Starting phenix.real_space_refine on Mon May 26 13:02:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pqy_17828/05_2025/8pqy_17828.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pqy_17828/05_2025/8pqy_17828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pqy_17828/05_2025/8pqy_17828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pqy_17828/05_2025/8pqy_17828.map" model { file = "/net/cci-nas-00/data/ceres_data/8pqy_17828/05_2025/8pqy_17828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pqy_17828/05_2025/8pqy_17828.cif" } resolution = 3.8 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 2 5.21 5 S 151 5.16 5 C 17748 2.51 5 N 4840 2.21 5 O 5166 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27916 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 22814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2892, 22814 Classifications: {'peptide': 2892} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PCIS': 4, 'PTRANS': 125, 'TRANS': 2762} Chain breaks: 13 Unresolved non-hydrogen bonds: 466 Unresolved non-hydrogen angles: 579 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 30, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 330 Chain: "B" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2494 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "C" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2494 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 114 Unusual residues: {' MG': 2, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 14.87, per 1000 atoms: 0.53 Number of scatterers: 27916 At special positions: 0 Unit cell: (129.198, 140.847, 210.741, 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 151 16.00 P 9 15.00 Mg 2 11.99 O 5166 8.00 N 4840 7.00 C 17748 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.74 Conformation dependent library (CDL) restraints added in 3.4 seconds 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6696 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 36 sheets defined 50.9% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.42 Creating SS restraints... Processing helix chain 'A' and resid 1444 through 1472 Processing helix chain 'A' and resid 1489 through 1507 removed outlier: 3.908A pdb=" N LEU A1493 " --> pdb=" O GLY A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1554 removed outlier: 3.921A pdb=" N ALA A1520 " --> pdb=" O PHE A1516 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A1546 " --> pdb=" O ARG A1542 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1585 removed outlier: 3.670A pdb=" N SER A1585 " --> pdb=" O LYS A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1593 Processing helix chain 'A' and resid 1596 through 1616 Processing helix chain 'A' and resid 1616 through 1624 removed outlier: 4.183A pdb=" N GLU A1620 " --> pdb=" O GLY A1616 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG A1621 " --> pdb=" O GLU A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1632 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1649 through 1652 removed outlier: 3.791A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1649 through 1652' Processing helix chain 'A' and resid 1653 through 1658 removed outlier: 3.954A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A1658 " --> pdb=" O PHE A1654 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1653 through 1658' Processing helix chain 'A' and resid 1693 through 1695 No H-bonds generated for 'chain 'A' and resid 1693 through 1695' Processing helix chain 'A' and resid 1697 through 1728 removed outlier: 3.521A pdb=" N ARG A1710 " --> pdb=" O GLU A1706 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1768 removed outlier: 4.183A pdb=" N SER A1768 " --> pdb=" O THR A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1776 through 1797 Processing helix chain 'A' and resid 1801 through 1827 Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1852 through 1855 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1912 through 1923 Processing helix chain 'A' and resid 1937 through 1952 Processing helix chain 'A' and resid 1965 through 1986 removed outlier: 3.847A pdb=" N GLN A1973 " --> pdb=" O SER A1969 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN A1974 " --> pdb=" O ALA A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2035 removed outlier: 3.586A pdb=" N LYS A2034 " --> pdb=" O ASP A2030 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU A2035 " --> pdb=" O ASN A2031 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2058 removed outlier: 3.599A pdb=" N ILE A2049 " --> pdb=" O ASP A2045 " (cutoff:3.500A) removed outlier: 3.541A 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 removed outlier: 3.798A pdb=" N GLU A2078 " --> pdb=" O LYS A2074 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU A2080 " --> pdb=" O CYS A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2114 removed outlier: 3.619A pdb=" N SER A2095 " --> pdb=" O ARG A2091 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU A2114 " --> pdb=" O LYS A2110 " (cutoff:3.500A) Processing helix chain 'A' and resid 2132 through 2146 Processing helix chain 'A' and resid 2153 through 2165 Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2260 through 2266 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2311 through 2315 Processing helix chain 'A' and resid 2352 through 2357 Processing helix chain 'A' and resid 2370 through 2384 removed outlier: 3.551A pdb=" N ILE A2374 " --> pdb=" O SER A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2410 through 2428 Proline residue: A2425 - end of helix removed outlier: 3.703A pdb=" N THR A2428 " --> pdb=" O GLN A2424 " (cutoff:3.500A) Processing helix chain 'A' and resid 2432 through 2443 removed outlier: 3.547A pdb=" N PHE A2441 " --> pdb=" O LEU A2437 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 4.436A pdb=" N CYS A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2503 removed outlier: 4.209A pdb=" N ARG A2492 " --> pdb=" O ARG A2488 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A2495 " --> pdb=" O GLN A2491 " (cutoff:3.500A) Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2548 