Starting phenix.real_space_refine on Tue Sep 24 03:50:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyu_27782/09_2024/8dyu_27782_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyu_27782/09_2024/8dyu_27782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyu_27782/09_2024/8dyu_27782.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyu_27782/09_2024/8dyu_27782.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyu_27782/09_2024/8dyu_27782_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyu_27782/09_2024/8dyu_27782_trim.cif" } resolution = 4.0 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= 0.025 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 S 142 5.16 5 C 15665 2.51 5 N 4260 2.21 5 O 4534 1.98 5 H 23568 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 48178 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 38760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2562, 38760 Classifications: {'peptide': 2562} Link IDs: {'PCIS': 2, 'PTRANS': 119, 'TRANS': 2440} Chain breaks: 19 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 919 Unresolved non-hydrogen angles: 1142 Unresolved non-hydrogen dihedrals: 750 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 21, 'ASP:plan': 29, 'TYR:plan': 8, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 31, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 574 Chain: "B" Number of atoms: 4721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 4721 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 295} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 4585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 4585 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 295} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 17.14, per 1000 atoms: 0.36 Number of scatterers: 48178 At special positions: 0 Unit cell: (105.56, 147.32, 190.24, 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 142 16.00 P 9 15.00 O 4534 8.00 N 4260 7.00 C 15665 6.00 H 23568 1.00 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: 9.31 Conformation dependent library (CDL) restraints added in 3.1 seconds 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6034 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 31 sheets defined 50.8% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.08 Creating SS restraints... Processing helix chain 'A' and resid 1652 through 1656 Processing helix chain 'A' and resid 1705 through 1725 removed outlier: 3.669A pdb=" N MET A1709 " --> pdb=" O VAL A1705 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A1722 " --> pdb=" O ALA A1718 " (cutoff:3.500A) Processing helix chain 'A' and resid 1726 through 1728 No H-bonds generated for 'chain 'A' and resid 1726 through 1728' Processing helix chain 'A' and resid 1734 through 1745 removed outlier: 3.639A pdb=" N TYR A1745 " --> pdb=" O TRP A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1768 removed outlier: 3.528A pdb=" N VAL A1751 " --> pdb=" O ALA A1747 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A1757 " --> pdb=" O SER A1753 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TRP A1758 " --> pdb=" O ALA A1754 " (cutoff:3.500A) Processing helix chain 'A' and resid 1776 through 1797 removed outlier: 3.779A pdb=" N VAL A1796 " --> pdb=" O LEU A1792 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1828 removed outlier: 3.786A pdb=" N LYS A1807 " --> pdb=" O LEU A1803 " (cutoff:3.500A) 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 removed outlier: 3.679A pdb=" N MET A1892 " --> pdb=" O CYS A1888 " (cutoff:3.500A) Processing helix chain 'A' and resid 1911 through 1924 Processing helix chain 'A' and resid 1937 through 1952 removed outlier: 3.672A pdb=" N VAL A1951 " --> pdb=" O GLY A1947 " (cutoff:3.500A) Processing helix chain 'A' and resid 1964 through 1987 removed outlier: 3.553A pdb=" N SER A1969 " --> pdb=" O GLU A1965 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN A1974 " --> pdb=" O ALA A1970 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN A1979 " --> pdb=" O VAL A1975 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A1981 " --> pdb=" O CYS A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2034 removed outlier: 3.954A pdb=" N LYS A2033 " --> pdb=" O PRO A2029 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS A2034 " --> pdb=" O ASP A2030 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2029 through 2034' Processing helix chain 'A' and resid 2045 through 2058 removed outlier: 3.709A pdb=" N ILE A2049 " --> pdb=" O ASP A2045 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET A2053 " --> pdb=" O ILE A2049 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A2054 " --> pdb=" O ALA A2050 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A2058 " --> pdb=" O LEU A2054 " (cutoff:3.500A) Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix Processing helix chain 'A' and resid 2089 through 2111 Processing helix chain 'A' and resid 2132 through 2145 removed outlier: 3.591A pdb=" N ILE A2136 " --> pdb=" O PRO A2132 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A2137 " --> pdb=" O GLU A2133 " (cutoff:3.500A) Processing helix chain 'A' and resid 2146 through 2149 Processing helix chain 'A' and resid 2153 through 2165 Processing helix chain 'A' and resid 2175 through 2187 removed outlier: 3.736A pdb=" N GLN A2187 " --> pdb=" O LYS A2183 " (cutoff:3.500A) Processing helix chain 'A' and resid 2200 through 2217 removed outlier: 3.747A pdb=" N VAL A2204 " --> pdb=" O GLY A2200 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A2216 " --> pdb=" O GLN A2212 " (cutoff:3.500A) Processing helix chain 'A' and resid 2229 through 2245 Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2293 through 2297 Processing helix chain 'A' and resid 2308 through 2313 removed outlier: 3.671A pdb=" N GLU A2313 " --> pdb=" O PRO A2309 " (cutoff:3.500A) Processing helix chain 'A' and resid 2314 through 2316 No H-bonds generated for 'chain 'A' and resid 2314 through 2316' Processing helix chain 'A' and resid 2352 through 2357 removed outlier: 3.669A pdb=" N SER A2357 " --> pdb=" O LEU A2353 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2385 removed outlier: 3.799A pdb=" N ILE A2374 " --> pdb=" O SER A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2410 through 2424 Processing helix chain 'A' and resid 2425 through 2427 No H-bonds generated for 'chain 'A' and resid 2425 through 2427' Processing helix chain 'A' and resid 2432 through 2441 Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.836A pdb=" N LEU A2458 " --> pdb=" O CYS A2454 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2503 removed outlier: 3.735A pdb=" N ARG A2488 " --> pdb=" O GLU A2484 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG A2492 " --> pdb=" O ARG A2488 " (cutoff:3.500A) Processing helix chain 'A' and resid 2507 through 2522 removed outlier: 3.642A pdb=" N THR A2522 " --> pdb=" O ILE A2518 " (cutoff:3.500A) 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 removed outlier: 3.816A pdb=" N VAL A2552 " --> pdb=" O GLN A2549 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2549 through 2552' Processing helix chain 'A' and resid 2558 through 2562 removed outlier: 3.663A pdb=" N VAL A2562 " --> pdb=" O THR A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.785A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2611 Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.234A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2690 removed outlier: 3.603A pdb=" N SER A2681 " --> pdb=" O GLN A2677 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS A2689 " --> pdb=" O GLN A2685 " (cutoff:3.500A) Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2740 through 2756 removed outlier: 3.711A pdb=" N THR A2745 " --> pdb=" O PRO A2741 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN A2746 " --> pdb=" O ALA A2742 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 4.736A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2782 removed outlier: 3.890A pdb=" N GLU A2782 " --> pdb=" O THR A2778 " (cutoff:3.500A) Processing helix chain 'A' and resid 2796 through 2811 Processing helix chain 'A' and resid 2817 through 2833 removed outlier: 3.538A pdb=" N LEU A2821 " --> pdb=" O PRO A2817 " (cutoff:3.500A) Processing helix chain 'A' and resid 2839 through 2858 removed outlier: 3.568A pdb=" N ARG A2843 " --> pdb=" O GLU A2839 " (cutoff:3.500A) Processing helix chain 'A' and resid 2885 through 2904 Processing helix chain 'A' and resid 2912 through 2928 removed outlier: 4.303A pdb=" N LEU A2916 " --> pdb=" O PHE A2912 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP A2917 " --> pdb=" O ASN A2913 " (cutoff:3.500A) Processing helix chain 'A' and resid 2944 through 2954 removed outlier: 3.716A pdb=" N MET A2953 " --> pdb=" O PHE A2949 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A2954 " --> pdb=" O VAL A2950 " (cutoff:3.500A) Processing helix chain 'A' and resid 2968 through 2985 removed outlier: 3.693A pdb=" N PHE A2972 " --> pdb=" O THR A2968 " (cutoff:3.500A) Processing helix chain 'A' and resid 2995 through 3000 removed outlier: 4.300A pdb=" N VAL A2999 " --> pdb=" O ASP A2995 " (cutoff:3.500A) Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 4.179A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU A3006 " --> pdb=" O SER A3002 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG A3007 " --> pdb=" O GLY A3003 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET A3008 " --> pdb=" O PHE A3004 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A3013 " --> pdb=" O ASN A3009 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 removed outlier: 3.770A pdb=" N ALA A3027 " --> pdb=" O GLY A3023 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU A3035 " --> pdb=" O THR A3031 " (cutoff:3.500A) Processing helix chain 'A' and resid 3046 through 3062 Processing helix chain 'A' and resid 3071 through 3082 Processing helix chain 'A' and resid 3082 through 3088 removed outlier: 3.658A pdb=" N PHE A3086 " --> pdb=" O SER A3082 " (cutoff:3.500A) Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3165 removed outlier: 3.521A pdb=" N HIS A3151 " --> pdb=" O CYS A3147 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A3154 " --> pdb=" O VAL A3150 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS A3155 " --> pdb=" O HIS A3151 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 3214 removed outlier: 4.002A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3474 through 3482 removed outlier: 3.606A pdb=" N LEU A3482 " --> pdb=" O LEU A3478 " (cutoff:3.500A) Processing helix chain 'A' and resid 3482 through 3495 removed outlier: 3.725A pdb=" N GLU A3494 " --> pdb=" O GLU A3490 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR A3495 " --> pdb=" O LYS A3491 " (cutoff:3.500A) Processing helix chain 'A' and resid 3495 through 3502 Processing helix chain 'A' and resid 3502 through 3517 removed outlier: 3.548A pdb=" N ALA A3517 " --> pdb=" O PHE A3513 " (cutoff:3.500A) Processing helix chain 'A' and resid 3518 through 3520 No H-bonds generated for 'chain 'A' and resid 3518 through 3520' Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3554 removed outlier: 3.626A pdb=" N LEU A3553 " --> pdb=" O ARG A3549 " (cutoff:3.500A) Processing helix chain 'A' and resid 3555 through 3564 Processing helix chain 'A' and resid 3570 through 3582 Processing helix chain 'A' and resid 3594 through 3604 removed outlier: 3.636A pdb=" N TYR A3604 " --> pdb=" O ILE A3600 " (cutoff:3.500A) Processing helix chain 'A' and resid 3605 through 3608 Processing helix chain 'A' and resid 3618 through 3630 removed outlier: 4.429A pdb=" N GLU A3624 " --> pdb=" O ARG A3620 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A3625 " --> pdb=" O LYS A3621 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE A3629 " --> pdb=" O SER A3625 " (cutoff:3.500A) 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 removed outlier: 3.789A pdb=" N ARG A3695 " --> pdb=" O ASP A3691 " (cutoff:3.500A) Processing helix chain 'A' and resid 3704 through 3721 removed outlier: 3.815A pdb=" N GLN A3711 " --> pdb=" O SER A3707 " (cutoff:3.500A) Processing helix chain 'A' and resid 3721 through 3755 removed outlier: 3.654A pdb=" N LEU A3753 " --> pdb=" O LEU A3749 " (cutoff:3.500A) Processing helix chain 'A' and resid 3764 through 3776 removed outlier: 3.550A pdb=" N THR A3768 " --> pdb=" O ASP A3764 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A3769 " --> pdb=" O THR A3765 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS A3774 " --> pdb=" O LEU A3770 " (cutoff:3.500A) Processing helix chain 'A' and resid 3778 through 3794 removed outlier: 4.104A pdb=" N ARG A3782 " --> pdb=" O ALA A3778 " (cutoff:3.500A) Processing helix chain 'A' and resid 3794 through 3799 removed outlier: 3.755A pdb=" N GLN A3799 " --> pdb=" O GLU A3795 " (cutoff:3.500A) Processing helix chain 'A' and resid 3801 through 3817 Processing helix chain 'A' and resid 3828 through 3843 removed outlier: 3.778A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR A3836 " --> pdb=" O PHE A3832 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR A3841 " --> pdb=" O HIS A3837 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 removed outlier: 3.842A pdb=" N PHE A3864 " --> pdb=" O THR A3860 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN A3865 " --> pdb=" O LYS A3861 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A3871 " --> pdb=" O ALA A3867 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG A3873 " --> pdb=" O ASN A3869 " (cutoff:3.500A) Processing helix chain 'A' and resid 3874 through 3875 No H-bonds generated for 'chain 'A' and resid 3874 through 3875' Processing helix chain 'A' and resid 3876 through 3878 No H-bonds generated for 'chain 'A' and resid 3876 through 3878' Processing helix chain 'A' and resid 3879 through 3892 Processing helix chain 'A' and resid 3901 through 3906 removed outlier: 4.027A pdb=" N GLN A3906 " --> pdb=" O ASP A3902 " (cutoff:3.500A) Processing helix chain 'A' and resid 3906 through 3911 Processing helix chain 'A' and resid 3928 through 3939 removed outlier: 3.665A pdb=" N ALA A3934 " --> pdb=" O GLU A3930 " (cutoff:3.500A) Processing helix chain 'A' and resid 3944 through 3948 removed outlier: 3.512A pdb=" N LEU A3947 " --> pdb=" O PHE A3944 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A3948 " --> pdb=" O LYS A3945 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3944 through 3948' Processing helix chain 'A' and resid 3949 through 3954 removed outlier: 3.683A pdb=" N ALA A3953 " --> pdb=" O ALA A3949 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP A3954 " --> pdb=" O LYS A3950 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3949 through 3954' Processing helix chain 'A' and resid 3956 through 3962 Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4013 removed outlier: 3.662A pdb=" N MET A4004 " --> pdb=" O ARG A4000 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A4010 " --> pdb=" O HIS A4006 " (cutoff:3.500A) Processing helix chain 'A' and resid 4014 through 4018 removed outlier: 4.431A pdb=" N MET A4018 " --> pdb=" O GLU A4015 " (cutoff:3.500A) Processing helix chain 'A' and resid 4026 through 4034 Processing helix chain 'A' and resid 4051 through 4063 removed outlier: 3.992A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A4056 " --> pdb=" O SER A4052 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4091 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: 3.537A pdb=" N GLU A4110 " --> pdb=" O LEU A4106 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS A4111 " --> pdb=" O MET A4107 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER A4115 " --> pdb=" O LYS A4111 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4142 removed outlier: 3.521A pdb=" N LEU A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) Processing helix chain 'A' and resid 4152 through 4164 removed outlier: 3.859A pdb=" N ASN A4156 " --> pdb=" O GLY A4152 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET A4157 " --> pdb=" O VAL A4153 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A4158 " --> pdb=" O LYS A4154 " (cutoff:3.500A) Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.731A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4174 through 4196 removed outlier: 4.023A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG A4195 " --> pdb=" O GLN A4191 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A4196 " --> pdb=" O GLU A4192 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4227 removed outlier: 3.573A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 removed outlier: 4.192A pdb=" N PHE A4305 " --> pdb=" O ARG A4301 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A4306 " --> pdb=" O ARG A4302 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN A4307 " --> pdb=" O GLU A4303 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TRP A4308 " --> pdb=" O GLU A4304 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A4309 " --> pdb=" O PHE A4305 