REVERT: A 4386 ASN cc_start: 0.7347 (m-40) cc_final: 0.7076 (m-40) REVERT: A 4412 PHE cc_start: 0.7969 (t80) cc_final: 0.7653 (t80) REVERT: A 4415 ARG cc_start: 0.7098 (ttp-110) cc_final: 0.6777 (ttp-110) REVERT: A 4425 GLN cc_start: 0.8193 (tp-100) cc_final: 0.7967 (tt0) REVERT: A 4426 ASP cc_start: 0.8136 (t70) cc_final: 0.7876 (m-30) REVERT: A 4571 ASN cc_start: 0.7481 (m-40) cc_final: 0.6876 (p0) REVERT: A 4592 TRP cc_start: 0.7028 (m100) cc_final: 0.6227 (m100) outliers start: 43 outliers final: 34 residues processed: 308 average time/residue: 0.3938 time to fit residues: 185.4429 Evaluate side-chains 305 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 265 time to evaluate : 2.519 ------------------------------------------------------------------------------- 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 2090 LEU 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 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 2968 THR Chi-restraints excluded: chain A residue 3009 ASN 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 3981 THR Chi-restraints excluded: chain A residue 4075 GLU Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4129 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 65 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 222 optimal weight: 3.9990 chunk 291 optimal weight: 0.2980 chunk 283 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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** A2707 GLN A3104 GLN A4038 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.128745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.099686 restraints weight = 30348.744| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.12 r_work: 0.3028 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24213 Z= 0.126 Angle : 0.473 6.640 32838 Z= 0.236 Chirality : 0.039 0.146 3692 Planarity : 0.004 0.046 4206 Dihedral : 5.432 86.777 3261 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.61 % Allowed : 11.21 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.42 (0.16), residues: 2929 helix: 2.58 (0.12), residues: 1731 sheet: -0.70 (0.32), residues: 252 loop : 0.51 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.003 0.001 HIS A3200 PHE 0.017 0.001 PHE A4620 TYR 0.021 0.001 TYR A1546 ARG 0.007 0.000 ARG A2863 Details of bonding type rmsd hydrogen bonds : bond 0.03871 ( 1440) hydrogen bonds : angle 3.81847 ( 4203) covalent geometry : bond 0.00294 (24213) covalent geometry : angle 0.47299 (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 325 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 283 time to evaluate : 2.821 Fit side-chains revert: symmetry clash REVERT: A 1464 LYS cc_start: 0.8084 (mmtt) cc_final: 0.7859 (mmmt) REVERT: A 1516 PHE cc_start: 0.7441 (m-80) cc_final: 0.7213 (m-80) REVERT: A 2012 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8573 (ttp) REVERT: A 2090 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8091 (tp) REVERT: A 2172 ARG cc_start: 0.7573 (tmm-80) cc_final: 0.6966 (tmm-80) REVERT: A 2180 GLU cc_start: 0.7697 (tp30) cc_final: 0.7189 (tp30) REVERT: A 2189 MET cc_start: 0.8276 (mtp) cc_final: 0.7791 (ttm) REVERT: A 2471 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7628 (tt0) REVERT: A 2558 GLU cc_start: 0.6811 (mp0) cc_final: 0.6589 (mp0) REVERT: A 2654 GLN cc_start: 0.8382 (tt0) cc_final: 0.7874 (tt0) REVERT: A 2782 GLU cc_start: 0.7589 (mt-10) cc_final: 0.6820 (mm-30) REVERT: A 2867 MET cc_start: 0.8438 (mmm) cc_final: 0.8066 (mtm) REVERT: A 2869 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6650 (tpm170) REVERT: A 3012 LEU cc_start: 0.8616 (mt) cc_final: 0.8353 (mt) REVERT: A 3068 MET cc_start: 0.9160 (ptm) cc_final: 0.8934 (ptm) REVERT: A 3478 LEU cc_start: 0.6629 (tp) cc_final: 0.6358 (mp) REVERT: A 3480 LYS cc_start: 0.8688 (mmmt) cc_final: 0.8147 (mttt) REVERT: A 3542 GLN cc_start: 0.8278 (mm110) cc_final: 0.7904 (mm-40) REVERT: A 3663 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8437 (p) REVERT: A 4075 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.6958 (tp30) REVERT: A 4274 THR cc_start: 0.9024 (OUTLIER) cc_final: 0.8731 (p) REVERT: A 4292 LYS cc_start: 0.7340 (mmtt) cc_final: 0.6749 (ttpp) REVERT: A 4307 GLN cc_start: 