through 2552 Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 4.157A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2612 removed outlier: 3.535A pdb=" N ALA A2611 " --> pdb=" O SER A2607 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A2612 " --> pdb=" O ALA A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.293A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2689 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2740 through 2756 removed outlier: 5.001A pdb=" N GLN A2746 " --> pdb=" O ALA A2742 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A2751 " --> pdb=" O ILE A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2762 through 2764 No H-bonds generated for 'chain 'A' and resid 2762 through 2764' Processing helix chain 'A' and resid 2765 through 2781 removed outlier: 3.570A pdb=" N GLU A2775 " --> pdb=" O ALA A2771 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A2776 " --> pdb=" O ALA A2772 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR A2777 " --> pdb=" O MET A2773 " (cutoff:3.500A) Processing helix chain 'A' and resid 2795 through 2810 removed outlier: 4.057A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 removed outlier: 3.506A pdb=" N GLN A2834 " --> pdb=" O LEU A2830 " (cutoff:3.500A) Processing helix chain 'A' and resid 2839 through 2858 removed outlier: 3.608A pdb=" N ARG A2843 " --> pdb=" O GLU A2839 " (cutoff:3.500A) Processing helix chain 'A' and resid 2862 through 2867 Processing helix chain 'A' and resid 2885 through 2901 removed outlier: 3.687A pdb=" N LEU A2889 " --> pdb=" O ASP A2885 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2928 removed outlier: 4.288A pdb=" N GLN A2928 " --> pdb=" O ARG A2924 " (cutoff:3.500A) Processing helix chain 'A' and resid 2942 through 2954 removed outlier: 3.522A pdb=" N LEU A2946 " --> pdb=" O GLY A2942 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A2947 " --> pdb=" O LYS A2943 " (cutoff:3.500A) Processing helix chain 'A' and resid 2968 through 2985 removed outlier: 3.609A pdb=" N PHE A2972 " --> pdb=" O THR A2968 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS A2985 " --> pdb=" O ARG A2981 " (cutoff:3.500A) Processing helix chain 'A' and resid 3001 through 3014 removed outlier: 3.775A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 removed outlier: 3.687A pdb=" N ALA A3027 " --> pdb=" O GLY A3023 " (cutoff:3.500A) Processing helix chain 'A' and resid 3047 through 3061 Processing helix chain 'A' and resid 3073 through 3082 removed outlier: 3.659A pdb=" N ALA A3080 " --> pdb=" O LYS A3076 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3088 Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3165 removed outlier: 3.711A pdb=" N ALA A3159 " --> pdb=" O HIS A3155 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A3165 " --> pdb=" O LEU A3161 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 3240 removed outlier: 3.508A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A3184 " --> pdb=" O ILE A3180 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A3203 " --> pdb=" O MET A3199 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A3209 " --> pdb=" O LEU A3205 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A3220 " --> pdb=" O GLU A3216 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A3237 " --> pdb=" O ASN A3233 " (cutoff:3.500A) Processing helix chain 'A' and resid 3451 through 3502 removed outlier: 4.009A pdb=" N ALA A3484 " --> pdb=" O LYS A3480 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU A3485 " --> pdb=" O SER A3481 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG A3488 " --> pdb=" O ALA A3484 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LYS A3491 " --> pdb=" O GLU A3487 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS A3497 " --> pdb=" O SER A3493 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN A3498 " --> pdb=" O GLU A3494 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A3501 " --> pdb=" O LYS A3497 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A3502 " --> pdb=" O ASN A3498 " (cutoff:3.500A) Processing helix chain 'A' and resid 3502 through 3516 Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3554 removed outlier: 4.133A pdb=" N LEU A3553 " --> pdb=" O ARG A3549 " (cutoff:3.500A) Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3582 Processing helix chain 'A' and resid 3594 through 3604 removed outlier: 3.844A pdb=" N GLU A3598 " --> pdb=" O GLY A3594 " (cutoff:3.500A) Processing helix chain 'A' and resid 3619 through 3630 Processing helix chain 'A' and resid 3637 through 3641 removed outlier: 3.559A pdb=" N SER A3640 " --> pdb=" O ASP A3637 " (cutoff:3.500A) Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3650 Processing helix chain 'A' and resid 3689 through 3696 removed outlier: 4.180A pdb=" N ARG A3695 " --> pdb=" O ASP A3691 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A3696 " --> pdb=" O LEU A3692 " (cutoff:3.500A) Processing helix chain 'A' and resid 3704 through 3721 Processing helix chain 'A' and resid 3721 through 3754 Processing helix chain 'A' and resid 3764 through 3818 removed outlier: 4.208A pdb=" N VAL A3784 " --> pdb=" O VAL A3780 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU A3785 " --> pdb=" O THR A3781 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A3786 " --> pdb=" O ARG A3782 " (cutoff:3.500A) Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3819 through 3821 No H-bonds generated for 'chain 'A' and resid 3819 through 3821' Processing helix chain 'A' and resid 3828 through 3841 removed outlier: 3.885A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR A3841 " --> pdb=" O HIS A3837 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 removed outlier: 3.996A pdb=" N SER A3857 " --> pdb=" O THR A3853 " (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 3894 removed outlier: 3.545A pdb=" N PHE A3883 " --> pdb=" O ASP A3879 " (cutoff:3.500A) Processing helix chain 'A' and resid 3901 through 3910 Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3946 through 3954 removed outlier: 3.776A pdb=" N GLN A3952 " --> pdb=" O ILE A3948 