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A4310 " --> pdb=" O VAL A4306 " (cutoff:3.500A) Processing helix chain 'A' and resid 4317 through 4321 Processing helix chain 'A' and resid 4326 through 4347 removed outlier: 4.043A pdb=" N VAL A4330 " --> pdb=" O ASN A4326 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A4331 " --> pdb=" O ALA A4327 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR A4333 " --> pdb=" O ARG A4329 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A4334 " --> pdb=" O VAL A4330 " (cutoff:3.500A) Processing helix chain 'A' and resid 4380 through 4395 removed outlier: 4.098A pdb=" N LEU A4390 " --> pdb=" O ASN A4386 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE A4391 " --> pdb=" O TRP A4387 " (cutoff:3.500A) Proline residue: A4392 - end of helix Processing helix chain 'A' and resid 4407 through 4440 removed outlier: 3.672A pdb=" N PHE A4412 " --> pdb=" O PRO A4408 " (cutoff:3.500A) Processing helix chain 'A' and resid 4448 through 4458 Processing helix chain 'A' and resid 4474 through 4498 removed outlier: 3.707A pdb=" N GLU A4484 " --> pdb=" O SER A4480 " (cutoff:3.500A) Processing helix chain 'A' and resid 4502 through 4507 removed outlier: 4.160A pdb=" N LYS A4505 " --> pdb=" O LYS A4502 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A4507 " --> pdb=" O LEU A4504 " (cutoff:3.500A) Processing helix chain 'A' and resid 4516 through 4533 Processing helix chain 'A' and resid 4631 through 4639 removed outlier: 3.727A pdb=" N PHE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR A4636 " --> pdb=" O PRO A4632 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A4637 " --> pdb=" O ARG A4633 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A4639 " --> pdb=" O PHE A4635 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 297 removed outlier: 4.637A pdb=" N SER B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 297 Processing sheet with id=AA1, first strand: chain 'A' and resid 1844 through 1846 Processing sheet with id=AA2, first strand: chain 'A' and resid 1901 through 1905 removed outlier: 3.516A pdb=" N LEU A2039 " --> pdb=" O SER A1903 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1927 through 1930 Processing sheet with id=AA4, first strand: chain 'A' and resid 1999 through 2000 Processing sheet with id=AA5, first strand: chain 'A' and resid 2249 through 2254 removed outlier: 6.541A pdb=" N VAL A2250 " --> pdb=" O TRP A2300 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL A2302 " --> pdb=" O VAL A2250 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N HIS A2252 " --> pdb=" O VAL A2302 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE A2303 " --> pdb=" O GLU A2344 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A2345 " --> pdb=" O MET A2222 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY A2219 " --> pdb=" O GLY A2360 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL A2362 " --> pdb=" O GLY A2219 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N MET A2221 " --> pdb=" O VAL A2362 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2266 through 2269 removed outlier: 3.709A pdb=" N GLU A2274 " --> pdb=" O ASP A2269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AA8, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AA9, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 6.551A pdb=" N GLU A2616 " --> pdb=" O VAL A2660 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE A2662 " --> pdb=" O GLU A2616 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL A2618 " --> pdb=" O PHE A2662 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2639 through 2644 removed outlier: 3.611A pdb=" N ARG A2642 " --> pdb=" O VAL A2649 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2873 through 2874 Processing sheet with id=AB3, first strand: chain 'A' and resid 2957 through 2959 removed outlier: 3.722A pdb=" N ILE A2993 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE A2990 " --> pdb=" O HIS A3063 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU A2935 " --> pdb=" O MET A3068 " (cutoff:3.500A) removed outlier: 10.629A pdb=" N LEU A2934 " --> pdb=" O TRP A3093 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N GLY A3095 " --> pdb=" O LEU A2934 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE A2936 " --> pdb=" O GLY A3095 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.319A pdb=" N LEU A3633 " --> pdb=" O PHE A3678 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N SER A3680 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A3635 " --> pdb=" O SER A3680 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N THR A3681 " --> pdb=" O PRO A3587 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE A3589 " --> pdb=" O THR A3681 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3654 through 3655 Processing sheet with id=AB6, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 3.839A pdb=" N LYS A4097 " --> pdb=" O ILE A4069 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL A4041 " --> pdb=" O LEU A4126 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N MET A4128 " --> pdb=" O VAL A4041 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N MET A4043 " --> pdb=" O MET A4128 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.100A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4564 through 4566 removed outlier: 4.111A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 95 through 104 removed outlier: 4.224A pdb=" N GLU B 408 " --> pdb=" O ARG B 97 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N VAL B 406 " --> pdb=" O PRO B 99 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N LYS B 101 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 11.356A pdb=" N VAL B 404 " --> pdb=" O LYS B 101 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 111 through 116 removed outlier: 3.783A pdb=" N ARG B 113 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASP B 136 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N PHE B 142 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 153 through 158 removed outlier: 3.516A pdb=" N ASP B 155 " --> pdb=" O CYS B 168 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 169 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 174 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR B 187 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU B 176 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 195 through 200 removed outlier: 6.557A pdb=" N GLU B 220 " --> pdb=" O CYS B 226 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS B 226 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 237 through 242 Processing sheet with id=AC5, first strand: chain 'B' and resid 279 through 284 removed outlier: 3.589A pdb=" N SER B 283 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASP B 324 " --> pdb=" O CYS B 330 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N CYS B 330 " --> pdb=" O ASP B 324 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 341 through 346 removed outlier: 3.650A pdb=" N ALA B 357 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ASP B 366 " --> pdb=" O CYS B 372 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N CYS B 372 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 95 through 104 removed outlier: 4.265A pdb=" N GLU C 408 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL C 406 " --> pdb=" O PRO C 99 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N LYS C 101 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 11.159A pdb=" N VAL C 404 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 396 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY C 398 " --> pdb=" O SER C 385 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER C 385 " --> pdb=" O GLY C 398 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 111 through 116 removed outlier: 4.388A pdb=" N ARG C 113 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG C 144 " --> pdb=" O VAL C 134 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 153 through 158 removed outlier: 3.621A pdb=" N ASP C 155 " --> pdb=" O CYS C 168 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE C 174 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG C 186 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASP C 178 " --> pdb=" O CYS C 184 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS C 184 " --> pdb=" O ASP C 178 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 195 through 200 removed outlier: 7.009A pdb=" N ALA C 210 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL C 198 " --> pdb=" O VAL C 208 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL C 208 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ILE C 200 " --> pdb=" O HIS C 206 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N HIS C 206 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER C 211 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS C 228 " --> pdb=" O MET C 218 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLU C 220 " --> pdb=" O CYS C 226 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N CYS C 226 " --> pdb=" O GLU C 220 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 239 through 242 removed outlier: 3.520A pdb=" N MET C 239 " --> pdb=" O CYS C 252 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA C 270 " --> pdb=" O VAL C 260 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 279 through 281 removed outlier: 3.579A pdb=" N SER C 315 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR C 319 " --> pdb=" O SER C 315 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP C 324 " --> pdb=" O CYS C 330 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N CYS C 330 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 341 through 346 removed outlier: 3.521A pdb=" N GLY C 343 " --> pdb=" O CYS C 356 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASP C 366 " --> pdb=" O CYS C 372 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N CYS C 372 " --> pdb=" O ASP C 366 " (cutoff:3.500A) 1227 hydrogen bonds defined for protein. 3552 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: 21.50 Time building geometry restraints manager: 11.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 23514 1.04 - 1.24: 2060 1.24 - 1.43: 8746 1.43 - 1.63: 14181 1.63 - 1.83: 228 Bond restraints: 48729 Sorted by residual: bond pdb=" C VAL B 278 " pdb=" O VAL B 278 " ideal model delta sigma weight residual 1.236 1.135 0.101 1.19e-02 7.06e+03 7.18e+01 bond pdb=" C4 ADP A4703 " pdb=" C5 ADP A4703 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C5 ADP A4703 " pdb=" C6 ADP A4703 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" CA SER C 399 " pdb=" CB SER C 399 " ideal model delta sigma weight residual 1.533 1.470 0.063 1.60e-02 3.91e+03 1.55e+01 bond pdb=" N VAL C 383 " pdb=" CA VAL C 383 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.15e-02 7.56e+03 1.16e+01 ... (remaining 48724 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 86365 2.39 - 4.78: 1335 4.78 - 7.17: 128 7.17 - 9.56: 19 9.56 - 11.95: 7 Bond angle restraints: 87854 Sorted by residual: angle pdb=" CA THR B 112 " pdb=" C THR B 112 " pdb=" O THR B 112 " ideal model delta sigma weight residual 119.67 110.07 9.60 1.15e+00 7.56e-01 6.97e+01 angle pdb=" CA THR C 384 " pdb=" C THR C 384 " pdb=" O THR C 384 " ideal model delta sigma weight residual 120.90 112.49 8.41 1.03e+00 9.43e-01 6.66e+01 angle pdb=" C THR B 319 " pdb=" CA THR B 319 " pdb=" CB THR B 319 " ideal model delta sigma weight residual 110.62 98.88 11.74 1.51e+00 4.39e-01 6.04e+01 angle pdb=" CA VAL B 278 " pdb=" C VAL B 278 " pdb=" O VAL B 278 " ideal model delta sigma weight residual 120.78 112.20 8.58 1.25e+00 6.40e-01 4.72e+01 angle pdb=" N LYS B 318 " pdb=" CA LYS B 318 " pdb=" C LYS B 318 " ideal model delta sigma weight residual 113.23 105.34 7.89 1.22e+00 6.72e-01 4.18e+01 ... (remaining 87849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 22476 35.38 - 70.75: 599 70.75 - 106.13: 32 106.13 - 141.51: 2 141.51 - 176.88: 1 Dihedral angle restraints: 23110 sinusoidal: 12213 harmonic: 10897 Sorted by residual: dihedral pdb=" O2A ADP A4704 " pdb=" O3A ADP A4704 " pdb=" PA ADP A4704 " pdb=" PB ADP A4704 " ideal model delta sinusoidal sigma weight residual -60.00 116.88 -176.88 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP A4704 " pdb=" O5' ADP A4704 " pdb=" PA ADP A4704 " pdb=" O2A ADP A4704 " ideal model delta sinusoidal sigma weight residual -60.00 70.59 -130.59 1 2.00e+01 2.50e-03 3.96e+01 dihedral pdb=" O1B ADP A4704 " pdb=" O3A ADP A4704 " pdb=" PB ADP A4704 " pdb=" PA ADP A4704 " ideal model delta sinusoidal sigma weight residual -60.00 -171.77 111.77 1 2.00e+01 2.50e-03 3.29e+01 ... (remaining 23107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3549 0.079 - 0.157: 349 0.157 - 0.236: 17 0.236 - 0.315: 5 0.315 - 0.394: 1 Chirality restraints: 3921 Sorted by residual: chirality pdb=" CA VAL B 278 " pdb=" N VAL B 278 " pdb=" C VAL B 278 " pdb=" CB VAL B 278 " both_signs ideal model delta sigma weight residual False 2.44 2.83 -0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CB VAL B 278 " pdb=" CA VAL B 278 " pdb=" CG1 VAL B 278 " pdb=" CG2 VAL B 278 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C2' ATP A4702 " pdb=" C1' ATP A4702 " pdb=" C3' ATP A4702 " pdb=" O2' ATP A4702 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 3918 not shown) Planarity restraints: 7367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 377 " 0.183 2.00e-02 2.50e+03 2.01e-01 6.03e+02 pdb=" CG ASN C 377 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN C 377 " -0.171 2.00e-02 2.50e+03 pdb=" ND2 ASN C 377 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN C 377 " -0.292 2.00e-02 2.50e+03 pdb="HD22 ASN C 377 " 0.304 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A3754 " 0.166 2.00e-02 2.50e+03 1.83e-01 5.03e+02 pdb=" CG ASN A3754 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A3754 " -0.154 2.00e-02 2.50e+03 pdb=" ND2 ASN A3754 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A3754 " 0.278 2.00e-02 2.50e+03 pdb="HD22 ASN A3754 " -0.268 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A3772 " 0.108 2.00e-02 2.50e+03 1.17e-01 2.04e+02 pdb=" CG ASN A3772 " -0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN A3772 " -0.107 2.00e-02 2.50e+03 pdb=" ND2 ASN A3772 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A3772 " 0.171 2.00e-02 2.50e+03 pdb="HD22 ASN A3772 " -0.171 2.00e-02 2.50e+03 ... (remaining 7364 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 1104 2.13 - 2.75: 85117 2.75 - 3.37: 136201 3.37 - 3.98: 169646 3.98 - 4.60: 267668 Nonbonded interactions: 659736 Sorted by model distance: nonbonded pdb=" HG SER B 313 " pdb=" HE1 TRP B 323 " model vdw 1.516 2.100 nonbonded pdb=" OE1 GLU A3720 " pdb=" HH TYR A3801 " model vdw 1.604 2.450 nonbonded pdb=" OD1 ASP C 213 " pdb=" HG1 THR C 215 " model vdw 1.615 2.450 nonbonded pdb=" O LEU A1873 " pdb="HE22 GLN A1876 " model vdw 1.624 2.450 nonbonded pdb=" HG SER C 313 " pdb=" HE1 TRP C 323 " model vdw 1.630 2.100 ... (remaining 659731 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 91 through 100 or (resid 101 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 102 through 107 or (re \ sid 108 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA )) or res \ id 109 through 162 or (resid 163 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 164 through 179 or (resid 180 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 181 \ through 268 or (resid 269 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 270 through 272 or (resid 273 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 274 throu \ gh 286 or (resid 287 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 288 through 294 or (resid 295 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 296 or (resid 2 \ 97 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 308 through 350 or (resid 351 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 352 through 369 or (resid 370 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 371 through 410)) selection = chain 'C' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.590 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: 0.670 Extract box with map and model: 1.450 Check model and map are aligned: 0.330 Set scattering table: 0.430 Process input model: 83.250 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 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 : 0.005 0.110 25161 Z= 0.305 Angle : 0.868 11.738 34237 Z= 0.489 Chirality : 0.048 0.394 3921 Planarity : 0.006 0.112 4362 Dihedral : 14.186 176.883 8989 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.14 % Favored : 96.83 % Rotamer: Outliers : 0.23 % Allowed : 0.74 % Favored : 99.02 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.26 % 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: -0.21 (0.15), residues: 3122 helix: 0.61 (0.14), residues: 1360 sheet: -0.53 (0.23), residues: 494 loop : -0.67 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A1758 HIS 0.023 