0.7546 (tt0) cc_final: 0.6897 (mt0) REVERT: A 4377 MET cc_start: 0.7167 (mtt) cc_final: 0.6654 (mtm) REVERT: A 4386 ASN cc_start: 0.7453 (m-40) cc_final: 0.7214 (m-40) REVERT: A 4412 PHE cc_start: 0.8002 (t80) cc_final: 0.7700 (t80) REVERT: A 4415 ARG cc_start: 0.7256 (ttp-110) cc_final: 0.6952 (ttp-110) REVERT: A 4425 GLN cc_start: 0.8197 (tp-100) cc_final: 0.7969 (tt0) REVERT: A 4426 ASP cc_start: 0.8136 (t70) cc_final: 0.7845 (m-30) REVERT: A 4571 ASN cc_start: 0.7472 (m-40) cc_final: 0.6869 (p0) REVERT: A 4592 TRP cc_start: 0.6711 (m100) cc_final: 0.6189 (m100) outliers start: 42 outliers final: 34 residues processed: 317 average time/residue: 0.3953 time to fit residues: 193.8345 Evaluate side-chains 305 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 265 time to evaluate : 2.551 ------------------------------------------------------------------------------- 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 1587 LEU Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2090 LEU 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 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 2699 THR 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 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 3981 THR Chi-restraints excluded: chain A residue 4075 GLU Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4129 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 78 optimal weight: 1.9990 chunk 246 optimal weight: 0.0670 chunk 123 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 229 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 286 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- 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** A2215 GLN A3104 GLN A4029 HIS A4038 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.128004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.098924 restraints weight = 30301.316| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.11 r_work: 0.3035 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24213 Z= 0.140 Angle : 0.487 7.805 32838 Z= 0.243 Chirality : 0.039 0.149 3692 Planarity : 0.004 0.047 4206 Dihedral : 5.469 89.312 3261 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.84 % Allowed : 11.63 % Favored : 86.53 % 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: 2.51 (0.12), residues: 1731 sheet: -0.67 (0.32), residues: 250 loop : 0.49 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.008 0.001 HIS A4029 PHE 0.018 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 0.03959 ( 1440) hydrogen bonds : angle 3.85846 ( 4203) covalent geometry : bond 0.00334 (24213) covalent geometry : angle 0.48720 (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 321 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 273 time to evaluate : 2.589 Fit side-chains revert: symmetry clash REVERT: A 1464 LYS cc_start: 0.8271 (mmtt) cc_final: 0.8024 (mmmt) REVERT: A 1873 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8844 (mt) REVERT: A 2012 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8604 (ttp) REVERT: A 2090 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8401 (tp) REVERT: A 2172 ARG cc_start: 0.7655 (tmm-80) cc_final: 0.7059 (tmm-80) REVERT: A 2180 GLU cc_start: 0.7921 (tp30) cc_final: 0.7412 (tp30) REVERT: A 2189 MET cc_start: 0.8521 (mtp) cc_final: 0.7998 (ttm) REVERT: A 2471 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7785 (tt0) REVERT: A 2558 GLU cc_start: 0.7261 (mp0) cc_final: 0.7054 (mp0) REVERT: A 2654 GLN cc_start: 0.8442 (tt0) cc_final: 0.7957 (tt0) REVERT: A 2782 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7076 (mm-30) REVERT: A 2867 MET cc_start: 0.8533 (mmm) cc_final: 0.8190 (mtm) REVERT: A 2869 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6672 (tpm170) REVERT: A 3012 LEU cc_start: 0.8834 (mt) cc_final: 0.8542 (mt) REVERT: A 3068 MET cc_start: 0.9286 (ptm) cc_final: 0.9080 (ptm) REVERT: A 3478 LEU cc_start: 0.6977 (tp) cc_final: 0.6688 (mp) REVERT: A 3480 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8271 (mttt) REVERT: A 3542 GLN cc_start: 0.8218 (mm110) cc_final: 0.7889 (mm-40) REVERT: A 3663 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8385 (p) REVERT: A 4049 TYR cc_start: 0.7434 (m-80) cc_final: 