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4013 Processing helix chain 'A' and resid 4026 through 4033 removed outlier: 3.767A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4062 removed outlier: 3.563A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4090 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: 4.371A pdb=" N GLN A4108 " --> pdb=" O GLY A4104 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4142 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.643A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4175 through 4193 removed outlier: 3.590A pdb=" N LEU A4179 " --> pdb=" O GLU A4175 " (cutoff:3.500A) Processing helix chain 'A' and resid 4209 through 4227 Processing helix chain 'A' and resid 4234 through 4238 removed outlier: 3.832A pdb=" N ILE A4238 " --> pdb=" O PRO A4235 " (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 removed outlier: 3.935A pdb=" N PHE A4278 " --> pdb=" O THR A4274 " (cutoff:3.500A) Processing helix chain 'A' and resid 4301 through 4310 Processing helix chain 'A' and resid 4317 through 4322 Processing helix chain 'A' and resid 4328 through 4347 removed outlier: 3.600A pdb=" N LYS A4345 " --> pdb=" O SER A4341 " (cutoff:3.500A) Processing helix chain 'A' and resid 4380 through 4391 Processing helix chain 'A' and resid 4392 through 4395 Processing helix chain 'A' and resid 4407 through 4439 removed outlier: 3.677A pdb=" N ARG A4411 " --> pdb=" O ASP A4407 " (cutoff:3.500A) Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4474 through 4497 removed outlier: 3.647A pdb=" N SER A4480 " --> pdb=" O ILE A4476 " (cutoff:3.500A) Processing helix chain 'A' and resid 4503 through 4506 Processing helix chain 'A' and resid 4512 through 4514 No H-bonds generated for 'chain 'A' and resid 4512 through 4514' Processing helix chain 'A' and resid 4516 through 4533 removed outlier: 3.647A pdb=" N TYR A4520 " --> pdb=" O VAL A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4631 through 4638 removed outlier: 3.520A pdb=" N PHE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 295 removed outlier: 4.062A pdb=" N SER B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 297 removed outlier: 3.876A pdb=" N SER C 294 " --> pdb=" O TYR C 290 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1476 through 1480 removed outlier: 4.540A pdb=" N ASP A1476 " --> pdb=" O ARG A1488 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1663 through 1666 removed outlier: 10.523A pdb=" N VAL A1672 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 11.212A pdb=" N THR A1688 " --> pdb=" O VAL A1672 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU A1674 " --> pdb=" O PHE A1686 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1928 removed outlier: 6.361A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N THR A2017 " --> pdb=" O GLY A1955 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE A1957 " --> pdb=" O THR A2017 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA7, first strand: chain 'A' and resid 2249 through 2254 removed outlier: 6.758A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE A2303 " --> pdb=" O GLU A2344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2324 through 2325 Processing sheet with id=AA9, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB1, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 6.203A pdb=" N GLU A2616 " --> pdb=" O VAL A2660 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N PHE A2662 " --> pdb=" O GLU A2616 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A2618 " --> pdb=" O PHE A2662 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A2591 " --> pdb=" O PHE A2708 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A2592 " --> pdb=" O VAL A2734 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2639 through 2644 removed outlier: 6.643A pdb=" N VAL A2648 " --> pdb=" O LYS A2702 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2873 through 2874 removed outlier: 3.539A pdb=" N SER A2874 " --> pdb=" O ILE A2882 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A2882 " --> pdb=" O SER A2874 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 6.300A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET A2994 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR A3067 " --> pdb=" O MET A2994 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU A2935 " --> pdb=" O MET A3068 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU A2934 " --> pdb=" O ASN A3092 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.109A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU A3633 " --> pdb=" O PHE A3678 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N SER A3680 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL A3635 " --> pdb=" O SER A3680 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR A3681 " --> pdb=" O PRO A3587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE A3589 " --> pdb=" O THR A3681 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU A3588 " --> pdb=" O VAL A3699 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 3654 through 3656 Processing sheet with id=AB7, first strand: chain 'A' and resid 4068 through 4070 Processing sheet with id=AB8, first strand: chain 'A' and resid 4283 through 4285 removed outlier: 6.871A pdb=" N ILE A4294 " --> pdb=" O LEU A4284 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4508 through 4510 removed outlier: 6.091A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4563 through 4564 removed outlier: 4.163A pdb=" N LEU A4563 " --> pdb=" O LEU A4585 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4568 through 4570 removed outlier: 3.877A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 95 through 96 Processing sheet with id=AC4, first strand: chain 'B' and resid 95 through 96 removed outlier: 4.585A pdb=" N THR B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER B 399 " --> pdb=" O THR B 403 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 111 through 116 removed outlier: 3.538A pdb=" N ARG B 113 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE B 132 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR B 145 