0.002 HIS C 193 PHE 0.026 0.002 PHE B 310 TYR 0.050 0.002 TYR A1889 ARG 0.016 0.001 ARG A1943 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1661 is missing expected H atoms. Skipping. Residue SER 1662 is missing expected H atoms. Skipping. Residue SER 1663 is missing expected H atoms. Skipping. Residue ILE 1664 is missing expected H atoms. Skipping. Residue LEU 1674 is missing expected H atoms. Skipping. Residue LYS 1729 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue SER 1732 is missing expected H atoms. Skipping. Residue ILE 1733 is missing expected H atoms. Skipping. Residue MET 1798 is missing expected H atoms. Skipping. Residue LYS 1849 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue LEU 1854 is missing expected H atoms. Skipping. Residue SER 1986 is missing expected H atoms. Skipping. Residue ILE 1997 is missing expected H atoms. Skipping. Residue SER 2081 is missing expected H atoms. Skipping. Residue SER 2082 is missing expected H atoms. Skipping. Residue MET 2175 is missing expected H atoms. Skipping. Residue LEU 2244 is missing expected H atoms. Skipping. Residue VAL 2247 is missing expected H atoms. Skipping. Residue THR 2272 is missing expected H atoms. Skipping. Residue SER 2290 is missing expected H atoms. Skipping. Residue VAL 2291 is missing expected H atoms. Skipping. Residue LYS 2349 is missing expected H atoms. Skipping. Residue TYR 2350 is missing expected H atoms. Skipping. Residue LEU 2443 is missing expected H atoms. Skipping. Residue MET 2481 is missing expected H atoms. Skipping. Residue LYS 2589 is missing expected H atoms. Skipping. Residue MET 2615 is missing expected H atoms. Skipping. Residue LYS 2633 is missing expected H atoms. Skipping. Residue MET 2671 is missing expected H atoms. Skipping. Residue LYS 2673 is missing expected H atoms. Skipping. Residue TYR 2674 is missing expected H atoms. Skipping. Residue THR 2676 is missing expected H atoms. Skipping. Residue THR 2815 is missing expected H atoms. Skipping. Residue LYS 2856 is missing expected H atoms. Skipping. Residue LYS 2865 is missing expected H atoms. Skipping. Residue LEU 2905 is missing expected H atoms. Skipping. Residue LYS 2962 is missing expected H atoms. Skipping. Residue LYS 2966 is missing expected H atoms. Skipping. Residue TYR 2967 is missing expected H atoms. Skipping. Residue THR 2968 is missing expected H atoms. Skipping. Residue SER 2997 is missing expected H atoms. Skipping. Residue VAL 2999 is missing expected H atoms. Skipping. Residue LEU 3000 is missing expected H atoms. Skipping. Residue SER 3002 is missing expected H atoms. Skipping. Residue TYR 3026 is missing expected H atoms. Skipping. Residue MET 3030 is missing expected H atoms. Skipping. Residue SER 3071 is missing expected H atoms. Skipping. Residue LYS 3163 is missing expected H atoms. Skipping. Residue THR 3545 is missing expected H atoms. Skipping. Residue SER 3593 is missing expected H atoms. Skipping. Residue LYS 3605 is missing expected H atoms. Skipping. Residue LEU 3615 is missing expected H atoms. Skipping. Residue LEU 3633 is missing expected H atoms. Skipping. Residue THR 3656 is missing expected H atoms. Skipping. Residue LEU 3664 is missing expected H atoms. Skipping. Residue THR 3685 is missing expected H atoms. Skipping. Residue THR 3702 is missing expected H atoms. Skipping. Residue LYS 3757 is missing expected H atoms. Skipping. Residue ILE 3760 is missing expected H atoms. Skipping. Residue LEU 3761 is missing expected H atoms. Skipping. Residue THR 3787 is missing expected H atoms. Skipping. Residue TYR 3825 is missing expected H atoms. Skipping. Residue LYS 3861 is missing expected H atoms. Skipping. Residue TYR 3901 is missing expected H atoms. Skipping. Residue LYS 3945 is missing expected H atoms. Skipping. Residue LEU 3947 is missing expected H atoms. Skipping. Residue ILE 3948 is missing expected H atoms. Skipping. Residue LYS 3950 is missing expected H atoms. Skipping. Residue ILE 3959 is missing expected H atoms. Skipping. Residue SER 3964 is missing expected H atoms. Skipping. Residue SER 3965 is missing expected H atoms. Skipping. Residue THR 3969 is missing expected H atoms. Skipping. Residue TYR 3972 is missing expected H atoms. Skipping. Residue LEU 3973 is missing expected H atoms. Skipping. Residue LEU 4106 is missing expected H atoms. Skipping. Residue LEU 4116 is missing expected H atoms. Skipping. Residue SER 4202 is missing expected H atoms. Skipping. Residue LYS 4203 is missing expected H atoms. Skipping. Residue LYS 4228 is missing expected H atoms. Skipping. Residue ILE 4233 is missing expected H atoms. Skipping. Residue SER 4280 is missing expected H atoms. Skipping. Residue VAL 4330 is missing expected H atoms. Skipping. Residue LEU 4331 is missing expected H atoms. Skipping. Residue LEU 4332 is missing expected H atoms. Skipping. Residue THR 4379 is missing expected H atoms. Skipping. Residue LEU 4380 is missing expected H atoms. Skipping. Residue THR 4382 is missing expected H atoms. Skipping. Residue THR 4383 is missing expected H atoms. Skipping. Residue LYS 4399 is missing expected H atoms. Skipping. Residue ILE 4405 is missing expected H atoms. Skipping. Residue LYS 4406 is missing expected H atoms. Skipping. Residue LYS 4441 is missing expected H atoms. Skipping. Residue LYS 4442 is missing expected H atoms. Skipping. Residue LYS 4443 is missing expected H atoms. Skipping. Residue TYR 4447 is missing expected H atoms. Skipping. Residue LYS 4457 is missing expected H atoms. Skipping. Residue VAL 4469 is missing expected H atoms. Skipping. Residue LYS 4502 is missing expected H atoms. Skipping. Residue LEU 4504 is missing expected H atoms. Skipping. Residue LYS 4505 is missing expected H atoms. Skipping. Residue ILE 4507 is missing expected H atoms. Skipping. Residue VAL 4509 is missing expected H atoms. Skipping. Residue VAL 4516 is missing expected H atoms. Skipping. Residue SER 4533 is missing expected H atoms. Skipping. Residue SER 4535 is missing expected H atoms. Skipping. Residue LEU 4536 is missing expected H atoms. Skipping. Residue LYS 4564 is missing expected H atoms. Skipping. Residue THR 4569 is missing expected H atoms. Skipping. Residue LYS 4574 is missing expected H atoms. Skipping. Residue LEU 4575 is missing expected H atoms. Skipping. Residue SER 4576 is missing expected H atoms. Skipping. Residue LYS 4594 is missing expected H atoms. Skipping. Residue LEU 4611 is missing expected H atoms. Skipping. Residue THR 4628 is missing expected H atoms. Skipping. Residue LYS 4629 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Evaluate side-chains 707 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 701 time to evaluate : 2.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1836 PHE cc_start: 0.6002 (t80) cc_final: 0.5743 (t80) REVERT: A 1897 GLU cc_start: 0.6359 (tp30) cc_final: 0.5932 (tp30) REVERT: A 1929 VAL cc_start: 0.8627 (t) cc_final: 0.8365 (p) REVERT: A 2034 LYS cc_start: 0.8196 (mmmm) cc_final: 0.7944 (ttmm) REVERT: A 2088 PHE cc_start: 0.7751 (m-10) cc_final: 0.7504 (m-10) REVERT: A 2097 LEU cc_start: 0.8485 (mt) cc_final: 0.8245 (mt) REVERT: A 2221 MET cc_start: 0.7065 (ttt) cc_final: 0.6579 (ttt) REVERT: A 2222 MET cc_start: 0.8204 (mtt) cc_final: 0.7890 (mpp) REVERT: A 2361 MET cc_start: 0.6190 (ttm) cc_final: 0.5925 (ttm) REVERT: A 2493 TYR cc_start: 0.7820 (t80) cc_final: 0.7539 (t80) REVERT: A 2823 ARG cc_start: 0.7828 (mmm-85) cc_final: 0.7384 (tpt170) REVERT: A 2852 THR cc_start: 0.8422 (p) cc_final: 0.8157 (t) REVERT: A 2910 VAL cc_start: 0.7950 (p) cc_final: 0.7551 (m) REVERT: A 2924 ARG cc_start: 0.8150 (mtp85) cc_final: 0.7921 (mtp-110) REVERT: A 3205 LEU cc_start: 0.8479 (mt) cc_final: 0.8202 (tt) REVERT: A 3747 LYS cc_start: 0.8662 (tttt) cc_final: 0.8432 (tppt) REVERT: A 4493 SER cc_start: 0.9008 (t) cc_final: 0.8508 (p) REVERT: B 141 ASP cc_start: 0.7662 (m-30) cc_final: 0.7230 (m-30) REVERT: B 254 ASN cc_start: 0.7380 (m110) cc_final: 0.7156 (m110) REVERT: B 356 CYS cc_start: 0.6729 (p) cc_final: 0.6366 (p) REVERT: C 387 ASP cc_start: 0.7619 (t70) cc_final: 0.7197 (t70) outliers start: 6 outliers final: 1 residues processed: 704 average time/residue: 0.7186 time to fit residues: 778.2108 Evaluate side-chains 445 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 444 time to evaluate : 2.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 318 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 7.9990 chunk 239 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 247 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 286 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1856 GLN A2468 ASN ** A2476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3063 HIS A3104 GLN A3155 HIS A3584 ASN A3711 GLN ** A4573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 GLN ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25161 Z= 0.344 Angle : 0.684 7.125 34237 Z= 0.364 Chirality : 0.042 0.184 3921 Planarity : 0.005 0.086 4362 Dihedral : 7.559 163.582 3461 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.72 % Allowed : 10.20 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.08 (0.15), residues: 3122 helix: 0.91 (0.13), residues: 1378 sheet: -0.60 (0.23), residues: 515 loop : -0.80 (0.18), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1758 HIS 0.007 0.001 HIS A3837 PHE 0.027 0.002 PHE A3054 TYR 0.027 0.002 TYR A2748 ARG 0.007 0.001 ARG A3474 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1661 is missing expected H atoms. Skipping. Residue SER 1662 is missing expected H atoms. Skipping. Residue SER 1663 is missing expected H atoms. Skipping. Residue ILE 1664 is missing expected H atoms. Skipping. Residue LEU 1674 is missing expected H atoms. Skipping. Residue LYS 1729 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue SER 1732 is missing expected H atoms. Skipping. Residue ILE 1733 is missing expected H atoms. Skipping. Residue MET 1798 is missing expected H atoms. Skipping. Residue LYS 1849 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue LEU 1854 is missing expected H atoms. Skipping. Residue SER 1986 is missing expected H atoms. Skipping. Residue ILE 1997 is missing expected H atoms. Skipping. Residue SER 2081 is missing expected H atoms. Skipping. Residue SER 2082 is missing expected H atoms. Skipping. Residue MET 2175 is missing expected H atoms. Skipping. Residue LEU 2244 is missing expected H atoms. Skipping. Residue VAL 2247 is missing expected H atoms. Skipping. Residue THR 2272 is missing expected H atoms. Skipping. Residue SER 2290 is missing expected H atoms. Skipping. Residue VAL 2291 is missing expected H atoms. Skipping. Residue LYS 2349 is missing expected H atoms. Skipping. Residue TYR 2350 is missing expected H atoms. Skipping. Residue LEU 2443 is missing expected H atoms. Skipping. Residue MET 2481 is missing expected H atoms. Skipping. Residue LYS 2589 is missing expected H atoms. Skipping. Residue MET 2615 is missing expected H atoms. Skipping. Residue LYS 2633 is missing expected H atoms. Skipping. Residue MET 2671 is missing expected H atoms. Skipping. Residue LYS 2673 is missing expected H atoms. Skipping. Residue TYR 2674 is missing expected H atoms. Skipping. Residue THR 2676 is missing expected H atoms. Skipping. Residue THR 2815 is missing expected H atoms. Skipping. Residue LYS 2856 is missing expected H atoms. Skipping. Residue LYS 2865 is missing expected H atoms. Skipping. Residue LEU 2905 is missing expected H atoms. Skipping. Residue LYS 2962 is missing expected H atoms. Skipping. Residue LYS 2966 is missing expected H atoms. Skipping. Residue TYR 2967 is missing expected H atoms. Skipping. Residue THR 2968 is missing expected H atoms. Skipping. Residue SER 2997 is missing expected H atoms. Skipping. Residue VAL 2999 is missing expected H atoms. Skipping. Residue LEU 3000 is missing expected H atoms. Skipping. Residue SER 3002 is missing expected H atoms. Skipping. Residue TYR 3026 is missing expected H atoms. Skipping. Residue MET 3030 is missing expected H atoms. Skipping. Residue SER 3071 is missing expected H atoms. Skipping. Residue LYS 3163 is missing expected H atoms. Skipping. Residue THR 3545 is missing expected H atoms. Skipping. Residue SER 3593 is missing expected H atoms. Skipping. Residue LYS 3605 is missing expected H atoms. Skipping. Residue LEU 3615 is missing expected H atoms. Skipping. Residue LEU 3633 is missing expected H atoms. Skipping. Residue THR 3656 is missing expected H atoms. Skipping. Residue LEU 3664 is missing expected H atoms. Skipping. Residue THR 3685 is missing expected H atoms. Skipping. Residue THR 3702 is missing expected H atoms. Skipping. Residue LYS 3757 is missing expected H atoms. Skipping. Residue ILE 3760 is missing expected H atoms. Skipping. Residue LEU 3761 is missing expected H atoms. Skipping. Residue THR 3787 is missing expected H atoms. Skipping. Residue TYR 3825 is missing expected H atoms. Skipping. Residue LYS 3861 is missing expected H atoms. Skipping. Residue TYR 3901 is missing expected H atoms. Skipping. Residue LYS 3945 is missing expected H atoms. Skipping. Residue LEU 3947 is missing expected H atoms. Skipping. Residue ILE 3948 is missing expected H atoms. Skipping. Residue LYS 3950 is missing expected H atoms. Skipping. Residue ILE 3959 is missing expected H atoms. Skipping. Residue SER 3964 is missing expected H atoms. Skipping. Residue SER 3965 is missing expected H atoms. Skipping. Residue THR 3969 is missing expected H atoms. Skipping. Residue TYR 3972 is missing expected H atoms. Skipping. Residue LEU 3973 is missing expected H atoms. Skipping. Residue LEU 4106 is missing expected H atoms. Skipping. Residue LEU 4116 is missing expected H atoms. Skipping. Residue SER 4202 is missing expected H atoms. Skipping. Residue LYS 4203 is missing expected H atoms. Skipping. Residue LYS 4228 is missing expected H atoms. Skipping. Residue ILE 4233 is missing expected H atoms. Skipping. Residue SER 4280 is missing expected H atoms. Skipping. Residue VAL 4330 is missing expected H atoms. Skipping. Residue LEU 4331 is missing expected H atoms. Skipping. Residue LEU 4332 is missing expected H atoms. Skipping. Residue THR 4379 is missing expected H atoms. Skipping. Residue LEU 4380 is missing expected H atoms. Skipping. Residue THR 4382 is missing expected H atoms. Skipping. Residue THR 4383 is missing expected H atoms. Skipping. Residue LYS 4399 is missing expected H atoms. Skipping. Residue ILE 4405 is missing expected H atoms. Skipping. Residue LYS 4406 is missing expected H atoms. Skipping. Residue LYS 4441 is missing expected H atoms. Skipping. Residue LYS 4442 is missing expected H atoms. Skipping. Residue LYS 4443 is missing expected H atoms. Skipping. Residue TYR 4447 is missing expected H atoms. Skipping. Residue LYS 4457 is missing expected H atoms. Skipping. Residue VAL 4469 is missing expected H atoms. Skipping. Residue LYS 4502 is missing expected H atoms. Skipping. Residue LEU 4504 is missing expected H atoms. Skipping. Residue LYS 4505 is missing expected H atoms. Skipping. Residue ILE 4507 is missing expected H atoms. Skipping. Residue VAL 4509 is missing expected H atoms. Skipping. Residue VAL 4516 is missing expected H atoms. Skipping. Residue SER 4533 is missing expected H atoms. Skipping. Residue SER 4535 is missing expected H atoms. Skipping. Residue LEU 4536 is missing expected H atoms. Skipping. Residue LYS 4564 is missing expected H atoms. Skipping. Residue THR 4569 is missing expected H atoms. Skipping. Residue LYS 4574 is missing expected H atoms. Skipping. Residue LEU 4575 is missing expected H atoms. Skipping. Residue SER 4576 is missing expected H atoms. Skipping. Residue LYS 4594 is missing expected H atoms. Skipping. Residue LEU 4611 is missing expected H atoms. Skipping. Residue THR 4628 is missing expected H atoms. Skipping. Residue LYS 4629 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Evaluate side-chains 490 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 446 time to evaluate : 2.