0.6794 (m-80) REVERT: A 4075 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7207 (tp30) REVERT: A 4157 MET cc_start: 0.8727 (mtp) cc_final: 0.7935 (mtp) REVERT: A 4274 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8861 (p) REVERT: A 4276 ARG cc_start: 0.8093 (mtm110) cc_final: 0.7874 (mtm110) REVERT: A 4298 ASP cc_start: 0.8232 (t0) cc_final: 0.7412 (t0) REVERT: A 4377 MET cc_start: 0.7366 (mtt) cc_final: 0.6827 (mtm) REVERT: A 4386 ASN cc_start: 0.7380 (m-40) cc_final: 0.7134 (m-40) REVERT: A 4412 PHE cc_start: 0.8226 (t80) cc_final: 0.7984 (t80) REVERT: A 4415 ARG cc_start: 0.7592 (ttp-110) cc_final: 0.7254 (ttp-110) REVERT: A 4426 ASP cc_start: 0.8344 (t70) cc_final: 0.8019 (m-30) REVERT: A 4566 GLN cc_start: 0.8411 (mm110) cc_final: 0.7816 (mm110) REVERT: A 4571 ASN cc_start: 0.7672 (m-40) cc_final: 0.7127 (p0) REVERT: A 4594 LYS cc_start: 0.5811 (mmmt) cc_final: 0.5295 (mmtt) outliers start: 48 outliers final: 37 residues processed: 310 average time/residue: 0.4044 time to fit residues: 193.4490 Evaluate side-chains 304 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 260 time to evaluate : 2.902 ------------------------------------------------------------------------------- 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 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 2090 LEU Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2212 GLN 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 2699 THR 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 2968 THR 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 3981 THR Chi-restraints excluded: chain A residue 4020 ILE Chi-restraints excluded: chain A residue 4068 SER Chi-restraints excluded: chain A residue 4075 GLU Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4129 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 285 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 273 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 235 optimal weight: 0.8980 chunk 258 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1695 HIS A1755 GLN ** A1810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3104 GLN ** 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 = 0.3554 r_free = 0.3554 target = 0.129266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099744 restraints weight = 30333.077| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.13 r_work: 0.3015 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3324 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= 0.136 Angle : 0.491 6.843 32838 Z= 0.246 Chirality : 0.039 0.149 3692 Planarity : 0.004 0.055 4206 Dihedral : 5.456 88.975 3261 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.69 % Allowed : 12.13 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.53 (0.12), residues: 1730 sheet: -0.70 (0.32), residues: 250 loop : 0.48 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.003 0.001 HIS A2085 PHE 0.020 0.001 PHE A3996 TYR 0.022 0.001 TYR A1546 ARG 0.006 0.000 ARG A2863 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 1440) hydrogen bonds : angle 3.84864 ( 4203) covalent geometry : bond 0.00321 (24213) covalent geometry : angle 0.49134 (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 311 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 267 time to evaluate : 2.848 Fit side-chains revert: symmetry clash REVERT: A 1464 LYS cc_start: 0.8099 (mmtt) cc_final: 0.7857 (mmmt) REVERT: A 1873 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8670 (mt) REVERT: A 2012 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8594 (ttp) REVERT: A 2090 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8098 (tp) REVERT: A 2172 ARG cc_start: 0.7571 (tmm-80) cc_final: 0.6945 (tmm-80) REVERT: A 2180 GLU cc_start: 0.7720 (tp30) cc_final: 0.7160 (tp30) REVERT: A 2189 MET cc_start: 0.8328 (mtp) cc_final: 0.7816 (ttm) REVERT: A 2471 GLN cc_start: 0.7922 (tm-30) cc_final: 0.7662 (tt0) REVERT: A 2558 GLU cc_start: 0.7082 (mp0) cc_final: 0.6869 (mp0) REVERT: A 2654 GLN cc_start: 0.8396 (tt0) cc_final: 0.7868 (tt0) REVERT: A 2782 GLU cc_start: 0.7588 (mt-10) cc_final: 0.6814 (mm-30) REVERT: A 2867 MET cc_start: 0.8410 (mmm) cc_final: 0.8066 (mtm) REVERT: A 2869 