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL B 134 " --> pdb=" O GLU B 143 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 153 through 157 removed outlier: 3.984A pdb=" N ASP B 155 " --> pdb=" O CYS B 168 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 169 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE B 174 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR B 187 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU B 176 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU B 183 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 206 through 210 removed outlier: 3.724A pdb=" N LYS B 228 " --> pdb=" O MET B 218 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU B 220 " --> pdb=" O CYS B 226 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N CYS B 226 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 237 through 242 removed outlier: 3.701A pdb=" N MET B 239 " --> pdb=" O CYS B 252 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL B 262 " --> pdb=" O CYS B 268 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N CYS B 268 " --> pdb=" O VAL B 262 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 279 through 284 removed outlier: 3.504A pdb=" N SER B 283 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET B 332 " --> pdb=" O MET B 322 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP B 324 " --> pdb=" O CYS B 330 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N CYS B 330 " --> pdb=" O ASP B 324 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 341 through 346 removed outlier: 3.613A pdb=" N THR B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS B 374 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ASP B 366 " --> pdb=" O CYS B 372 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N CYS B 372 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 95 through 96 Processing sheet with id=AD3, first strand: chain 'C' and resid 95 through 96 removed outlier: 4.891A pdb=" N THR C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER C 399 " --> pdb=" O THR C 403 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 111 through 116 removed outlier: 5.830A pdb=" N ASP C 136 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE C 142 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 155 through 157 removed outlier: 3.820A pdb=" N ASP C 155 " --> pdb=" O CYS C 168 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP C 178 " --> pdb=" O CYS C 184 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N CYS C 184 " --> pdb=" O ASP C 178 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 195 through 200 removed outlier: 3.583A pdb=" N SER C 211 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N THR C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLU C 220 " --> pdb=" O CYS C 226 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N CYS C 226 " --> pdb=" O GLU C 220 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 237 through 242 removed outlier: 6.514A pdb=" N VAL C 262 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N CYS C 268 " --> pdb=" O VAL C 262 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 279 through 284 removed outlier: 4.581A pdb=" N THR C 319 " --> pdb=" O SER C 315 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET C 332 " --> pdb=" O MET C 322 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ASP C 324 " --> pdb=" O CYS C 330 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS C 330 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 341 through 346 removed outlier: 3.684A pdb=" N ALA C 357 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASP C 366 " --> pdb=" O CYS C 372 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N CYS C 372 " --> pdb=" O ASP C 366 " (cutoff:3.500A) 1492 hydrogen bonds defined for protein. 4353 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: 16.86 Time building geometry restraints manager: 7.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9075 1.34 - 1.46: 6496 1.46 - 1.59: 12697 1.59 - 1.71: 13 1.71 - 1.83: 245 Bond restraints: 28526 Sorted by residual: bond pdb=" C ARG A2869 " pdb=" N PRO A2870 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.64e+01 bond pdb=" CB PRO A3643 " pdb=" CG PRO A3643 " ideal model delta sigma weight residual 1.492 1.645 -0.153 5.00e-02 4.00e+02 9.42e+00 bond pdb=" CA GLU A1567 " pdb=" C GLU A1567 " ideal model delta sigma weight residual 1.524 1.492 0.032 1.27e-02 6.20e+03 6.31e+00 bond pdb=" CA GLU A1610 " pdb=" C GLU A1610 " ideal model delta sigma weight residual 1.524 1.495 0.029 1.24e-02 6.50e+03 5.50e+00 bond pdb=" CB PRO A2817 " pdb=" CG PRO A2817 " ideal model delta sigma weight residual 1.492 1.608 -0.116 5.00e-02 4.00e+02 5.36e+00 ... (remaining 28521 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 38304 3.41 - 6.83: 333 6.83 - 10.24: 64 10.24 - 13.66: 21 13.66 - 17.07: 7 Bond angle restraints: 38729 Sorted by residual: angle pdb=" CA PRO A3643 " pdb=" N PRO A3643 " pdb=" CD PRO A3643 " ideal model delta sigma weight residual 112.00 94.93 17.07 1.40e+00 5.10e-01 1.49e+02 angle pdb=" CG ARG A2729 " pdb=" CD ARG A2729 " pdb=" NE ARG A2729 " ideal model delta sigma weight residual 112.00 126.62 -14.62 2.20e+00 2.07e-01 4.42e+01 angle pdb=" CA PRO A2817 " pdb=" N PRO A2817 " pdb=" CD PRO A2817 " ideal model delta sigma weight residual 112.00 103.34 8.66 1.40e+00 5.10e-01 3.83e+01 angle pdb=" N ILE A1557 " pdb=" CA ILE A1557 " pdb=" C ILE A1557 " ideal model delta sigma weight residual 111.81 106.79 5.02 8.60e-01 1.35e+00 3.41e+01 angle pdb=" CB MET A1531 " pdb=" CG MET A1531 " pdb=" SD MET A1531 " ideal model delta sigma weight residual 112.70 129.34 -16.64 3.00e+00 1.11e-01 3.08e+01 ... (remaining 38724 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.38: 16067 28.38 - 56.77: 1029 56.77 - 85.15: 69 85.15 - 113.54: 5 113.54 - 141.92: 3 Dihedral angle restraints: 17173 sinusoidal: 6889 harmonic: 10284 Sorted by residual: dihedral pdb=" CA LEU A1963 " pdb=" C LEU A1963 " pdb=" N GLU A1964 " pdb=" CA GLU A1964 " ideal model delta harmonic sigma weight residual 180.00 143.22 36.78 0 5.00e+00 4.00e-02 