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1929 VAL cc_start: 0.8705 (t) cc_final: 0.8362 (p) REVERT: A 1934 GLU cc_start: 0.8546 (mp0) cc_final: 0.8192 (mp0) REVERT: A 2034 LYS cc_start: 0.8396 (mmmm) cc_final: 0.8111 (ttmm) REVERT: A 2088 PHE cc_start: 0.7991 (m-10) cc_final: 0.7571 (m-10) REVERT: A 2202 MET cc_start: 0.7544 (mpp) cc_final: 0.7161 (mtm) REVERT: A 2222 MET cc_start: 0.8172 (mtt) cc_final: 0.7516 (mpp) REVERT: A 2823 ARG cc_start: 0.7972 (mmm-85) cc_final: 0.7499 (tpt170) REVERT: A 3176 TYR cc_start: 0.7667 (t80) cc_final: 0.7462 (t80) REVERT: A 3579 MET cc_start: 0.7735 (mmp) cc_final: 0.7307 (mmp) REVERT: A 3735 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7018 (tm-30) REVERT: A 3747 LYS cc_start: 0.8728 (tttt) cc_final: 0.8416 (tppt) REVERT: A 4211 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.7029 (m-30) REVERT: A 4493 SER cc_start: 0.9019 (t) cc_final: 0.8503 (p) REVERT: B 141 ASP cc_start: 0.7450 (m-30) cc_final: 0.7112 (m-30) REVERT: B 254 ASN cc_start: 0.7879 (m110) cc_final: 0.7529 (m110) REVERT: B 339 ASN cc_start: 0.7791 (t0) cc_final: 0.7072 (m-40) REVERT: B 356 CYS cc_start: 0.6386 (p) cc_final: 0.6076 (p) REVERT: C 387 ASP cc_start: 0.7836 (t70) cc_final: 0.7566 (t0) outliers start: 44 outliers final: 34 residues processed: 473 average time/residue: 0.6807 time to fit residues: 511.9381 Evaluate side-chains 441 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 405 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1824 SER Chi-restraints excluded: chain A residue 1969 SER Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2778 THR Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2868 SER Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 3098 SER Chi-restraints excluded: chain A residue 3138 SER Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3212 VAL Chi-restraints excluded: chain A residue 3635 VAL Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3735 GLN Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3819 LYS Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 4073 SER Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4211 ASP Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4427 VAL Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4522 THR Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 159 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 238 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 287 optimal weight: 0.9990 chunk 310 optimal weight: 8.9990 chunk 256 optimal weight: 0.9990 chunk 285 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 230 optimal weight: 0.0970 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1856 GLN ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3014 ASN A4573 ASN ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25161 Z= 0.191 Angle : 0.580 6.808 34237 Z= 0.298 Chirality : 0.040 0.184 3921 Planarity : 0.004 0.074 4362 Dihedral : 6.803 151.724 3457 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.29 % Allowed : 12.67 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.27 (0.15), residues: 3122 helix: 1.34 (0.14), residues: 1383 sheet: -0.63 (0.22), residues: 524 loop : -0.73 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A4387 HIS 0.020 0.001 HIS A3155 PHE 0.020 0.001 PHE A3908 TYR 0.021 0.001 TYR A1889 ARG 0.007 0.000 ARG A1843 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1661 is missing expected H atoms. Skipping. Residue SER 1662 is missing expected H atoms. Skipping. Residue SER 1663 is missing expected H atoms. Skipping. Residue ILE 1664 is missing expected H atoms. Skipping. Residue LEU 1674 is missing expected H atoms. Skipping. Residue LYS 1729 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue SER 1732 is missing expected H atoms. Skipping. Residue ILE 1733 is missing expected H atoms. Skipping. Residue MET 1798 is missing expected H atoms. Skipping. Residue LYS 1849 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue LEU 1854 is missing expected H atoms. Skipping. Residue SER 1986 is missing expected H atoms. Skipping. Residue ILE 1997 is missing expected H atoms. Skipping. Residue SER 2081 is missing expected H atoms. Skipping. Residue SER 2082 is missing expected H atoms. Skipping. Residue MET 2175 is missing expected H atoms. Skipping. Residue LEU 2244 is missing expected H atoms. Skipping. Residue VAL 2247 is missing expected H atoms. Skipping. Residue THR 2272 is missing expected H atoms. Skipping. Residue SER 2290 is missing expected H atoms. Skipping. Residue VAL 2291 is missing expected H atoms. Skipping. Residue LYS 2349 is missing expected H atoms. Skipping. Residue TYR 2350 is missing expected H atoms. Skipping. Residue LEU 2443 is missing expected H atoms. Skipping. Residue MET 2481 is missing expected H atoms. Skipping. Residue LYS 2589 is missing expected H atoms. Skipping. Residue MET 2615 is missing expected H atoms. Skipping. Residue LYS 2633 is missing expected H atoms. Skipping. Residue MET 2671 is missing expected H atoms. Skipping. Residue LYS 2673 is missing expected H atoms. Skipping. Residue TYR 2674 is missing expected H atoms. Skipping. Residue THR 2676 is missing expected H atoms. Skipping. Residue THR 2815 is missing expected H atoms. Skipping. Residue LYS 2856 is missing expected H atoms. Skipping. Residue LYS 2865 is missing expected H atoms. Skipping. Residue LEU 2905 is missing expected H atoms. Skipping. Residue LYS 2962 is missing expected H atoms. Skipping. Residue LYS 2966 is missing expected H atoms. Skipping. Residue TYR 2967 is missing expected H atoms. Skipping. Residue THR 2968 is missing expected H atoms. Skipping. Residue SER 2997 is missing expected H atoms. Skipping. Residue VAL 2999 is missing expected H atoms. Skipping. Residue LEU 3000 is missing expected H atoms. Skipping. Residue SER 3002 is missing expected H atoms. Skipping. Residue TYR 3026 is missing expected H atoms. Skipping. Residue MET 3030 is missing expected H atoms. Skipping. Residue SER 3071 is missing expected H atoms. Skipping. Residue LYS 3163 is missing expected H atoms. Skipping. Residue THR 3545 is missing expected H atoms. Skipping. Residue SER 3593 is missing expected H atoms. Skipping. Residue LYS 3605 is missing expected H atoms. Skipping. Residue LEU 3615 is missing expected H atoms. Skipping. Residue LEU 3633 is missing expected H atoms. Skipping. Residue THR 3656 is missing expected H atoms. Skipping. Residue LEU 3664 is missing expected H atoms. Skipping. Residue THR 3685 is missing expected H atoms. Skipping. Residue THR 3702 is missing expected H atoms. Skipping. Residue LYS 3757 is missing expected H atoms. Skipping. Residue ILE 3760 is missing expected H atoms. Skipping. Residue LEU 3761 is missing expected H atoms. Skipping. Residue THR 3787 is missing expected H atoms. Skipping. Residue TYR 3825 is missing expected H atoms. Skipping. Residue LYS 3861 is missing expected H atoms. Skipping. Residue TYR 3901 is missing expected H atoms. Skipping. Residue LYS 3945 is missing expected H atoms. Skipping. Residue LEU 3947 is missing expected H atoms. Skipping. Residue ILE 3948 is missing expected H atoms. Skipping. Residue LYS 3950 is missing expected H atoms. Skipping. Residue ILE 3959 is missing expected H atoms. Skipping. Residue SER 3964 is missing expected H atoms. Skipping. Residue SER 3965 is missing expected H atoms. Skipping. Residue THR 3969 is missing expected H atoms. Skipping. Residue TYR 3972 is missing expected H atoms. Skipping. Residue LEU 3973 is missing expected H atoms. Skipping. Residue LEU 4106 is missing expected H atoms. Skipping. Residue LEU 4116 is missing expected H atoms. Skipping. Residue SER 4202 is missing expected H atoms. Skipping. Residue LYS 4203 is missing expected H atoms. Skipping. Residue LYS 4228 is missing expected H atoms. Skipping. Residue ILE 4233 is missing expected H atoms. Skipping. Residue SER 4280 is missing expected H atoms. Skipping. Residue VAL 4330 is missing expected H atoms. Skipping. Residue LEU 4331 is missing expected H atoms. Skipping. Residue LEU 4332 is missing expected H atoms. Skipping. Residue THR 4379 is missing expected H atoms. Skipping. Residue LEU 4380 is missing expected H atoms. Skipping. Residue THR 4382 is missing expected H atoms. Skipping. Residue THR 4383 is missing expected H atoms. Skipping. Residue LYS 4399 is missing expected H atoms. Skipping. Residue ILE 4405 is missing expected H atoms. Skipping. Residue LYS 4406 is missing expected H atoms. Skipping. Residue LYS 4441 is missing expected H atoms. Skipping. Residue LYS 4442 is missing expected H atoms. Skipping. Residue LYS 4443 is missing expected H atoms. Skipping. Residue TYR 4447 is missing expected H atoms. Skipping. Residue LYS 4457 is missing expected H atoms. Skipping. Residue VAL 4469 is missing expected H atoms. Skipping. Residue LYS 4502 is missing expected H atoms. Skipping. Residue LEU 4504 is missing expected H atoms. Skipping. Residue LYS 4505 is missing expected H atoms. Skipping. Residue ILE 4507 is missing expected H atoms. Skipping. Residue VAL 4509 is missing expected H atoms. Skipping. Residue VAL 4516 is missing expected H atoms. Skipping. Residue SER 4533 is missing expected H atoms. Skipping. Residue SER 4535 is missing expected H atoms. Skipping. Residue LEU 4536 is missing expected H atoms. Skipping. Residue LYS 4564 is missing expected H atoms. Skipping. Residue THR 4569 is missing expected H atoms. Skipping. Residue LYS 4574 is missing expected H atoms. Skipping. Residue LEU 4575 is missing expected H atoms. Skipping. Residue SER 4576 is missing expected H atoms. Skipping. Residue LYS 4594 is missing expected H atoms. Skipping. Residue LEU 4611 is missing expected H atoms. Skipping. Residue THR 4628 is missing expected H atoms. Skipping. Residue LYS 4629 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Evaluate side-chains 459 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 426 time to evaluate : 2.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1759 SER cc_start: 0.8995 (m) cc_final: 0.8654 (p) REVERT: A 1929 VAL cc_start: 0.8634 (t) cc_final: 0.8277 (p) REVERT: A 2034 LYS cc_start: 0.8361 (mmmm) cc_final: 0.8110 (ttmm) REVERT: A 2202 MET cc_start: 0.7477 (mpp) cc_final: 0.7174 (mtm) REVERT: A 2222 MET cc_start: 0.8044 (mtt) cc_final: 0.7398 (mpp) REVERT: A 2773 MET cc_start: 0.6372 (ptp) cc_final: 0.5964 (ptm) REVERT: A 2823 ARG cc_start: 0.7937 (mmm-85) cc_final: 0.7065 (tpt170) REVERT: A 3579 MET cc_start: 0.7771 (mmp) cc_final: 0.7422 (mmp) REVERT: A 3735 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.6813 (tm-30) REVERT: A 3747 LYS cc_start: 0.8720 (tttt) cc_final: 0.8424 (tppt) REVERT: A 4157 MET cc_start: 0.7619 (mpp) cc_final: 0.7134 (mpp) REVERT: A 4493 SER cc_start: 0.8964 (t) cc_final: 0.8461 (p) REVERT: B 141 ASP cc_start: 0.7541 (m-30) cc_final: 0.7195 (m-30) REVERT: B 254 ASN cc_start: 0.8074 (m110) cc_final: 0.7712 (m110) REVERT: B 339 ASN cc_start: 0.7677 (t0) cc_final: 0.7332 (m110) REVERT: B 365 TRP cc_start: 0.8141 (m100) cc_final: 0.7740 (m100) REVERT: C 195 VAL cc_start: 0.7510 (t) cc_final: 0.7040 (p) outliers start: 33 outliers final: 23 residues processed: 444 average time/residue: 0.6772 time to fit residues: 476.2059 Evaluate side-chains 428 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 404 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1969 SER Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2487 GLU Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2947 SER Chi-restraints excluded: chain A residue 3098 SER Chi-restraints excluded: chain A residue 3212 VAL Chi-restraints excluded: chain A residue 3735 GLN Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 4073 SER Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4427 VAL Chi-restraints excluded: chain A residue 4522 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 284 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 193 optimal weight: 10.0000 chunk 288 optimal weight: 0.4980 chunk 305 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 273 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3155 HIS A4174 ASN A4262 GLN ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25161 Z= 0.192 Angle : 0.559 8.454 34237 Z= 0.286 Chirality : 0.039 0.151 3921 Planarity : 0.004 0.064 4362 Dihedral : 6.374 137.414 3457 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.52 % Allowed : 13.02 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.42 (0.15), residues: 3122 helix: 1.56 (0.14), residues: 1382 sheet: -0.55 (0.23), residues: 510 loop : -0.78 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A4387 HIS 0.008 0.001 HIS A2218 PHE 0.020 0.001 PHE A3054 TYR 0.018 0.001 TYR A1889 ARG 0.006 0.000 ARG A2453 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1661 is missing expected H atoms. Skipping. Residue SER 1662 is missing expected H atoms. Skipping. Residue SER 1663 is missing expected H atoms. Skipping. Residue ILE 1664 is missing expected H atoms. Skipping. Residue LEU 1674 is missing expected H atoms. Skipping. Residue LYS 1729 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue SER 1732 is missing expected H atoms. Skipping. Residue ILE 1733 is missing expected H atoms. Skipping. Residue MET 1798 is missing expected H atoms. Skipping. Residue LYS 1849 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue LEU 1854 is missing expected H atoms. Skipping. Residue SER 1986 is missing expected H atoms. Skipping. Residue ILE 1997 is missing expected H atoms. Skipping. Residue SER 2081 is missing expected H atoms. Skipping. Residue SER 2082 is missing expected H atoms. Skipping. Residue MET 2175 is missing expected H atoms. Skipping. Residue LEU 2244 is missing expected H atoms. Skipping. Residue VAL 2247 is missing expected H atoms. Skipping. Residue THR 2272 is missing expected H atoms. Skipping. Residue SER 2290 is missing expected H atoms. Skipping. Residue VAL 2291 is missing expected H atoms. Skipping. Residue LYS 2349 is missing expected H atoms. Skipping. Residue TYR 2350 is missing expected H atoms. Skipping. Residue LEU 2443 is missing expected H atoms. Skipping. Residue MET 2481 is missing expected H atoms. Skipping. Residue LYS 2589 is missing expected H atoms. Skipping. Residue MET 2615 is missing expected H atoms. Skipping. Residue LYS 2633 is missing expected H atoms. Skipping. Residue MET 2671 is missing expected H atoms. Skipping. Residue LYS 2673 is missing expected H atoms. Skipping. Residue TYR 2674 is missing expected H atoms. Skipping. Residue THR 2676 is missing expected H atoms. Skipping. Residue THR 2815 is missing expected H atoms. Skipping. Residue LYS 2856 is missing expected H atoms. Skipping. Residue LYS 2865 is missing expected H atoms. Skipping. Residue LEU 2905 is missing expected H atoms. Skipping. Residue LYS 2962 is missing expected H atoms. Skipping. Residue LYS 2966 is missing expected H atoms. Skipping. Residue TYR 2967 is missing expected H atoms. Skipping. Residue THR 2968 is missing expected H atoms. Skipping. Residue SER 2997 is missing expected H atoms. Skipping. Residue VAL 2999 is missing expected H atoms. Skipping. Residue LEU 3000 is missing expected H atoms. Skipping. Residue SER 3002 is missing expected H atoms. Skipping. Residue TYR 3026 is missing expected H atoms. Skipping. Residue MET 3030 is missing expected H atoms. Skipping. Residue SER 3071 is missing expected H atoms. Skipping. Residue LYS 3163 is missing expected H atoms. Skipping. Residue THR 3545 is missing expected H atoms. Skipping. Residue SER 3593 is missing expected H atoms. Skipping. Residue LYS 3605 is missing expected H atoms. Skipping. Residue LEU 3615 is missing expected H atoms. Skipping. Residue LEU 3633 is missing expected H atoms. Skipping. Residue THR 3656 is missing expected H atoms. Skipping. Residue LEU 3664 is missing expected H atoms. Skipping. Residue THR 3685 is missing expected H atoms. Skipping. Residue THR 3702 is missing expected H atoms. Skipping. Residue LYS 3757 is missing expected H atoms. Skipping. Residue ILE 3760 is missing expected H atoms. Skipping. Residue LEU 3761 is missing expected H atoms. Skipping. Residue THR 3787 is missing expected H atoms. Skipping. Residue TYR 3825 is missing expected H atoms. Skipping. Residue LYS 3861 is missing expected H atoms. Skipping. Residue TYR 3901 is missing expected H atoms. Skipping. Residue LYS 3945 is missing expected H atoms. Skipping. Residue LEU 3947 is missing expected H atoms. Skipping. Residue ILE 3948 is missing expected H atoms. Skipping. Residue LYS 3950 is missing expected H atoms. Skipping. Residue ILE 3959 is missing expected H atoms. Skipping. Residue SER 3964 is missing expected H atoms. Skipping. Residue SER 3965 is missing expected H atoms. Skipping. Residue THR 3969 is missing expected H atoms. Skipping. Residue TYR 3972 is missing expected H atoms. Skipping. Residue LEU 3973 is missing expected H atoms. Skipping. Residue LEU 4106 is missing expected H atoms. Skipping. Residue LEU 4116 is missing expected H atoms. Skipping. Residue SER 4202 is missing expected H atoms. Skipping. Residue LYS 4203 is missing expected H atoms. Skipping. Residue LYS 4228 is missing expected H atoms. Skipping. Residue ILE 4233 is missing expected H atoms. Skipping. Residue SER 4280 is missing expected H atoms. Skipping. Residue VAL 4330 is missing expected H atoms. Skipping. Residue LEU 4331 is missing expected H atoms. Skipping. Residue LEU 4332 is missing expected H atoms. Skipping. Residue THR 4379 is missing expected H atoms. Skipping. Residue LEU 4380 is missing expected H atoms. Skipping. Residue THR 4382 is missing expected H atoms. Skipping. Residue THR 4383 is missing expected H atoms. Skipping. Residue LYS 4399 is missing expected H atoms. Skipping. Residue ILE 4405 is missing expected H atoms. Skipping. Residue LYS 4406 is missing expected H atoms. Skipping. Residue LYS 4441 is missing expected H atoms. Skipping. Residue LYS 4442 is missing expected H atoms. Skipping. Residue LYS 4443 is missing expected H atoms. Skipping. Residue TYR 4447 is missing expected H atoms. Skipping. Residue LYS 4457 is missing expected H atoms. Skipping. Residue VAL 4469 is missing expected H atoms. Skipping. Residue LYS 4502 is missing expected H atoms. Skipping. Residue LEU 4504 is missing expected H atoms. Skipping. Residue LYS 4505 is missing expected H atoms. Skipping. Residue ILE 4507 is missing expected H atoms. Skipping. Residue VAL 4509 is missing expected H atoms. Skipping. Residue VAL 4516 is missing expected H atoms. Skipping. Residue SER 4533 is missing expected H atoms. Skipping. Residue SER 4535 is missing expected H atoms. Skipping. Residue LEU 4536 is missing expected H atoms. Skipping. Residue LYS 4564 is missing expected H atoms. Skipping. Residue THR 4569 is missing expected H atoms. Skipping. Residue LYS 4574 is missing expected H atoms. Skipping. Residue LEU 4575 is missing expected H atoms. Skipping. Residue SER 4576 is missing expected H atoms. Skipping. Residue LYS 4594 is missing expected H atoms. Skipping. Residue LEU 4611 is missing expected H atoms. Skipping. Residue THR 4628 is missing expected H atoms. Skipping. Residue LYS 4629 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Evaluate side-chains 449 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 410 time to evaluate : 2.