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6637 (tpm170) REVERT: A 3012 LEU cc_start: 0.8681 (mt) cc_final: 0.8387 (mt) REVERT: A 3068 MET cc_start: 0.9157 (ptm) cc_final: 0.8933 (ptm) REVERT: A 3478 LEU cc_start: 0.6671 (tp) cc_final: 0.6394 (mp) REVERT: A 3480 LYS cc_start: 0.8759 (mmmt) cc_final: 0.8223 (mttt) REVERT: A 3542 GLN cc_start: 0.8131 (mm110) cc_final: 0.7751 (mm-40) REVERT: A 3663 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8515 (p) REVERT: A 4049 TYR cc_start: 0.7387 (m-80) cc_final: 0.6630 (m-80) REVERT: A 4075 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6970 (tp30) REVERT: A 4274 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8746 (p) REVERT: A 4276 ARG cc_start: 0.7974 (mtm110) cc_final: 0.7709 (mtm110) REVERT: A 4292 LYS cc_start: 0.7341 (mmtt) cc_final: 0.6672 (ttpp) REVERT: A 4298 ASP cc_start: 0.8266 (t0) cc_final: 0.7442 (t0) REVERT: A 4377 MET cc_start: 0.7219 (mtt) cc_final: 0.6678 (mtm) REVERT: A 4386 ASN cc_start: 0.7339 (m-40) cc_final: 0.7133 (m-40) REVERT: A 4412 PHE cc_start: 0.8017 (t80) cc_final: 0.7798 (t80) REVERT: A 4415 ARG cc_start: 0.7456 (ttp-110) cc_final: 0.7128 (ttp-110) REVERT: A 4426 ASP cc_start: 0.8183 (t70) cc_final: 0.7867 (m-30) REVERT: A 4566 GLN cc_start: 0.8198 (mm110) cc_final: 0.7727 (mm-40) REVERT: A 4571 ASN cc_start: 0.7645 (m-40) cc_final: 0.6990 (p0) REVERT: A 4594 LYS cc_start: 0.5829 (mmmt) cc_final: 0.5283 (mmtt) outliers start: 44 outliers final: 36 residues processed: 301 average time/residue: 0.3877 time to fit residues: 179.9648 Evaluate side-chains 304 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 261 time to evaluate : 2.458 ------------------------------------------------------------------------------- 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 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 2090 LEU 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 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 2699 THR 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 2968 THR 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 3784 VAL 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 4068 SER Chi-restraints excluded: chain A residue 4075 GLU Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4129 GLU 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: 0.0170 chunk 253 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 234 optimal weight: 4.9990 chunk 131 optimal weight: 0.0040 chunk 186 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 115 optimal weight: 0.0770 chunk 287 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.2988 ------------------------------------------------------------------------------- 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** A2215 GLN A3104 GLN A4038 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.129166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.101727 restraints weight = 30191.582| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.03 r_work: 0.3055 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3373 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= 0.100 Angle : 0.470 7.893 32838 Z= 0.235 Chirality : 0.038 0.146 3692 Planarity : 0.004 0.045 4206 Dihedral : 5.317 83.445 3261 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.54 % Allowed : 12.40 % Favored : 86.07 % 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: 2.49 (0.16), residues: 2929 helix: 2.63 (0.12), residues: 1733 sheet: -0.65 (0.32), residues: 249 loop : 0.53 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.002 0.000 HIS A3200 PHE 0.015 0.001 PHE A4620 TYR 0.025 0.001 TYR A1546 ARG 0.008 0.000 ARG A2863 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 1440) hydrogen bonds : angle 3.76435 ( 4203) covalent geometry : bond 0.00215 (24213) covalent geometry : angle 0.47038 (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 320 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 280 time to evaluate : 2.559 Fit side-chains revert: symmetry clash REVERT: A 1464 LYS cc_start: 0.8322 (mmtt) cc_final: 0.8009 (mmmt) REVERT: A 1516 PHE cc_start: 0.7688 (m-80) cc_final: 0.7444 (m-80) REVERT: A 1873 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8834 (mt) REVERT: A 2012 