5.41e+01 dihedral pdb=" O2A ADP A4806 " pdb=" O3A ADP A4806 " pdb=" PA ADP A4806 " pdb=" PB ADP A4806 " ideal model delta sinusoidal sigma weight residual -60.00 81.93 -141.92 1 2.00e+01 2.50e-03 4.29e+01 dihedral pdb=" O1B ADP A4806 " pdb=" O3A ADP A4806 " pdb=" PB ADP A4806 " pdb=" PA ADP A4806 " ideal model delta sinusoidal sigma weight residual -60.00 81.34 -141.35 1 2.00e+01 2.50e-03 4.27e+01 ... (remaining 17170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3680 0.065 - 0.129: 635 0.129 - 0.194: 75 0.194 - 0.258: 3 0.258 - 0.323: 5 Chirality restraints: 4398 Sorted by residual: chirality pdb=" CB VAL B 122 " pdb=" CA VAL B 122 " pdb=" CG1 VAL B 122 " pdb=" CG2 VAL B 122 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB VAL A2557 " pdb=" CA VAL A2557 " pdb=" CG1 VAL A2557 " pdb=" CG2 VAL A2557 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CG LEU A3745 " pdb=" CB LEU A3745 " pdb=" CD1 LEU A3745 " pdb=" CD2 LEU A3745 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 4395 not shown) Planarity restraints: 4930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A3642 " 0.129 5.00e-02 4.00e+02 1.79e-01 5.15e+01 pdb=" N PRO A3643 " -0.310 5.00e-02 4.00e+02 pdb=" CA PRO A3643 " 0.094 5.00e-02 4.00e+02 pdb=" CD PRO A3643 " 0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A2928 " 0.057 5.00e-02 4.00e+02 8.72e-02 1.22e+01 pdb=" N PRO A2929 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO A2929 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A2929 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A3109 " -0.016 2.00e-02 2.50e+03 2.48e-02 1.08e+01 pdb=" CG PHE A3109 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE A3109 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A3109 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE A3109 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A3109 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A3109 " -0.001 2.00e-02 2.50e+03 ... (remaining 4927 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 166 2.50 - 3.10: 18059 3.10 - 3.70: 45368 3.70 - 4.30: 62968 4.30 - 4.90: 103119 Nonbonded interactions: 229680 Sorted by model distance: nonbonded pdb=" NH2 ARG A2729 " pdb="MG MG A4804 " model vdw 1.902 2.250 nonbonded pdb=" OG SER A2231 " pdb=" O2B ATP A4803 " model vdw 1.971 3.040 nonbonded pdb=" O2B ADP A4801 " pdb="MG MG A4802 " model vdw 1.981 2.170 nonbonded pdb=" OG SER A2231 " pdb=" OE2 GLU A2344 " model vdw 2.012 3.040 nonbonded pdb=" OD2 ASP A1958 " pdb="MG MG A4802 " model vdw 2.066 2.170 ... (remaining 229675 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' 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.100 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 66.160 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.153 28526 Z= 0.192 Angle : 0.892 17.074 38729 Z= 0.452 Chirality : 0.050 0.323 4398 Planarity : 0.007 0.179 4930 Dihedral : 17.214 141.924 10477 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.18 % Rotamer: Outliers : 0.36 % Allowed : 22.29 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.12), residues: 3482 helix: -1.08 (0.11), residues: 1650 sheet: -0.78 (0.22), residues: 491 loop : -1.48 (0.15), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 261 HIS 0.006 0.001 HIS A2730 PHE 0.056 0.002 PHE A3109 TYR 0.033 0.002 TYR C 225 ARG 0.011 0.000 ARG B 144 Details of bonding type rmsd hydrogen bonds : bond 0.14771 ( 1488) hydrogen bonds : angle 6.56008 ( 4353) covalent geometry : bond 0.00412 (28526) covalent geometry : angle 0.89189 (38729) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 2.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1467 ARG cc_start: 0.9119 (tpp-160) cc_final: 0.8900 (tpp80) REVERT: A 2762 LEU cc_start: 0.7126 (mt) cc_final: 0.6818 (mp) REVERT: A 3500 MET cc_start: 0.8112 (tmm) cc_final: 0.7685 (tmm) REVERT: A 3924 ILE cc_start: 0.6524 (OUTLIER) cc_final: 0.6090 (mm) REVERT: B 201 MET cc_start: 0.4875 (pmm) cc_final: 0.4674 (pmm) outliers start: 11 outliers final: 2 residues processed: 181 average time/residue: 0.4217 time to fit residues: 121.5228 Evaluate side-chains 162 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 159 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1610 GLU Chi-restraints excluded: chain A residue 3924 ILE Chi-restraints excluded: chain C residue 290 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 4.9990 chunk 266 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 275 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 318 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1667 ASN ** A2468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2560 HIS ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2730 HIS A2964 HIS A3032 GLN ** A3878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4023 GLN ** A4335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4389 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.057798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.049834 restraints weight = 187393.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.050997 restraints weight = 102627.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.051838 restraints weight = 67299.581| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 28526 Z= 0.180 Angle : 0.624 11.065 38729 Z= 0.316 Chirality : 0.042 0.154 4398 Planarity : 0.005 0.090 4930 Dihedral : 7.023 142.206 3862 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.33 % Favored : 96.64 % Rotamer: Outliers : 2.48 % Allowed : 20.87 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: -0.55 (0.14), residues: 3482 helix: 0.45 (0.12), residues: 1670 sheet: -0.68 (0.22), residues: 504 loop : -1.20 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 261 HIS 0.006 0.001 HIS A2588 PHE 0.018 0.002 PHE A2912 TYR 0.027 0.002 TYR A3836 ARG 0.009 0.000 ARG A2729 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 1488) hydrogen bonds : angle 4.63504 ( 4353) covalent geometry : bond 0.00402 (28526) covalent geometry : angle 0.62418 (38729) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 163 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1467 