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1759 SER cc_start: 0.8945 (m) cc_final: 0.8610 (p) REVERT: A 1836 PHE cc_start: 0.6441 (t80) cc_final: 0.5940 (t80) REVERT: A 1929 VAL cc_start: 0.8630 (t) cc_final: 0.8286 (p) REVERT: A 2034 LYS cc_start: 0.8389 (mmmm) cc_final: 0.8133 (ttmm) REVERT: A 2202 MET cc_start: 0.7461 (mpp) cc_final: 0.7181 (mtm) REVERT: A 2222 MET cc_start: 0.8089 (mtt) cc_final: 0.7469 (mpp) REVERT: A 2773 MET cc_start: 0.6454 (ptp) cc_final: 0.6034 (ptm) REVERT: A 2849 ASN cc_start: 0.7862 (m110) cc_final: 0.7498 (m110) REVERT: A 3579 MET cc_start: 0.7927 (mmp) cc_final: 0.7529 (mmp) REVERT: A 3735 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.6911 (tm-30) REVERT: A 3747 LYS cc_start: 0.8741 (tttt) cc_final: 0.8448 (tppt) REVERT: A 3890 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8114 (mt) REVERT: A 4157 MET cc_start: 0.7633 (mpp) cc_final: 0.7160 (mpp) REVERT: B 141 ASP cc_start: 0.7537 (m-30) cc_final: 0.7228 (m-30) REVERT: B 339 ASN cc_start: 0.7665 (t0) cc_final: 0.7260 (m110) REVERT: B 365 TRP cc_start: 0.8186 (m100) cc_final: 0.7726 (m100) REVERT: C 203 ASN cc_start: 0.7715 (p0) cc_final: 0.7017 (p0) REVERT: C 405 LYS cc_start: 0.8087 (mttm) cc_final: 0.7475 (mttt) outliers start: 39 outliers final: 30 residues processed: 435 average time/residue: 0.6718 time to fit residues: 463.3584 Evaluate side-chains 416 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 384 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1969 SER Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2487 GLU Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 3098 SER Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3212 VAL Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3735 GLN Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3890 ILE Chi-restraints excluded: chain A residue 4073 SER Chi-restraints excluded: chain A residue 4174 ASN Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4211 ASP Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4427 VAL Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4522 THR Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 254 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 227 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 260 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 274 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3155 HIS A4262 GLN ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25161 Z= 0.278 Angle : 0.599 6.570 34237 Z= 0.313 Chirality : 0.040 0.150 3921 Planarity : 0.004 0.067 4362 Dihedral : 6.381 117.106 3457 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.26 % Favored : 95.71 % Rotamer: Outliers : 1.92 % Allowed : 13.96 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.15 (0.15), residues: 3122 helix: 1.30 (0.13), residues: 1387 sheet: -0.65 (0.22), residues: 522 loop : -0.90 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A4387 HIS 0.009 0.001 HIS C 191 PHE 0.022 0.002 PHE A3054 TYR 0.016 0.002 TYR A1889 ARG 0.005 0.000 ARG A1843 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1661 is missing expected H atoms. Skipping. Residue SER 1662 is missing expected H atoms. Skipping. Residue SER 1663 is missing expected H atoms. Skipping. Residue ILE 1664 is missing expected H atoms. Skipping. Residue LEU 1674 is missing expected H atoms. Skipping. Residue LYS 1729 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue SER 1732 is missing expected H atoms. Skipping. Residue ILE 1733 is missing expected H atoms. Skipping. Residue MET 1798 is missing expected H atoms. Skipping. Residue LYS 1849 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue LEU 1854 is missing expected H atoms. Skipping. Residue SER 1986 is missing expected H atoms. Skipping. Residue ILE 1997 is missing expected H atoms. Skipping. Residue SER 2081 is missing expected H atoms. Skipping. Residue SER 2082 is missing expected H atoms. Skipping. Residue MET 2175 is missing expected H atoms. Skipping. Residue LEU 2244 is missing expected H atoms. Skipping. Residue VAL 2247 is missing expected H atoms. Skipping. Residue THR 2272 is missing expected H atoms. Skipping. Residue SER 2290 is missing expected H atoms. Skipping. Residue VAL 2291 is missing expected H atoms. Skipping. Residue LYS 2349 is missing expected H atoms. Skipping. Residue TYR 2350 is missing expected H atoms. Skipping. Residue LEU 2443 is missing expected H atoms. Skipping. Residue MET 2481 is missing expected H atoms. Skipping. Residue LYS 2589 is missing expected H atoms. Skipping. Residue MET 2615 is missing expected H atoms. Skipping. Residue LYS 2633 is missing expected H atoms. Skipping. Residue MET 2671 is missing expected H atoms. Skipping. Residue LYS 2673 is missing expected H atoms. Skipping. Residue TYR 2674 is missing expected H atoms. Skipping. Residue THR 2676 is missing expected H atoms. Skipping. Residue THR 2815 is missing expected H atoms. Skipping. Residue LYS 2856 is missing expected H atoms. Skipping. Residue LYS 2865 is missing expected H atoms. Skipping. Residue LEU 2905 is missing expected H atoms. Skipping. Residue LYS 2962 is missing expected H atoms. Skipping. Residue LYS 2966 is missing expected H atoms. Skipping. Residue TYR 2967 is missing expected H atoms. Skipping. Residue THR 2968 is missing expected H atoms. Skipping. Residue SER 2997 is missing expected H atoms. Skipping. Residue VAL 2999 is missing expected H atoms. Skipping. Residue LEU 3000 is missing expected H atoms. Skipping. Residue SER 3002 is missing expected H atoms. Skipping. Residue TYR 3026 is missing expected H atoms. Skipping. Residue MET 3030 is missing expected H atoms. Skipping. Residue SER 3071 is missing expected H atoms. Skipping. Residue LYS 3163 is missing expected H atoms. Skipping. Residue THR 3545 is missing expected H atoms. Skipping. Residue SER 3593 is missing expected H atoms. Skipping. Residue LYS 3605 is missing expected H atoms. Skipping. Residue LEU 3615 is missing expected H atoms. Skipping. Residue LEU 3633 is missing expected H atoms. Skipping. Residue THR 3656 is missing expected H atoms. Skipping. Residue LEU 3664 is missing expected H atoms. Skipping. Residue THR 3685 is missing expected H atoms. Skipping. Residue THR 3702 is missing expected H atoms. Skipping. Residue LYS 3757 is missing expected H atoms. Skipping. Residue ILE 3760 is missing expected H atoms. Skipping. Residue LEU 3761 is missing expected H atoms. Skipping. Residue THR 3787 is missing expected H atoms. Skipping. Residue TYR 3825 is missing expected H atoms. Skipping. Residue LYS 3861 is missing expected H atoms. Skipping. Residue TYR 3901 is missing expected H atoms. Skipping. Residue LYS 3945 is missing expected H atoms. Skipping. Residue LEU 3947 is missing expected H atoms. Skipping. Residue ILE 3948 is missing expected H atoms. Skipping. Residue LYS 3950 is missing expected H atoms. Skipping. Residue ILE 3959 is missing expected H atoms. Skipping. Residue SER 3964 is missing expected H atoms. Skipping. Residue SER 3965 is missing expected H atoms. Skipping. Residue THR 3969 is missing expected H atoms. Skipping. Residue TYR 3972 is missing expected H atoms. Skipping. Residue LEU 3973 is missing expected H atoms. Skipping. Residue LEU 4106 is missing expected H atoms. Skipping. Residue LEU 4116 is missing expected H atoms. Skipping. Residue SER 4202 is missing expected H atoms. Skipping. Residue LYS 4203 is missing expected H atoms. Skipping. Residue LYS 4228 is missing expected H atoms. Skipping. Residue ILE 4233 is missing expected H atoms. Skipping. Residue SER 4280 is missing expected H atoms. Skipping. Residue VAL 4330 is missing expected H atoms. Skipping. Residue LEU 4331 is missing expected H atoms. Skipping. Residue LEU 4332 is missing expected H atoms. Skipping. Residue THR 4379 is missing expected H atoms. Skipping. Residue LEU 4380 is missing expected H atoms. Skipping. Residue THR 4382 is missing expected H atoms. Skipping. Residue THR 4383 is missing expected H atoms. Skipping. Residue LYS 4399 is missing expected H atoms. Skipping. Residue ILE 4405 is missing expected H atoms. Skipping. Residue LYS 4406 is missing expected H atoms. Skipping. Residue LYS 4441 is missing expected H atoms. Skipping. Residue LYS 4442 is missing expected H atoms. Skipping. Residue LYS 4443 is missing expected H atoms. Skipping. Residue TYR 4447 is missing expected H atoms. Skipping. Residue LYS 4457 is missing expected H atoms. Skipping. Residue VAL 4469 is missing expected H atoms. Skipping. Residue LYS 4502 is missing expected H atoms. Skipping. Residue LEU 4504 is missing expected H atoms. Skipping. Residue LYS 4505 is missing expected H atoms. Skipping. Residue ILE 4507 is missing expected H atoms. Skipping. Residue VAL 4509 is missing expected H atoms. Skipping. Residue VAL 4516 is missing expected H atoms. Skipping. Residue SER 4533 is missing expected H atoms. Skipping. Residue SER 4535 is missing expected H atoms. Skipping. Residue LEU 4536 is missing expected H atoms. Skipping. Residue LYS 4564 is missing expected H atoms. Skipping. Residue THR 4569 is missing expected H atoms. Skipping. Residue LYS 4574 is missing expected H atoms. Skipping. Residue LEU 4575 is missing expected H atoms. Skipping. Residue SER 4576 is missing expected H atoms. Skipping. Residue LYS 4594 is missing expected H atoms. Skipping. Residue LEU 4611 is missing expected H atoms. Skipping. Residue THR 4628 is missing expected H atoms. Skipping. Residue LYS 4629 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Evaluate side-chains 438 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 389 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.5121 (tpt) cc_final: 0.4907 (tpt) REVERT: A 1759 SER cc_start: 0.9009 (m) cc_final: 0.8682 (p) REVERT: A 1846 PHE cc_start: 0.7778 (t80) cc_final: 0.7438 (t80) REVERT: A 1897 GLU cc_start: 0.7085 (tp30) cc_final: 0.6761 (tp30) REVERT: A 1929 VAL cc_start: 0.8561 (t) cc_final: 0.8221 (p) REVERT: A 2034 LYS cc_start: 0.8558 (mmmm) cc_final: 0.8217 (ttmm) REVERT: A 2202 MET cc_start: 0.7545 (mpp) cc_final: 0.7272 (mtm) REVERT: A 2773 MET cc_start: 0.6563 (ptp) cc_final: 0.6133 (ptm) REVERT: A 2849 ASN cc_start: 0.7954 (m110) cc_final: 0.7555 (m110) REVERT: A 3094 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.6498 (t80) REVERT: A 3198 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7547 (tm-30) REVERT: A 3579 MET cc_start: 0.8081 (mmp) cc_final: 0.6690 (mmp) REVERT: A 3735 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7008 (tm-30) REVERT: A 3747 LYS cc_start: 0.8775 (tttt) cc_final: 0.8477 (tppt) REVERT: A 3890 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8233 (mt) REVERT: A 4004 MET cc_start: 0.6859 (tpt) cc_final: 0.6297 (tpt) REVERT: A 4493 SER cc_start: 0.9066 (t) cc_final: 0.8629 (p) REVERT: B 141 ASP cc_start: 0.7604 (m-30) cc_final: 0.7324 (m-30) REVERT: C 203 ASN cc_start: 0.7626 (p0) cc_final: 0.6971 (p0) REVERT: C 405 LYS cc_start: 0.8075 (mttm) cc_final: 0.7466 (mttt) outliers start: 49 outliers final: 40 residues processed: 421 average time/residue: 0.6409 time to fit residues: 435.0699 Evaluate side-chains 414 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 371 time to evaluate : 2.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1824 SER Chi-restraints excluded: chain A residue 1969 SER Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2487 GLU Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2659 LEU Chi-restraints excluded: chain A residue 2778 THR Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2992 PHE Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3098 SER Chi-restraints excluded: chain A residue 3138 SER Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3212 VAL Chi-restraints excluded: chain A residue 3578 ILE Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3735 GLN Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3890 ILE Chi-restraints excluded: chain A residue 4073 SER Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4211 ASP Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4427 VAL Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4486 ILE Chi-restraints excluded: chain A residue 4522 THR Chi-restraints excluded: chain B residue 135 TRP Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 102 optimal weight: 1.9990 chunk 275 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 179 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 305 optimal weight: 9.9990 chunk 253 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4262 GLN A4573 ASN C 379 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25161 Z= 0.192 Angle : 0.560 7.832 34237 Z= 0.286 Chirality : 0.040 0.160 3921 Planarity : 0.004 0.068 4362 Dihedral : 6.054 105.045 3457 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.86 % Rotamer: Outliers : 1.92 % Allowed : 14.50 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.43 (0.15), residues: 3122 helix: 1.56 (0.14), residues: 1387 sheet: -0.61 (0.22), residues: 523 loop : -0.73 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A4387 HIS 0.009 0.001 HIS A2218 PHE 0.021 0.001 PHE A3086 TYR 0.012 0.001 TYR A2748 ARG 0.004 0.000 ARG A1843 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1661 is missing expected H atoms. Skipping. Residue SER 1662 is missing expected H atoms. Skipping. Residue SER 1663 is missing expected H atoms. Skipping. Residue ILE 1664 is missing expected H atoms. Skipping. Residue LEU 1674 is missing expected H atoms. Skipping. Residue LYS 1729 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue SER 1732 is missing expected H atoms. Skipping. Residue ILE 1733 is missing expected H atoms. Skipping. Residue MET 1798 is missing expected H atoms. Skipping. Residue LYS 1849 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue LEU 1854 is missing expected H atoms. Skipping. Residue SER 1986 is missing expected H atoms. Skipping. Residue ILE 1997 is missing expected H atoms. Skipping. Residue SER 2081 is missing expected H atoms. Skipping. Residue SER 2082 is missing expected H atoms. Skipping. Residue MET 2175 is missing expected H atoms. Skipping. Residue LEU 2244 is missing expected H atoms. Skipping. Residue VAL 2247 is missing expected H atoms. Skipping. Residue THR 2272 is missing expected H atoms. Skipping. Residue SER 2290 is missing expected H atoms. Skipping. Residue VAL 2291 is missing expected H atoms. Skipping. Residue LYS 2349 is missing expected H atoms. Skipping. Residue TYR 2350 is missing expected H atoms. Skipping. Residue LEU 2443 is missing expected H atoms. Skipping. Residue MET 2481 is missing expected H atoms. Skipping. Residue LYS 2589 is missing expected H atoms. Skipping. Residue MET 2615 is missing expected H atoms. Skipping. Residue LYS 2633 is missing expected H atoms. Skipping. Residue MET 2671 is missing expected H atoms. Skipping. Residue LYS 2673 is missing expected H atoms. Skipping. Residue TYR 2674 is missing expected H atoms. Skipping. Residue THR 2676 is missing expected H atoms. Skipping. Residue THR 2815 is missing expected H atoms. Skipping. Residue LYS 2856 is missing expected H atoms. Skipping. Residue LYS 2865 is missing expected H atoms. Skipping. Residue LEU 2905 is missing expected H atoms. Skipping. Residue LYS 2962 is missing expected H atoms. Skipping. Residue LYS 2966 is missing expected H atoms. Skipping. Residue TYR 2967 is missing expected H atoms. Skipping. Residue THR 2968 is missing expected H atoms. Skipping. Residue SER 2997 is missing expected H atoms. Skipping. Residue VAL 2999 is missing expected H atoms. Skipping. Residue LEU 3000 is missing expected H atoms. Skipping. Residue SER 3002 is missing expected H atoms. Skipping. Residue TYR 3026 is missing expected