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8552 (ttp) REVERT: A 2090 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8323 (tp) REVERT: A 2172 ARG cc_start: 0.7645 (tmm-80) cc_final: 0.7040 (tmm-80) REVERT: A 2180 GLU cc_start: 0.7788 (tp30) cc_final: 0.7290 (tp30) REVERT: A 2189 MET cc_start: 0.8446 (mtp) cc_final: 0.7958 (ttm) REVERT: A 2435 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8414 (mtpt) REVERT: A 2471 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7791 (tt0) REVERT: A 2654 GLN cc_start: 0.8427 (tt0) cc_final: 0.7934 (tt0) REVERT: A 2782 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7070 (mm-30) REVERT: A 2869 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6592 (tpm170) REVERT: A 2885 ASP cc_start: 0.8036 (t70) cc_final: 0.7474 (t0) REVERT: A 3012 LEU cc_start: 0.8812 (mt) cc_final: 0.8548 (mt) REVERT: A 3068 MET cc_start: 0.9262 (ptm) cc_final: 0.9053 (ptm) REVERT: A 3478 LEU cc_start: 0.6938 (tp) cc_final: 0.6666 (mp) REVERT: A 3480 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8268 (mttt) REVERT: A 3542 GLN cc_start: 0.8260 (mm110) cc_final: 0.7936 (mm-40) REVERT: A 3663 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8387 (p) REVERT: A 4049 TYR cc_start: 0.7416 (m-80) cc_final: 0.6784 (m-80) REVERT: A 4075 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7116 (tp30) REVERT: A 4274 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8807 (p) REVERT: A 4276 ARG cc_start: 0.8069 (mtm110) cc_final: 0.7832 (mtm110) REVERT: A 4292 LYS cc_start: 0.7364 (mmtt) cc_final: 0.6766 (ttpp) REVERT: A 4298 ASP cc_start: 0.8237 (t0) cc_final: 0.7417 (t0) REVERT: A 4307 GLN cc_start: 0.7757 (tt0) cc_final: 0.7406 (tt0) REVERT: A 4377 MET cc_start: 0.7383 (mtt) cc_final: 0.6823 (mtm) REVERT: A 4386 ASN cc_start: 0.7367 (m-40) cc_final: 0.7106 (m-40) REVERT: A 4426 ASP cc_start: 0.8327 (t70) cc_final: 0.7990 (m-30) REVERT: A 4566 GLN cc_start: 0.8277 (mm110) cc_final: 0.7825 (mm-40) REVERT: A 4571 ASN cc_start: 0.7710 (m-40) cc_final: 0.7105 (p0) REVERT: A 4593 VAL cc_start: 0.5941 (m) cc_final: 0.5685 (p) outliers start: 40 outliers final: 32 residues processed: 308 average time/residue: 0.3938 time to fit residues: 188.0800 Evaluate side-chains 303 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 264 time to evaluate : 2.666 ------------------------------------------------------------------------------- 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 1666 LEU Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2090 LEU Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2212 GLN 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 2699 THR 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 4068 SER Chi-restraints excluded: chain A residue 4075 GLU 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 20 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.0470 chunk 127 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 291 optimal weight: 4.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- 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** A2752 ASN A4038 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.130248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.100830 restraints weight = 30228.043| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.13 r_work: 0.3030 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24213 Z= 0.129 Angle : 0.491 8.457 32838 Z= 0.246 Chirality : 0.039 0.165 3692 Planarity : 0.004 0.070 4206 Dihedral : 5.336 81.634 3261 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.69 % Allowed : 12.51 % Favored : 85.80 % 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: 2.42 (0.16), residues: 2929 helix: 2.58 (0.12), residues: 1731 sheet: -0.72 (0.32), residues: 250 loop : 0.51 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.004 0.001 HIS A1559 PHE 0.050 0.001 PHE A4412 TYR 0.028 0.001 TYR A1546 ARG 0.007 0.000 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 1440) hydrogen bonds : angle 3.79956 ( 4203) covalent geometry : bond 0.00302 (24213) covalent geometry : angle 0.49147 (32838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12273.77 seconds wall clock time: 213 minutes 5.95 seconds (12785.95 seconds total)