ARG cc_start: 0.9140 (tpp-160) cc_final: 0.8885 (tpt-90) REVERT: A 1892 MET cc_start: 0.7829 (mmt) cc_final: 0.7456 (mmt) REVERT: A 1960 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7483 (t80) REVERT: A 2358 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6633 (ttp-110) REVERT: A 2438 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: A 2538 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8349 (pt0) REVERT: A 2578 GLU cc_start: 0.7784 (tp30) cc_final: 0.7479 (tp30) REVERT: A 3043 MET cc_start: 0.5366 (mmm) cc_final: 0.4949 (mmt) REVERT: A 3199 MET cc_start: 0.7748 (mmm) cc_final: 0.7444 (tpt) REVERT: A 3825 TYR cc_start: 0.7397 (OUTLIER) cc_final: 0.6120 (p90) REVERT: A 3875 MET cc_start: 0.8518 (tpp) cc_final: 0.8046 (ttm) REVERT: A 4004 MET cc_start: 0.6746 (mmp) cc_final: 0.6531 (mmp) REVERT: C 322 MET cc_start: 0.7688 (tpp) cc_final: 0.7353 (tpp) outliers start: 75 outliers final: 32 residues processed: 225 average time/residue: 0.4099 time to fit residues: 149.3802 Evaluate side-chains 191 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1615 LEU Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 1999 CYS Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2146 VAL Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2438 GLU Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2538 GLU Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 3058 VAL Chi-restraints excluded: chain A residue 3131 ASP Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3223 ARG Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3768 THR Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3782 ARG Chi-restraints excluded: chain A residue 3802 LEU Chi-restraints excluded: chain A residue 3823 PHE Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 4190 ILE Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 391 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 148 optimal weight: 0.9980 chunk 306 optimal weight: 20.0000 chunk 315 optimal weight: 20.0000 chunk 301 optimal weight: 0.4980 chunk 97 optimal weight: 5.9990 chunk 257 optimal weight: 9.9990 chunk 147 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 331 optimal weight: 8.9990 chunk 142 optimal weight: 7.9990 chunk 260 optimal weight: 0.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN A2134 GLN A2560 HIS ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3735 GLN A3878 GLN ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4335 GLN A4389 HIS B 381 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.057708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.049898 restraints weight = 186324.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.051010 restraints weight = 101950.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.051823 restraints weight = 67478.638| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28526 Z= 0.145 Angle : 0.579 11.879 38729 Z= 0.291 Chirality : 0.041 0.150 4398 Planarity : 0.004 0.059 4930 Dihedral : 6.678 138.640 3855 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.98 % Rotamer: Outliers : 2.98 % Allowed : 20.83 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: -0.00 (0.14), residues: 3482 helix: 1.07 (0.12), residues: 1670 sheet: -0.68 (0.22), residues: 504 loop : -1.06 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 261 HIS 0.004 0.001 HIS C 389 PHE 0.013 0.001 PHE A3823 TYR 0.023 0.001 TYR A3836 ARG 0.003 0.000 ARG C 113 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 1488) hydrogen bonds : angle 4.36835 ( 4353) covalent geometry : bond 0.00325 (28526) covalent geometry : angle 0.57891 (38729) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 162 time to evaluate : 3.002 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: A 1467 ARG cc_start: 0.9144 (tpp-160) cc_final: 0.8865 (tpt-90) REVERT: A 1892 MET cc_start: 0.7958 (mmt) cc_final: 0.7713 (mmt) REVERT: A 1960 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.7414 (t80) REVERT: A 2189 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7226 (ttm) REVERT: A 2358 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6990 (ttp-170) REVERT: A 2438 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: A 2461 MET cc_start: 0.8394 (mmm) cc_final: 0.8155 (mmm) REVERT: A 2671 MET cc_start: 0.7999 (tmm) cc_final: 0.7756 (tmm) REVERT: A 2994 MET cc_start: 0.7995 (ppp) cc_final: 0.7731 (ptm) REVERT: A 3008 MET cc_start: 0.8356 (mmm) cc_final: 0.7997 (mmm) REVERT: A 3199 MET cc_start: 0.7687 (mmm) cc_final: 0.7379 (tpt) REVERT: A 3825 TYR cc_start: 0.7443 (OUTLIER) cc_final: 0.6395 (p90) REVERT: A 3875 MET cc_start: 0.8552 (tpp) cc_final: 0.8064 (ttm) REVERT: B 205 ASP cc_start: 0.7876 (t0) cc_final: 0.7597 (t70) REVERT: B 218 MET cc_start: 0.7219 (tpp) cc_final: 0.6850 (tpp) REVERT: B 222 GLN cc_start: 0.7869 (mp10) cc_final: 0.7472 (mm-40) REVERT: B 261 TRP cc_start: 0.6660 (OUTLIER) cc_final: 0.5027 (m100) REVERT: C 311 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.6801 (tt) REVERT: C 322 MET cc_start: 0.7882 (tpp) cc_final: 0.7427 (tpp) outliers start: 90 outliers final: 46 residues processed: 239 average time/residue: 0.3821 time to fit residues: 149.6315 Evaluate side-chains 207 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 154 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1615 LEU Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1932 CYS Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 1971 VAL Chi-restraints excluded: chain A residue 1999 CYS Chi-restraints excluded: chain A residue 2004 LYS Chi-restraints excluded: chain A residue 2146 VAL Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2438 GLU Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 3131 ASP Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3472 VAL Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3802 LEU Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3858 ILE Chi-restraints excluded: chain A residue 3887 LEU Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 4162 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4391 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 381 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 141 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 226 optimal weight: 8.9990 chunk 341 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 217 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2377 ASN A2482 GLN A2560 HIS A2707 GLN A3038 GLN ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4389 HIS A4566 GLN ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.056095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.048379 restraints weight = 192951.