H atoms. Skipping. Residue MET 3030 is missing expected H atoms. Skipping. Residue SER 3071 is missing expected H atoms. Skipping. Residue LYS 3163 is missing expected H atoms. Skipping. Residue THR 3545 is missing expected H atoms. Skipping. Residue SER 3593 is missing expected H atoms. Skipping. Residue LYS 3605 is missing expected H atoms. Skipping. Residue LEU 3615 is missing expected H atoms. Skipping. Residue LEU 3633 is missing expected H atoms. Skipping. Residue THR 3656 is missing expected H atoms. Skipping. Residue LEU 3664 is missing expected H atoms. Skipping. Residue THR 3685 is missing expected H atoms. Skipping. Residue THR 3702 is missing expected H atoms. Skipping. Residue LYS 3757 is missing expected H atoms. Skipping. Residue ILE 3760 is missing expected H atoms. Skipping. Residue LEU 3761 is missing expected H atoms. Skipping. Residue THR 3787 is missing expected H atoms. Skipping. Residue TYR 3825 is missing expected H atoms. Skipping. Residue LYS 3861 is missing expected H atoms. Skipping. Residue TYR 3901 is missing expected H atoms. Skipping. Residue LYS 3945 is missing expected H atoms. Skipping. Residue LEU 3947 is missing expected H atoms. Skipping. Residue ILE 3948 is missing expected H atoms. Skipping. Residue LYS 3950 is missing expected H atoms. Skipping. Residue ILE 3959 is missing expected H atoms. Skipping. Residue SER 3964 is missing expected H atoms. Skipping. Residue SER 3965 is missing expected H atoms. Skipping. Residue THR 3969 is missing expected H atoms. Skipping. Residue TYR 3972 is missing expected H atoms. Skipping. Residue LEU 3973 is missing expected H atoms. Skipping. Residue LEU 4106 is missing expected H atoms. Skipping. Residue LEU 4116 is missing expected H atoms. Skipping. Residue SER 4202 is missing expected H atoms. Skipping. Residue LYS 4203 is missing expected H atoms. Skipping. Residue LYS 4228 is missing expected H atoms. Skipping. Residue ILE 4233 is missing expected H atoms. Skipping. Residue SER 4280 is missing expected H atoms. Skipping. Residue VAL 4330 is missing expected H atoms. Skipping. Residue LEU 4331 is missing expected H atoms. Skipping. Residue LEU 4332 is missing expected H atoms. Skipping. Residue THR 4379 is missing expected H atoms. Skipping. Residue LEU 4380 is missing expected H atoms. Skipping. Residue THR 4382 is missing expected H atoms. Skipping. Residue THR 4383 is missing expected H atoms. Skipping. Residue LYS 4399 is missing expected H atoms. Skipping. Residue ILE 4405 is missing expected H atoms. Skipping. Residue LYS 4406 is missing expected H atoms. Skipping. Residue LYS 4441 is missing expected H atoms. Skipping. Residue LYS 4442 is missing expected H atoms. Skipping. Residue LYS 4443 is missing expected H atoms. Skipping. Residue TYR 4447 is missing expected H atoms. Skipping. Residue LYS 4457 is missing expected H atoms. Skipping. Residue VAL 4469 is missing expected H atoms. Skipping. Residue LYS 4502 is missing expected H atoms. Skipping. Residue LEU 4504 is missing expected H atoms. Skipping. Residue LYS 4505 is missing expected H atoms. Skipping. Residue ILE 4507 is missing expected H atoms. Skipping. Residue VAL 4509 is missing expected H atoms. Skipping. Residue VAL 4516 is missing expected H atoms. Skipping. Residue SER 4533 is missing expected H atoms. Skipping. Residue SER 4535 is missing expected H atoms. Skipping. Residue LEU 4536 is missing expected H atoms. Skipping. Residue LYS 4564 is missing expected H atoms. Skipping. Residue THR 4569 is missing expected H atoms. Skipping. Residue LYS 4574 is missing expected H atoms. Skipping. Residue LEU 4575 is missing expected H atoms. Skipping. Residue SER 4576 is missing expected H atoms. Skipping. Residue LYS 4594 is missing expected H atoms. Skipping. Residue LEU 4611 is missing expected H atoms. Skipping. Residue THR 4628 is missing expected H atoms. Skipping. Residue LYS 4629 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Evaluate side-chains 440 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 391 time to evaluate : 2.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1657 MET cc_start: 0.5131 (tpt) cc_final: 0.4911 (tpt) REVERT: A 1759 SER cc_start: 0.9042 (m) cc_final: 0.8717 (p) REVERT: A 1836 PHE cc_start: 0.6400 (t80) cc_final: 0.5857 (t80) REVERT: A 1846 PHE cc_start: 0.7645 (t80) cc_final: 0.7371 (t80) REVERT: A 1897 GLU cc_start: 0.7007 (tp30) cc_final: 0.6733 (tp30) REVERT: A 1929 VAL cc_start: 0.8637 (t) cc_final: 0.8296 (p) REVERT: A 2034 LYS cc_start: 0.8493 (mmmm) cc_final: 0.8176 (ttmm) REVERT: A 2202 MET cc_start: 0.7482 (mpp) cc_final: 0.7217 (mtm) REVERT: A 2222 MET cc_start: 0.8009 (mtt) cc_final: 0.7415 (mpp) REVERT: A 2773 MET cc_start: 0.6466 (ptp) cc_final: 0.6055 (ptm) REVERT: A 2823 ARG cc_start: 0.8158 (mmm-85) cc_final: 0.7634 (tpt-90) REVERT: A 2849 ASN cc_start: 0.7955 (m110) cc_final: 0.7578 (m110) REVERT: A 3094 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.6375 (t80) REVERT: A 3176 TYR cc_start: 0.7107 (t80) cc_final: 0.6804 (t80) REVERT: A 3198 GLN cc_start: 0.7818 (tm-30) cc_final: 0.7481 (tm-30) REVERT: A 3579 MET cc_start: 0.8108 (mmp) cc_final: 0.6847 (mmp) REVERT: A 3735 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.6992 (tm-30) REVERT: A 3747 LYS cc_start: 0.8750 (tttt) cc_final: 0.8460 (tppt) REVERT: A 3890 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8138 (mt) REVERT: A 4493 SER cc_start: 0.9086 (t) cc_final: 0.8626 (p) REVERT: B 141 ASP cc_start: 0.7596 (m-30) cc_final: 0.7246 (m-30) REVERT: B 339 ASN cc_start: 0.7673 (t0) cc_final: 0.7269 (m110) REVERT: C 203 ASN cc_start: 0.7606 (p0) cc_final: 0.6972 (p0) REVERT: C 405 LYS cc_start: 0.8048 (mttm) cc_final: 0.7365 (mtpt) outliers start: 49 outliers final: 39 residues processed: 422 average time/residue: 0.7501 time to fit residues: 514.3635 Evaluate side-chains 419 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 377 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1969 SER Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2306 ASP Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2487 GLU Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2778 THR Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2992 PHE Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3098 SER Chi-restraints excluded: chain A residue 3138 SER Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3212 VAL Chi-restraints excluded: chain A residue 3578 ILE Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3735 GLN Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3890 ILE Chi-restraints excluded: chain A residue 4073 SER Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4211 ASP Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4427 VAL Chi-restraints excluded: chain A residue 4522 THR Chi-restraints excluded: chain B residue 135 TRP Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 294 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 257 optimal weight: 0.7980 chunk 170 optimal weight: 0.7980 chunk 304 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4262 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25161 Z= 0.225 Angle : 0.569 8.171 34237 Z= 0.294 Chirality : 0.039 0.155 3921 Planarity : 0.004 0.066 4362 Dihedral : 5.994 90.968 3457 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.07 % Favored : 95.90 % Rotamer: Outliers : 2.11 % Allowed : 14.66 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.41 (0.15), residues: 3122 helix: 1.56 (0.14), residues: 1389 sheet: -0.60 (0.23), residues: 520 loop : -0.79 (0.18), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 135 HIS 0.009 0.001 HIS A2218 PHE 0.021 0.001 PHE A3054 TYR 0.014 0.001 TYR A2496 ARG 0.005 0.000 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1661 is missing expected H atoms. Skipping. Residue SER 1662 is missing expected H atoms. Skipping. Residue SER 1663 is missing expected H atoms. Skipping. Residue ILE 1664 is missing expected H atoms. Skipping. Residue LEU 1674 is missing expected H atoms. Skipping. Residue LYS 1729 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue SER 1732 is missing expected H atoms. Skipping. Residue ILE 1733 is missing expected H atoms. Skipping. Residue MET 1798 is missing expected H atoms. Skipping. Residue LYS 1849 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue LEU 1854 is missing expected H atoms. Skipping. Residue SER 1986 is missing expected H atoms. Skipping. Residue ILE 1997 is missing expected H atoms. Skipping. Residue SER 2081 is missing expected H atoms. Skipping. Residue SER 2082 is missing expected H atoms. Skipping. Residue MET 2175 is missing expected H atoms. Skipping. Residue LEU 2244 is missing expected H atoms. Skipping. Residue VAL 2247 is missing expected H atoms. Skipping. Residue THR 2272 is missing expected H atoms. Skipping. Residue SER 2290 is missing expected H atoms. Skipping. Residue VAL 2291 is missing expected H atoms. Skipping. Residue LYS 2349 is missing expected H atoms. Skipping. Residue TYR 2350 is missing expected H atoms. Skipping. Residue LEU 2443 is missing expected H atoms. Skipping. Residue MET 2481 is missing expected H atoms. Skipping. Residue LYS 2589 is missing expected H atoms. Skipping. Residue MET 2615 is missing expected H atoms. Skipping. Residue LYS 2633 is missing expected H atoms. Skipping. Residue MET 2671 is missing expected H atoms. Skipping. Residue LYS 2673 is missing expected H atoms. Skipping. Residue TYR 2674 is missing expected H atoms. Skipping. Residue THR 2676 is missing expected H atoms. Skipping. Residue THR 2815 is missing expected H atoms. Skipping. Residue LYS 2856 is missing expected H atoms. Skipping. Residue LYS 2865 is missing expected H atoms. Skipping. Residue LEU 2905 is missing expected H atoms. Skipping. Residue LYS 2962 is missing expected H atoms. Skipping. Residue LYS 2966 is missing expected H atoms. Skipping. Residue TYR 2967 is missing expected H atoms. Skipping. Residue THR 2968 is missing expected H atoms. Skipping. Residue SER 2997 is missing expected H atoms. Skipping. Residue VAL 2999 is missing expected H atoms. Skipping. Residue LEU 3000 is missing expected H atoms. Skipping. Residue SER 3002 is missing expected H atoms. Skipping. Residue TYR 3026 is missing expected H atoms. Skipping. Residue MET 3030 is missing expected H atoms. Skipping. Residue SER 3071 is missing expected H atoms. Skipping. Residue LYS 3163 is missing expected H atoms. Skipping. Residue THR 3545 is missing expected H atoms. Skipping. Residue SER 3593 is missing expected H atoms. Skipping. Residue LYS 3605 is missing expected H atoms. Skipping. Residue LEU 3615 is missing expected H atoms. Skipping. Residue LEU 3633 is missing expected H atoms. Skipping. Residue THR 3656 is missing expected H atoms. Skipping. Residue LEU 3664 is missing expected H atoms. Skipping. Residue THR 3685 is missing expected H atoms. Skipping. Residue THR 3702 is missing expected H atoms. Skipping. Residue LYS 3757 is missing expected H atoms. Skipping. Residue ILE 3760 is missing expected H atoms. Skipping. Residue LEU 3761 is missing expected H atoms. Skipping. Residue THR 3787 is missing expected H atoms. Skipping. Residue TYR 3825 is missing expected H atoms. Skipping. Residue LYS 3861 is missing expected H atoms. Skipping. Residue TYR 3901 is missing expected H atoms. Skipping. Residue LYS 3945 is missing expected H atoms. Skipping. Residue LEU 3947 is missing expected H atoms. Skipping. Residue ILE 3948 is missing expected H atoms. Skipping. Residue LYS 3950 is missing expected H atoms. Skipping. Residue ILE 3959 is missing expected H atoms. Skipping. Residue SER 3964 is missing expected H atoms. Skipping. Residue SER 3965 is missing expected H atoms. Skipping. Residue THR 3969 is missing expected H atoms. Skipping. Residue TYR 3972 is missing expected H atoms. Skipping. Residue LEU 3973 is missing expected H atoms. Skipping. Residue LEU 4106 is missing expected H atoms. Skipping. Residue LEU 4116 is missing expected H atoms. Skipping. Residue SER 4202 is missing expected H atoms. Skipping. Residue LYS 4203 is missing expected H atoms. Skipping. Residue LYS 4228 is missing expected H atoms. Skipping. Residue ILE 4233 is missing expected H atoms. Skipping. Residue SER 4280 is missing expected H atoms. Skipping. Residue VAL 4330 is missing expected H atoms. Skipping. Residue LEU 4331 is missing expected H atoms. Skipping. Residue LEU 4332 is missing expected H atoms. Skipping. Residue THR 4379 is missing expected H atoms. Skipping. Residue LEU 4380 is missing expected H atoms. Skipping. Residue THR 4382 is missing expected H atoms. Skipping. Residue THR 4383 is missing expected H atoms. Skipping. Residue LYS 4399 is missing expected H atoms. Skipping. Residue ILE 4405 is missing expected H atoms. Skipping. Residue LYS 4406 is missing expected H atoms. Skipping. Residue LYS 4441 is missing expected H atoms. Skipping. Residue LYS 4442 is missing expected H atoms. Skipping. Residue LYS 4443 is missing expected H atoms. Skipping. Residue TYR 4447 is missing expected H atoms. Skipping. Residue LYS 4457 is missing expected H atoms. Skipping. Residue VAL 4469 is missing expected H atoms. Skipping. Residue LYS 4502 is missing expected H atoms. Skipping. Residue LEU 4504 is missing expected H atoms. Skipping. Residue LYS 4505 is missing expected H atoms. Skipping. Residue ILE 4507 is missing expected H atoms. Skipping. Residue VAL 4509 is missing expected H atoms. Skipping. Residue VAL 4516 is missing expected H atoms. Skipping. Residue SER 4533 is missing expected H atoms. Skipping. Residue SER 4535 is missing expected H atoms. Skipping. Residue LEU 4536 is missing expected H atoms. Skipping. Residue LYS 4564 is missing expected H atoms. Skipping. Residue THR 4569 is missing expected H atoms. Skipping. Residue LYS 4574 is missing expected H atoms. Skipping. Residue LEU 4575 is missing expected H atoms. Skipping. Residue SER 4576 is missing expected H atoms. Skipping. Residue LYS 4594 is missing expected H atoms. Skipping. Residue LEU 4611 is missing expected H atoms. Skipping. Residue THR 4628 is missing expected H atoms. Skipping. Residue LYS 4629 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Evaluate side-chains 435 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 381 time to evaluate : 2.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1759 SER cc_start: 0.9034 (m) cc_final: 0.8692 (p) REVERT: A 1836 PHE cc_start: 0.6354 (t80) cc_final: 0.5927 (t80) REVERT: A 1846 PHE cc_start: 0.7744 (t80) cc_final: 0.7442 (t80) REVERT: A 1897 GLU cc_start: 0.7109 (tp30) cc_final: 0.6848 (tp30) REVERT: A 1929 VAL cc_start: 0.8618 (t) cc_final: 0.8255 (p) REVERT: A 2034 LYS cc_start: 0.8531 (mmmm) cc_final: 0.8199 (ttmm) REVERT: A 2202 MET cc_start: 0.7520 (mpp) cc_final: 0.7241 (mtm) REVERT: A 2222 MET cc_start: 0.8016 (mtt) cc_final: 0.7418 (mpp) REVERT: A 2773 MET cc_start: 0.6501 (ptp) cc_final: 0.6077 (ptm) REVERT: A 2849 ASN cc_start: 0.7860 (m110) cc_final: 0.7487 (m110) REVERT: A 2872 LEU cc_start: 0.8495 (mt) cc_final: 0.7940 (mp) REVERT: A 3094 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.6458 (t80) REVERT: A 3176 TYR cc_start: 0.7240 (t80) cc_final: 0.6899 (t80) REVERT: A 3198 GLN cc_start: 0.7835 (tm-30) cc_final: 0.7528 (tm-30) REVERT: A 3579 MET cc_start: 0.8239 (mmp) cc_final: 0.7086 (mmp) REVERT: A 3735 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7037 (tm-30) REVERT: A 3747 LYS cc_start: 0.8779 (tttt) cc_final: 0.8472 (tppt) REVERT: A 3890 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8046 (mt) REVERT: A 4004 MET cc_start: 0.6800 (tpt) cc_final: 0.6224 (tpt) REVERT: A 4493 SER cc_start: 0.9111 (t) cc_final: 0.8650 (p) REVERT: B 141 ASP cc_start: 0.7426 (m-30) cc_final: 0.7155 (m-30) REVERT: B 269 LYS cc_start: 0.7993 (mmpt) cc_final: 0.7337 (mmmt) REVERT: B 339 ASN cc_start: 0.7688 (t0) cc_final: 0.7184 (m110) REVERT: C 203 ASN cc_start: 0.7567 (p0) cc_final: 0.6946 (p0) REVERT: C 405 LYS cc_start: 0.8036 (mttm) cc_final: 0.7371 (mtmt) outliers start: 54 outliers final: 44 residues processed: 414 average time/residue: 0.6647 time to fit residues: 443.4398 Evaluate side-chains 417 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 370 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1969 SER Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2306 ASP Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2487 GLU Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2778 THR Chi-restraints excluded: chain A residue 2909 LEU Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2992 PHE Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3098 SER Chi-restraints excluded: chain A residue 3138 SER Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3212 VAL Chi-restraints excluded: chain A residue 3578 ILE Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3735 GLN Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3890 ILE Chi-restraints excluded: chain A residue 4073 SER Chi-restraints excluded: chain A residue 4139 LEU Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4211 ASP Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4427 VAL Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4522 THR Chi-restraints excluded: chain B residue 135 TRP Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 384 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 188 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 181 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 193 optimal weight: 6.9990 chunk 207 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 239 optimal weight: 0.9990 chunk 277 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2031 ASN ** A2476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4262 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25161 Z= 0.189 Angle : 0.554 7.660 34237 Z= 0.283 Chirality : 0.039 0.150 3921 Planarity : 0.004 0.067 4362 Dihedral : 5.814 77.841 3457 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.54 % Rotamer: Outliers : 1.99 % Allowed : 14.93 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.54 (0.15), residues: 3122 helix: 1.71 (0.14), residues: 1386 sheet: -0.58 (0.22), residues: 521 loop : -0.74 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A4387 HIS 0.007 0.001 HIS A2218 PHE 0.020 0.001 PHE A1866 TYR 0.013 0.001 TYR A2748 ARG 0.004 0.000 ARG A1843 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1661 is missing expected H atoms. Skipping. Residue SER 1662 is missing expected H atoms. Skipping. Residue SER 1663 is missing expected H atoms. Skipping. Residue ILE 1664 is missing expected H atoms. Skipping. Residue LEU 1674 is missing expected H atoms. Skipping. Residue LYS 1729 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue SER 1732 is missing expected H atoms. Skipping. Residue ILE 1733 is missing expected H atoms. Skipping. Residue MET 1798 is missing expected H atoms. Skipping. Residue LYS 1849 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue LEU 1854 is missing expected H atoms. Skipping. Residue SER 1986 is missing expected H atoms. Skipping. Residue ILE 1997 is missing expected H atoms. Skipping. Residue SER 2081 is missing expected H atoms. Skipping. Residue SER 2082 is missing expected H atoms. Skipping. Residue MET 2175 is missing expected H atoms. Skipping. Residue LEU 2244 is missing expected H atoms. Skipping. Residue VAL 2247 is missing expected H atoms. Skipping. Residue THR 2272 is missing expected H atoms. Skipping. Residue SER 2290 is missing expected H atoms. Skipping. Residue VAL 2291 is missing expected H atoms. Skipping. Residue LYS 2349 is missing expected H atoms. Skipping. Residue TYR 2350 is missing expected H atoms. Skipping. Residue LEU 2443 is missing expected H atoms. Skipping. Residue MET 2481 is missing expected H atoms. Skipping. Residue LYS 2589 is missing expected H atoms. Skipping. Residue MET 2615 is missing expected H atoms. Skipping. Residue LYS 2633 is missing expected H atoms. Skipping. Residue MET 2671 is missing expected H atoms. Skipping. Residue LYS 2673 is missing expected H atoms. Skipping. Residue TYR 2674 is missing expected H atoms. Skipping. Residue THR 2676 is missing expected H atoms. Skipping. Residue THR 2815 is missing expected H atoms. Skipping. Residue LYS 2856 is missing expected H atoms. Skipping. Residue LYS 2865 is missing expected H atoms. Skipping. Residue LEU 2905 is missing expected H atoms. Skipping. Residue LYS 2962 is missing expected H atoms. Skipping. Residue LYS 2966 is missing expected H atoms. Skipping. Residue TYR 2967 is missing expected H atoms. Skipping. Residue THR 2968 is missing expected H atoms. Skipping. Residue SER 2997 is missing expected H atoms. Skipping. Residue VAL 2999 is missing expected H atoms. Skipping. Residue LEU 3000 is missing expected H atoms. Skipping. Residue SER 3002 is missing expected H atoms. Skipping. Residue TYR 3026 is missing expected H atoms. Skipping. Residue MET 3030 is missing expected H atoms. Skipping. Residue SER 3071 is missing expected H atoms. Skipping. Residue LYS 3163 is missing expected H atoms. Skipping. Residue THR 3545 is missing expected H atoms. Skipping. Residue SER 3593 is missing expected H atoms. Skipping. Residue LYS 3605 is missing expected H atoms. Skipping. Residue LEU 3615 is missing expected H atoms. Skipping. Residue LEU 3633 is missing expected H atoms. Skipping. Residue THR 3656 is missing expected H atoms. Skipping. Residue LEU 3664 is missing expected H atoms. Skipping. Residue THR 3685 is missing expected H atoms. Skipping. Residue THR 3702 is missing expected H atoms. Skipping. Residue LYS 3757 is missing expected H atoms. Skipping. Residue ILE 3760 is missing expected H atoms. Skipping. Residue LEU 3761 is missing expected H atoms. Skipping. Residue THR 3787 is missing expected H atoms. Skipping. Residue TYR 3825 is missing expected H atoms. Skipping. Residue LYS 3861 is missing expected H atoms. Skipping. Residue TYR 3901 is missing expected H atoms. Skipping. Residue LYS 3945 is missing expected H atoms. Skipping. Residue LEU 3947 is missing expected H atoms. Skipping. Residue ILE 3948 is missing expected H atoms. Skipping. Residue LYS 3950 is missing expected H atoms. Skipping. Residue ILE 3959 is missing expected H atoms. Skipping. Residue SER 3964 is missing expected H atoms. Skipping. Residue SER 3965 is missing expected H atoms. Skipping. Residue THR 3969 is missing expected H atoms. Skipping. Residue TYR 3972 is missing expected H atoms. Skipping. Residue LEU 3973 is missing expected H atoms. Skipping. Residue LEU 4106 is missing expected H atoms. Skipping. Residue LEU 4116 is missing expected H atoms. Skipping. Residue SER 4202 is missing expected H atoms. Skipping. Residue LYS 4203 is missing expected H atoms. Skipping. Residue LYS 4228 is missing expected H atoms. Skipping. Residue ILE 4233 is missing expected H atoms. Skipping. Residue SER 4280 is missing expected H atoms. Skipping. Residue VAL 4330 is missing expected H atoms. Skipping. Residue LEU 4331 is missing expected H atoms. Skipping. Residue LEU 4332 is missing expected H atoms. Skipping. Residue THR 4379 is missing expected H atoms. Skipping. Residue LEU 4380 is missing expected H atoms. Skipping. Residue THR 4382 is missing expected H atoms. Skipping. Residue THR 4383 is missing expected H atoms. Skipping. Residue LYS 4399 is missing expected H atoms. Skipping. Residue ILE 4405 is missing expected H atoms. Skipping. Residue LYS 4406 is missing expected H atoms. Skipping. Residue LYS 4441 is missing expected H atoms. Skipping. Residue LYS 4442 is missing expected H atoms. Skipping. Residue LYS 4443 is missing expected H atoms. Skipping. Residue TYR 4447 is missing expected H atoms. Skipping. Residue LYS 4457 is missing expected H atoms. Skipping. Residue VAL 4469 is missing expected H atoms. Skipping. Residue LYS 4502 is missing expected H atoms. Skipping. Residue LEU 4504 is missing expected H atoms. Skipping. Residue LYS 4505 is missing expected H atoms. Skipping. Residue ILE 4507 is missing expected H atoms. Skipping. Residue VAL 4509 is missing expected H atoms. Skipping. Residue VAL 4516 is missing expected H atoms. Skipping. Residue SER 4533 is missing expected H atoms. Skipping. Residue SER 4535 is missing expected H atoms. Skipping. Residue LEU 4536 is missing expected H atoms. Skipping. Residue LYS 4564 is missing expected H atoms. Skipping. Residue THR 4569 is missing expected H atoms. Skipping. Residue LYS 4574 is missing expected H atoms. Skipping. Residue LEU 4575 is missing expected H atoms. Skipping. Residue SER 4576 is missing expected H atoms. Skipping. Residue LYS 4594 is missing expected H atoms. Skipping. Residue LEU 4611 is missing expected H atoms. Skipping. Residue THR 4628 is missing expected H atoms. Skipping. Residue LYS 4629 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Evaluate side-chains 434 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 383 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1709 MET cc_start: 0.6950 (tmm) cc_final: 0.6521 (tmm) REVERT: A 1759 SER cc_start: 0.9081 (m) cc_final: 0.8749 (p) REVERT: A 1836 PHE cc_start: 0.6377 (t80) cc_final: 0.5873 (t80) REVERT: A 1846 PHE cc_start: 0.7747 (t80) cc_final: 0.7477 (t80) REVERT: A 1897 GLU cc_start: 0.6983 (tp30) cc_final: 0.6720 (tp30) REVERT: A 1929 VAL cc_start: 0.8572 (t) cc_final: 0.8229 (p) REVERT: A 2034 LYS cc_start: 0.8515 (mmmm) cc_final: 0.8190 (ttmm) REVERT: A 2202 MET cc_start: 0.7373 (mpp) cc_final: 0.7094 (mtm) REVERT: A 2222 MET cc_start: 0.7963 (mtt) cc_final: 0.7427 (mpp) REVERT: A 2773 MET cc_start: 0.6452 (ptp) cc_final: 0.6035 (ptm) REVERT: A 2849 ASN cc_start: 0.7859 (m110) cc_final: 0.7463 (m110) REVERT: A 2872 LEU cc_start: 0.8497 (mt) cc_final: 0.7928 (mp) REVERT: A 3094 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.6557 (t80) REVERT: A 3176 TYR cc_start: 0.7172 (t80) cc_final: 0.6795 (t80) REVERT: A 3198 GLN cc_start: 0.7783 (tm-30) cc_final: 0.7482 (tm-30) REVERT: A 3579 MET cc_start: 0.8231 (mmp) cc_final: 0.7114 (mmp) REVERT: A 3735 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.6983 (tm-30) REVERT: A 3747 LYS cc_start: 0.8784 (tttt) cc_final: 0.8430 (tppt) REVERT: A 3890 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7981 (mt) REVERT: A 4004 MET cc_start: 0.6815 (tpt) cc_final: 0.6312 (tpt) REVERT: A 4038 ASN cc_start: 0.4992 (OUTLIER) cc_final: 0.4644 (m-40) REVERT: A 4105 TRP cc_start: 0.7098 (OUTLIER) cc_final: 0.5659 (t60) REVERT: A 4168 ARG cc_start: 0.8026 (mmp80) cc_final: 0.7679 (mmp80) REVERT: A 4397 HIS cc_start: 0.4150 (OUTLIER) cc_final: 0.2075 (m-70) REVERT: A 4493 SER cc_start: 0.9105 (t) cc_final: 0.8641 (p) REVERT: B 141 ASP cc_start: 0.7316 (m-30) cc_final: 0.7098 (m-30) REVERT: B 269 LYS cc_start: 0.7954 (mmpt) cc_final: 0.7280 (mmmt) REVERT: B 339 ASN cc_start: 0.7659 (t0) cc_final: 0.7142 (m110) REVERT: C 203 ASN cc_start: 0.7572 (p0) cc_final: 0.6976 (p0) outliers start: 51 outliers final: 41 residues processed: 416 average time/residue: 0.6563 time to fit residues: 437.3350 Evaluate side-chains 416 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 369 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2085 HIS Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2306 ASP Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain A residue 2326 THR Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2487 GLU Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2778 THR Chi-restraints excluded: chain A residue 2909 LEU Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2992 PHE Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3138 SER Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3212 VAL Chi-restraints excluded: chain A residue 3578 ILE Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3735 GLN Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3890 ILE Chi-restraints excluded: chain A residue 4038 ASN Chi-restraints excluded: chain A residue 4073 SER Chi-restraints excluded: chain A residue 4105 TRP Chi-restraints excluded: chain A residue 4139 LEU Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4211 ASP Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4397 HIS Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4427 VAL Chi-restraints excluded: chain A residue 4463 SER Chi-restraints excluded: chain A residue 4522 THR Chi-restraints excluded: chain B residue 135 TRP Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 384 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 291 optimal weight: 3.9990 chunk 266 optimal weight: 7.9990 chunk 283 optimal weight: 5.9990 chunk 170 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 222 optimal weight: 0.5980 chunk 87 optimal weight: 0.4980 chunk 256 optimal weight: 0.9980 chunk 268 optimal weight: 0.9990 chunk 282 optimal weight: 0.6980 chunk 186 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2476 HIS A3087 ASN A3155 HIS ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25161 Z= 0.160 Angle : 0.542 7.224 34237 Z= 0.274 Chirality : 0.039 0.149 3921 Planarity : 0.004 0.066 4362 Dihedral : 5.553 68.892 3457 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.17 % Favored : 96.80 % Rotamer: Outliers : 1.56 % Allowed : 15.60 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.75 (0.15), residues: 3122 helix: 1.90 (0.14), residues: 1379 sheet: -0.46 (0.23), residues: 501 loop : -0.64 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A4387 HIS 0.006 0.001 HIS A2218 PHE 0.027 0.001 PHE A1866 TYR 0.036 0.001 TYR A1889 ARG 0.004 0.000 ARG A1843 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1661 is missing expected H atoms. Skipping. Residue SER 1662 is missing expected H atoms. Skipping. Residue SER 1663 is missing expected H atoms. Skipping. Residue ILE 1664 is missing expected H atoms. Skipping. Residue LEU 1674 is missing expected H atoms. Skipping. Residue LYS 1729 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue SER 1732 is missing expected H atoms. Skipping. Residue ILE 1733 is missing expected H atoms. Skipping. Residue MET 1798 is missing expected H atoms. Skipping. Residue LYS 1849 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue LEU 1854 is missing expected H atoms. Skipping. Residue SER 1986 is missing expected H atoms. Skipping. Residue ILE 1997 is missing expected H atoms. Skipping. Residue SER 2081 is missing expected H atoms. Skipping. Residue SER 2082 is missing expected H atoms. Skipping. Residue MET 2175 is missing expected H atoms. Skipping. Residue LEU 2244 is missing expected H atoms. Skipping. Residue VAL 2247 is missing expected H atoms. Skipping. Residue THR 2272 is missing expected H atoms. Skipping. Residue SER 2290 is missing expected H atoms. Skipping. Residue VAL 2291 is missing expected H atoms. Skipping. Residue LYS 2349 is missing expected H atoms. Skipping. Residue TYR 2350 is missing expected H atoms. Skipping. Residue LEU 2443 is missing expected H atoms. Skipping. Residue MET 2481 is missing expected H atoms. Skipping. Residue LYS 2589 is missing expected H atoms. Skipping. Residue MET 2615 is missing expected H atoms. Skipping. Residue LYS 2633 is missing expected H atoms. Skipping. Residue MET 2671 is missing expected H atoms. Skipping. Residue LYS 2673 is missing expected H atoms. Skipping. Residue TYR 2674 is missing expected H atoms. Skipping. Residue THR 2676 is missing expected H atoms. Skipping. Residue THR 2815 is missing expected H atoms. Skipping. Residue LYS 2856 is missing expected H atoms. Skipping. Residue LYS 2865 is missing expected H atoms. Skipping. Residue LEU 2905 is missing expected H atoms. Skipping. Residue LYS 2962 is missing expected H atoms. Skipping. Residue LYS 2966 is missing expected H atoms. Skipping. Residue TYR 2967 is missing expected H atoms. Skipping. Residue THR 2968 is missing expected H atoms. Skipping. Residue SER 2997 is missing expected H atoms. Skipping. Residue VAL 2999 is missing expected H atoms. Skipping. Residue LEU 3000 is missing expected H atoms. Skipping. Residue SER 3002 is missing expected H atoms. Skipping. Residue TYR 3026 is missing expected H atoms. Skipping. Residue MET 3030 is missing expected H atoms. Skipping. Residue SER 3071 is missing expected H atoms. Skipping. Residue LYS 3163 is missing expected H atoms. Skipping. Residue THR 3545 is missing expected H atoms. Skipping. Residue SER 3593 is missing expected H atoms. Skipping. Residue LYS 3605 is missing expected H atoms. Skipping. Residue LEU 3615 is missing expected H atoms. Skipping. Residue LEU 3633 is missing expected H atoms. Skipping. Residue THR 3656 is missing expected H atoms. Skipping. Residue LEU 3664 is missing expected H atoms. Skipping. Residue THR 3685 is missing expected H atoms. Skipping. Residue THR 3702 is missing expected H atoms. Skipping. Residue LYS 3757 is missing expected H atoms. Skipping. Residue ILE 3760 is missing expected H atoms. Skipping. Residue LEU 3761 is missing expected H atoms. Skipping. Residue THR 3787 is missing expected H atoms. Skipping. Residue TYR 3825 is missing expected H atoms. Skipping. Residue LYS 3861 is missing expected H atoms. Skipping. Residue TYR 3901 is missing expected H atoms. Skipping. Residue LYS 3945 is missing expected H atoms. Skipping. Residue LEU 3947 is missing expected H atoms. Skipping. Residue ILE 3948 is missing expected H atoms. Skipping. Residue LYS 3950 is missing expected H atoms. Skipping. Residue ILE 3959 is missing expected H atoms. Skipping. Residue SER 3964 is missing expected H atoms. Skipping. Residue SER 3965 is missing expected H atoms. Skipping. Residue THR 3969 is missing expected H atoms. Skipping. Residue TYR 3972 is missing expected H atoms. Skipping. Residue LEU 3973 is missing expected H atoms. Skipping. Residue LEU 4106 is missing expected H atoms. Skipping. Residue LEU 4116 is missing expected H atoms. Skipping. Residue SER 4202 is missing expected H atoms. Skipping. Residue LYS 4203 is missing expected H atoms. Skipping. Residue LYS 4228 is missing expected H atoms. Skipping. Residue ILE 4233 is missing expected H atoms. Skipping. Residue