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.049438 restraints weight = 106553.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.050206 restraints weight = 71137.927| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 28526 Z= 0.235 Angle : 0.691 17.618 38729 Z= 0.345 Chirality : 0.044 0.158 4398 Planarity : 0.005 0.058 4930 Dihedral : 6.805 137.669 3855 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.31 % Favored : 95.66 % Rotamer: Outliers : 4.84 % Allowed : 21.17 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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 (0.14), residues: 3482 helix: 0.94 (0.12), residues: 1672 sheet: -0.92 (0.22), residues: 508 loop : -1.15 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1523 HIS 0.010 0.002 HIS A2857 PHE 0.019 0.002 PHE A2912 TYR 0.025 0.002 TYR A3836 ARG 0.009 0.001 ARG A2757 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 1488) hydrogen bonds : angle 4.59267 ( 4353) covalent geometry : bond 0.00532 (28526) covalent geometry : angle 0.69094 (38729) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 163 time to evaluate : 3.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1467 ARG cc_start: 0.9118 (tpp-160) cc_final: 0.8830 (tpt-90) REVERT: A 1592 LEU cc_start: 0.4654 (tp) cc_final: 0.3860 (tp) REVERT: A 1826 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8730 (tt) REVERT: A 1894 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7777 (mm110) REVERT: A 1960 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7351 (t80) REVERT: A 1982 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7354 (mm) REVERT: A 2053 MET cc_start: 0.8712 (mmm) cc_final: 0.8501 (mmm) REVERT: A 2358 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6982 (ttp-170) REVERT: A 2438 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7198 (tm-30) REVERT: A 2671 MET cc_start: 0.8134 (tmm) cc_final: 0.7538 (tmm) REVERT: A 3008 MET cc_start: 0.8453 (mmm) cc_final: 0.8124 (mmm) REVERT: A 3199 MET cc_start: 0.7722 (mmm) cc_final: 0.7462 (tpt) REVERT: A 3747 LYS cc_start: 0.9214 (tmtt) cc_final: 0.8942 (mmtt) REVERT: A 3825 TYR cc_start: 0.7829 (OUTLIER) cc_final: 0.6549 (p90) REVERT: A 3836 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.7769 (t80) REVERT: A 3875 MET cc_start: 0.8705 (tpp) cc_final: 0.8044 (ttm) REVERT: A 4128 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.6646 (pmm) REVERT: A 4419 MET cc_start: 0.7842 (tpp) cc_final: 0.7598 (tpp) REVERT: A 4518 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8487 (mp0) REVERT: B 205 ASP cc_start: 0.7863 (t0) cc_final: 0.7609 (t70) REVERT: B 261 TRP cc_start: 0.6757 (OUTLIER) cc_final: 0.4961 (m100) REVERT: C 164 LEU cc_start: 0.8625 (tp) cc_final: 0.8214 (tt) REVERT: C 267 GLU cc_start: 0.6586 (pp20) cc_final: 0.6380 (pp20) REVERT: C 311 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.6698 (tt) REVERT: C 322 MET cc_start: 0.7900 (tpp) cc_final: 0.7405 (tpp) outliers start: 146 outliers final: 83 residues processed: 294 average time/residue: 0.4091 time to fit residues: 195.0766 Evaluate side-chains 250 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 155 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1540 VAL Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1615 LEU Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1861 MET Chi-restraints excluded: chain A residue 1894 GLN Chi-restraints excluded: chain A residue 1932 CYS Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 1971 VAL Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 1999 CYS Chi-restraints excluded: chain A residue 2002 LEU Chi-restraints excluded: chain A residue 2079 GLN Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2146 VAL Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2371 THR Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2438 GLU Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2538 GLU Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2681 SER Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2912 PHE Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 3058 VAL Chi-restraints excluded: chain A residue 3099 THR Chi-restraints excluded: chain A residue 3213 ASP Chi-restraints excluded: chain A residue 3223 ARG Chi-restraints excluded: chain A residue 3472 VAL Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3662 ILE Chi-restraints excluded: chain A residue 3768 THR Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3782 ARG Chi-restraints excluded: chain A residue 3802 LEU Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3837 HIS Chi-restraints excluded: chain A residue 3858 ILE Chi-restraints excluded: chain A residue 3859 ILE Chi-restraints excluded: chain A residue 3882 THR Chi-restraints excluded: chain A residue 3887 LEU Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 4004 MET Chi-restraints excluded: chain A residue 4009 VAL Chi-restraints excluded: chain A residue 4066 ILE Chi-restraints excluded: chain A residue 4084 ILE Chi-restraints excluded: chain A residue 4128 MET Chi-restraints excluded: chain A residue 4162 SER Chi-restraints excluded: chain A residue 4190 ILE Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4230 ARG Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4391 ILE Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4518 GLU Chi-restraints excluded: chain A residue 4604 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain C residue 135 TRP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 381 HIS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 400 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 227 optimal weight: 0.0470 chunk 39 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 195 optimal weight: 20.0000 chunk 336 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1921 HIS A3175 HIS ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4389 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.056840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.049103 restraints weight = 188483.