SER 4280 is missing expected H atoms. Skipping. Residue VAL 4330 is missing expected H atoms. Skipping. Residue LEU 4331 is missing expected H atoms. Skipping. Residue LEU 4332 is missing expected H atoms. Skipping. Residue THR 4379 is missing expected H atoms. Skipping. Residue LEU 4380 is missing expected H atoms. Skipping. Residue THR 4382 is missing expected H atoms. Skipping. Residue THR 4383 is missing expected H atoms. Skipping. Residue LYS 4399 is missing expected H atoms. Skipping. Residue ILE 4405 is missing expected H atoms. Skipping. Residue LYS 4406 is missing expected H atoms. Skipping. Residue LYS 4441 is missing expected H atoms. Skipping. Residue LYS 4442 is missing expected H atoms. Skipping. Residue LYS 4443 is missing expected H atoms. Skipping. Residue TYR 4447 is missing expected H atoms. Skipping. Residue LYS 4457 is missing expected H atoms. Skipping. Residue VAL 4469 is missing expected H atoms. Skipping. Residue LYS 4502 is missing expected H atoms. Skipping. Residue LEU 4504 is missing expected H atoms. Skipping. Residue LYS 4505 is missing expected H atoms. Skipping. Residue ILE 4507 is missing expected H atoms. Skipping. Residue VAL 4509 is missing expected H atoms. Skipping. Residue VAL 4516 is missing expected H atoms. Skipping. Residue SER 4533 is missing expected H atoms. Skipping. Residue SER 4535 is missing expected H atoms. Skipping. Residue LEU 4536 is missing expected H atoms. Skipping. Residue LYS 4564 is missing expected H atoms. Skipping. Residue THR 4569 is missing expected H atoms. Skipping. Residue LYS 4574 is missing expected H atoms. Skipping. Residue LEU 4575 is missing expected H atoms. Skipping. Residue SER 4576 is missing expected H atoms. Skipping. Residue LYS 4594 is missing expected H atoms. Skipping. Residue LEU 4611 is missing expected H atoms. Skipping. Residue THR 4628 is missing expected H atoms. Skipping. Residue LYS 4629 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Evaluate side-chains 425 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 385 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1709 MET cc_start: 0.6952 (tmm) cc_final: 0.6529 (tmm) REVERT: A 1759 SER cc_start: 0.9072 (m) cc_final: 0.8758 (p) REVERT: A 1836 PHE cc_start: 0.6382 (t80) cc_final: 0.5806 (t80) REVERT: A 1846 PHE cc_start: 0.7704 (t80) cc_final: 0.7440 (t80) REVERT: A 1897 GLU cc_start: 0.6911 (tp30) cc_final: 0.6664 (tp30) REVERT: A 1929 VAL cc_start: 0.8543 (t) cc_final: 0.8210 (p) REVERT: A 2034 LYS cc_start: 0.8495 (mmmm) cc_final: 0.8200 (ttmm) REVERT: A 2202 MET cc_start: 0.7319 (mpp) cc_final: 0.7043 (mtm) REVERT: A 2222 MET cc_start: 0.8000 (mtt) cc_final: 0.7468 (mpp) REVERT: A 2773 MET cc_start: 0.6387 (ptp) cc_final: 0.5982 (ptm) REVERT: A 2823 ARG cc_start: 0.7966 (mmm-85) cc_final: 0.7530 (tpt-90) REVERT: A 2849 ASN cc_start: 0.7882 (m110) cc_final: 0.7481 (m110) REVERT: A 2872 LEU cc_start: 0.8467 (mt) cc_final: 0.7862 (mp) REVERT: A 3094 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.6722 (t80) REVERT: A 3176 TYR cc_start: 0.7063 (t80) cc_final: 0.6715 (t80) REVERT: A 3198 GLN cc_start: 0.7722 (tm-30) cc_final: 0.7423 (tm-30) REVERT: A 3579 MET cc_start: 0.8241 (mmp) cc_final: 0.7219 (mmp) REVERT: A 3735 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7016 (tm-30) REVERT: A 3747 LYS cc_start: 0.8733 (tttt) cc_final: 0.8392 (tppt) REVERT: A 3890 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7867 (mt) REVERT: A 4004 MET cc_start: 0.6703 (tpt) cc_final: 0.6383 (tpt) REVERT: A 4038 ASN cc_start: 0.5022 (OUTLIER) cc_final: 0.4658 (m-40) REVERT: A 4105 TRP cc_start: 0.7067 (OUTLIER) cc_final: 0.5603 (t60) REVERT: A 4168 ARG cc_start: 0.7933 (mmp80) cc_final: 0.7578 (mmp80) REVERT: A 4493 SER cc_start: 0.9068 (t) cc_final: 0.8594 (p) REVERT: A 4515 PHE cc_start: 0.7511 (m-80) cc_final: 0.7290 (m-80) REVERT: B 141 ASP cc_start: 0.7309 (m-30) cc_final: 0.7069 (m-30) REVERT: B 269 LYS cc_start: 0.7925 (mmpt) cc_final: 0.7259 (mmmt) REVERT: B 339 ASN cc_start: 0.7612 (t0) cc_final: 0.7119 (m110) REVERT: C 203 ASN cc_start: 0.7567 (p0) cc_final: 0.6989 (p0) outliers start: 40 outliers final: 32 residues processed: 410 average time/residue: 0.6732 time to fit residues: 444.6589 Evaluate side-chains 412 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 375 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1755 GLN Chi-restraints excluded: chain A residue 2085 HIS Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2306 ASP Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2992 PHE Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3138 SER Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3735 GLN Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3890 ILE Chi-restraints excluded: chain A residue 4038 ASN Chi-restraints excluded: chain A residue 4062 GLN Chi-restraints excluded: chain A residue 4073 SER Chi-restraints excluded: chain A residue 4105 TRP Chi-restraints excluded: chain A residue 4139 LEU Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4211 ASP Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4427 VAL Chi-restraints excluded: chain B residue 135 TRP Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 300 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 208 optimal weight: 0.0870 chunk 314 optimal weight: 7.9990 chunk 289 optimal weight: 0.8980 chunk 250 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 chunk 199 optimal weight: 0.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25161 Z= 0.170 Angle : 0.547 8.055 34237 Z= 0.276 Chirality : 0.039 0.148 3921 Planarity : 0.004 0.067 4362 Dihedral : 5.316 64.600 3457 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.64 % Allowed : 15.79 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.84 (0.15), residues: 3122 helix: 2.00 (0.14), residues: 1374 sheet: -0.45 (0.23), residues: 501 loop : -0.62 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A4387 HIS 0.005 0.001 HIS A2218 PHE 0.020 0.001 PHE A3054 TYR 0.029 0.001 TYR A1889 ARG 0.005 0.000 ARG A1843 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1661 is missing expected H atoms. Skipping. Residue SER 1662 is missing expected H atoms. Skipping. Residue SER 1663 is missing expected H atoms. Skipping. Residue ILE 1664 is missing expected H atoms. Skipping. Residue LEU 1674 is missing expected H atoms. Skipping. Residue LYS 1729 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue SER 1732 is missing expected H atoms. Skipping. Residue ILE 1733 is missing expected H atoms. Skipping. Residue MET 1798 is missing expected H atoms. Skipping. Residue LYS 1849 is missing expected H atoms. Skipping. Residue THR 1851 is missing expected H atoms. Skipping. Residue LEU 1854 is missing expected H atoms. Skipping. Residue SER 1986 is missing expected H atoms. Skipping. Residue ILE 1997 is missing expected H atoms. Skipping. Residue SER 2081 is missing expected H atoms. Skipping. Residue SER 2082 is missing expected H atoms. Skipping. Residue MET 2175 is missing expected H atoms. Skipping. Residue LEU 2244 is missing expected H atoms. Skipping. Residue VAL 2247 is missing expected H atoms. Skipping. Residue THR 2272 is missing expected H atoms. Skipping. Residue SER 2290 is missing expected H atoms. Skipping. Residue VAL 2291 is missing expected H atoms. Skipping. Residue LYS 2349 is missing expected H atoms. Skipping. Residue TYR 2350 is missing expected H atoms. Skipping. Residue LEU 2443 is missing expected H atoms. Skipping. Residue MET 2481 is missing expected H atoms. Skipping. Residue LYS 2589 is missing expected H atoms. Skipping. Residue MET 2615 is missing expected H atoms. Skipping. Residue LYS 2633 is missing expected H atoms. Skipping. Residue MET 2671 is missing expected H atoms. Skipping. Residue LYS 2673 is missing expected H atoms. Skipping. Residue TYR 2674 is missing expected H atoms. Skipping. Residue THR 2676 is missing expected H atoms. Skipping. Residue THR 2815 is missing expected H atoms. Skipping. Residue LYS 2856 is missing expected H atoms. Skipping. Residue LYS 2865 is missing expected H atoms. Skipping. Residue LEU 2905 is missing expected H atoms. Skipping. Residue LYS 2962 is missing expected H atoms. Skipping. Residue LYS 2966 is missing expected H atoms. Skipping. Residue TYR 2967 is missing expected H atoms. Skipping. Residue THR 2968 is missing expected H atoms. Skipping. Residue SER 2997 is missing expected H atoms. Skipping. Residue VAL 2999 is missing expected H atoms. Skipping. Residue LEU 3000 is missing expected H atoms. Skipping. Residue SER 3002 is missing expected H atoms. Skipping. Residue TYR 3026 is missing expected H atoms. Skipping. Residue MET 3030 is missing expected H atoms. Skipping. Residue SER 3071 is missing expected H atoms. Skipping. Residue LYS 3163 is missing expected H atoms. Skipping. Residue THR 3545 is missing expected H atoms. Skipping. Residue SER 3593 is missing expected H atoms. Skipping. Residue LYS 3605 is missing expected H atoms. Skipping. Residue LEU 3615 is missing expected H atoms. Skipping. Residue LEU 3633 is missing expected H atoms. Skipping. Residue THR 3656 is missing expected H atoms. Skipping. Residue LEU 3664 is missing expected H atoms. Skipping. Residue THR 3685 is missing expected H atoms. Skipping. Residue THR 3702 is missing expected H atoms. Skipping. Residue LYS 3757 is missing expected H atoms. Skipping. Residue ILE 3760 is missing expected H atoms. Skipping. Residue LEU 3761 is missing expected H atoms. Skipping. Residue THR 3787 is missing expected H atoms. Skipping. Residue TYR 3825 is missing expected H atoms. Skipping. Residue LYS 3861 is missing expected H atoms. Skipping. Residue TYR 3901 is missing expected H atoms. Skipping. Residue LYS 3945 is missing expected H atoms. Skipping. Residue LEU 3947 is missing expected H atoms. Skipping. Residue ILE 3948 is missing expected H atoms. Skipping. Residue LYS 3950 is missing expected H atoms. Skipping. Residue ILE 3959 is missing expected H atoms. Skipping. Residue SER 3964 is missing expected H atoms. Skipping. Residue SER 3965 is missing expected H atoms. Skipping. Residue THR 3969 is missing expected H atoms. Skipping. Residue TYR 3972 is missing expected H atoms. Skipping. Residue LEU 3973 is missing expected H atoms. Skipping. Residue LEU 4106 is missing expected H atoms. Skipping. Residue LEU 4116 is missing expected H atoms. Skipping. Residue SER 4202 is missing expected H atoms. Skipping. Residue LYS 4203 is missing expected H atoms. Skipping. Residue LYS 4228 is missing expected H atoms. Skipping. Residue ILE 4233 is missing expected H atoms. Skipping. Residue SER 4280 is missing expected H atoms. Skipping. Residue VAL 4330 is missing expected H atoms. Skipping. Residue LEU 4331 is missing expected H atoms. Skipping. Residue LEU 4332 is missing expected H atoms. Skipping. Residue THR 4379 is missing expected H atoms. Skipping. Residue LEU 4380 is missing expected H atoms. Skipping. Residue THR 4382 is missing expected H atoms. Skipping. Residue THR 4383 is missing expected H atoms. Skipping. Residue LYS 4399 is missing expected H atoms. Skipping. Residue ILE 4405 is missing expected H atoms. Skipping. Residue LYS 4406 is missing expected H atoms. Skipping. Residue LYS 4441 is missing expected H atoms. Skipping. Residue LYS 4442 is missing expected H atoms. Skipping. Residue LYS 4443 is missing expected H atoms. Skipping. Residue TYR 4447 is missing expected H atoms. Skipping. Residue LYS 4457 is missing expected H atoms. Skipping. Residue VAL 4469 is missing expected H atoms. Skipping. Residue LYS 4502 is missing expected H atoms. Skipping. Residue LEU 4504 is missing expected H atoms. Skipping. Residue LYS 4505 is missing expected H atoms. Skipping. Residue ILE 4507 is missing expected H atoms. Skipping. Residue VAL 4509 is missing expected H atoms. Skipping. Residue VAL 4516 is missing expected H atoms. Skipping. Residue SER 4533 is missing expected H atoms. Skipping. Residue SER 4535 is missing expected H atoms. Skipping. Residue LEU 4536 is missing expected H atoms. Skipping. Residue LYS 4564 is missing expected H atoms. Skipping. Residue THR 4569 is missing expected H atoms. Skipping. Residue LYS 4574 is missing expected H atoms. Skipping. Residue LEU 4575 is missing expected H atoms. Skipping. Residue SER 4576 is missing expected H atoms. Skipping. Residue LYS 4594 is missing expected H atoms. Skipping. Residue LEU 4611 is missing expected H atoms. Skipping. Residue THR 4628 is missing expected H atoms. Skipping. Residue LYS 4629 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue THR 297 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Evaluate side-chains 420 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 378 time to evaluate : 2.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1759 SER cc_start: 0.9040 (m) cc_final: 0.8770 (p) REVERT: A 1836 PHE cc_start: 0.6431 (t80) cc_final: 0.5813 (t80) REVERT: A 1846 PHE cc_start: 0.7712 (t80) cc_final: 0.7435 (t80) REVERT: A 1897 GLU cc_start: 0.6921 (tp30) cc_final: 0.6695 (tp30) REVERT: A 1929 VAL cc_start: 0.8532 (t) cc_final: 0.8210 (p) REVERT: A 2034 LYS cc_start: 0.8510 (mmmm) cc_final: 0.8185 (ttmm) REVERT: A 2202 MET cc_start: 0.7386 (mpp) cc_final: 0.7078 (mtm) REVERT: A 2222 MET cc_start: 0.8022 (mtt) cc_final: 0.7495 (mpp) REVERT: A 2823 ARG cc_start: 0.7944 (mmm-85) cc_final: 0.7469 (tpt-90) REVERT: A 2849 ASN cc_start: 0.7871 (m110) cc_final: 0.7417 (m110) REVERT: A 2872 LEU cc_start: 0.8490 (mt) cc_final: 0.7889 (mp) REVERT: A 3094 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.6916 (t80) REVERT: A 3176 TYR cc_start: 0.7154 (t80) cc_final: 0.6820 (t80) REVERT: A 3198 GLN cc_start: 0.7723 (tm-30) cc_final: 0.7424 (tm-30) REVERT: A 3579 MET cc_start: 0.8162 (mmp) cc_final: 0.7170 (mmp) REVERT: A 3735 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7036 (tm-30) REVERT: A 3747 LYS cc_start: 0.8751 (tttt) cc_final: 0.8400 (tppt) REVERT: A 3890 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7897 (mt) REVERT: A 4105 TRP cc_start: 0.7100 (OUTLIER) cc_final: 0.5596 (t60) REVERT: B 141 ASP cc_start: 0.7266 (m-30) cc_final: 0.7062 (m-30) REVERT: B 269 LYS cc_start: 0.7922 (mmpt) cc_final: 0.7251 (mmmt) REVERT: B 339 ASN cc_start: 0.7620 (t0) cc_final: 0.7110 (m110) REVERT: C 203 ASN cc_start: 0.7578 (p0) cc_final: 0.7007 (p0) outliers start: 42 outliers final: 33 residues processed: 403 average time/residue: 0.6840 time to fit residues: 443.9027 Evaluate side-chains 411 residues out of total 2828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 374 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1755 GLN Chi-restraints excluded: chain A residue 2085 HIS Chi-restraints excluded: chain A residue 2131 LEU Chi-restraints excluded: chain A residue 2306 ASP Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain A residue 2374 ILE Chi-restraints excluded: chain A residue 2593 LEU Chi-restraints excluded: chain A residue 2909 LEU Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2992 PHE Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3059 ILE Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3138 SER Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3735 GLN Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3797 VAL Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3890 ILE Chi-restraints excluded: chain A residue 4073 SER Chi-restraints excluded: chain A residue 4105 TRP Chi-restraints excluded: chain A residue 4139 LEU Chi-restraints excluded: chain A residue 4194 LEU Chi-restraints excluded: chain A residue 4211 ASP Chi-restraints excluded: chain A residue 4338 ASP Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4427 VAL Chi-restraints excluded: chain B residue 135 TRP Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 353 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 267 optimal weight: 3.9990 chunk 76 optimal weight: 0.0030 chunk 231 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 257 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.129727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.115012 restraints weight = 186807.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.118808 restraints weight = 79874.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.121147 restraints weight = 43061.794| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25161 Z= 0.185 Angle : 0.554 7.995 34237 Z= 0.280 Chirality : 0.039 0.147 3921 Planarity : 0.004 0.067 4362 Dihedral : 5.237 64.440 3457 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.49 % Allowed : 15.95 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.85 (0.15), residues: 3122 helix: 2.03 (0.14), residues: 1370 sheet: -0.48 (0.23), residues: 503 loop : -0.61 (0.18), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A4387 HIS 0.006 0.001 HIS A2218 PHE 0.020 0.001 PHE A3054 TYR 0.030 0.001 TYR A2582 ARG 0.004 0.000 ARG A1843 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9193.07 seconds wall clock time: 157 minutes 54.99 seconds (9474.99 seconds total)