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.050203 restraints weight = 104557.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.050998 restraints weight = 69448.118| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28526 Z= 0.146 Angle : 0.592 12.918 38729 Z= 0.294 Chirality : 0.042 0.186 4398 Planarity : 0.004 0.053 4930 Dihedral : 6.590 136.209 3855 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 3.61 % Allowed : 22.56 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: 0.09 (0.14), residues: 3482 helix: 1.26 (0.12), residues: 1681 sheet: -0.93 (0.22), residues: 520 loop : -1.07 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2952 HIS 0.005 0.001 HIS A2857 PHE 0.015 0.001 PHE A2776 TYR 0.021 0.001 TYR A3836 ARG 0.005 0.000 ARG A1529 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 1488) hydrogen bonds : angle 4.34475 ( 4353) covalent geometry : bond 0.00333 (28526) covalent geometry : angle 0.59164 (38729) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 156 time to evaluate : 3.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1467 ARG cc_start: 0.9116 (tpp-160) cc_final: 0.8830 (tpt-90) REVERT: A 1826 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8625 (tt) REVERT: A 1894 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7726 (mm110) REVERT: A 1960 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7393 (t80) REVERT: A 1982 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7399 (mm) REVERT: A 2189 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7250 (ttm) REVERT: A 2358 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6791 (ttp-170) REVERT: A 2545 TRP cc_start: 0.6678 (OUTLIER) cc_final: 0.6370 (m-10) REVERT: A 2615 MET cc_start: 0.7323 (mmm) cc_final: 0.6925 (mtp) REVERT: A 2671 MET cc_start: 0.8162 (tmm) cc_final: 0.7621 (tmm) REVERT: A 3199 MET cc_start: 0.7595 (mmm) cc_final: 0.7334 (tpt) REVERT: A 3825 TYR cc_start: 0.7650 (OUTLIER) cc_final: 0.6471 (p90) REVERT: A 3875 MET cc_start: 0.8742 (tpp) cc_final: 0.8065 (ttm) REVERT: A 4419 MET cc_start: 0.7728 (tpp) cc_final: 0.7493 (tpp) REVERT: A 4455 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7597 (mm) REVERT: A 4518 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8411 (mp0) REVERT: B 205 ASP cc_start: 0.7757 (t0) cc_final: 0.7371 (t0) REVERT: B 218 MET cc_start: 0.7249 (tpp) cc_final: 0.6678 (tpp) REVERT: B 222 GLN cc_start: 0.8430 (mp10) cc_final: 0.7911 (mm-40) REVERT: B 261 TRP cc_start: 0.6746 (OUTLIER) cc_final: 0.4998 (m100) REVERT: B 332 MET cc_start: 0.6158 (tmm) cc_final: 0.5877 (tmm) REVERT: C 164 LEU cc_start: 0.8536 (tp) cc_final: 0.8072 (tt) REVERT: C 311 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.6770 (tt) REVERT: C 322 MET cc_start: 0.7826 (tpp) cc_final: 0.7345 (tpp) outliers start: 109 outliers final: 68 residues processed: 258 average time/residue: 0.4248 time to fit residues: 183.0794 Evaluate side-chains 229 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 149 time to evaluate : 3.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1615 LEU Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1861 MET Chi-restraints excluded: chain A residue 1894 GLN Chi-restraints excluded: chain A residue 1915 SER Chi-restraints excluded: chain A residue 1932 CYS Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 1971 VAL Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 1999 CYS Chi-restraints excluded: chain A residue 2002 LEU Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2111 ILE Chi-restraints excluded: chain A residue 2146 VAL Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2545 TRP Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2681 SER Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2945 THR Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 3058 VAL Chi-restraints excluded: chain A residue 3472 VAL Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3662 ILE Chi-restraints excluded: chain A residue 3672 SER Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3837 HIS Chi-restraints excluded: chain A residue 3858 ILE Chi-restraints excluded: chain A residue 3882 THR Chi-restraints excluded: chain A residue 3887 LEU Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3936 VAL Chi-restraints excluded: chain A residue 4009 VAL Chi-restraints excluded: chain A residue 4162 SER Chi-restraints excluded: chain A residue 4190 ILE Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4391 ILE Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4518 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 381 HIS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 400 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 251 optimal weight: 5.9990 chunk 287 optimal weight: 6.9990 chunk 224 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 252 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 280 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 337 optimal weight: 2.9990 chunk 303 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4389 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.056953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.049248 restraints weight = 189665.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.050348 restraints weight = 104145.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.051124 restraints weight = 69062.576| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28526 Z= 0.141 Angle : 0.586 13.300 38729 Z= 0.290 Chirality : 0.041 0.176 4398 Planarity : 0.004 0.054 4930 Dihedral : 6.451 136.210 3855 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.08 % Favored : 95.89 % Rotamer: Outliers : 4.04 % Allowed : 22.29 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: 0.24 (0.14), residues: 3482 helix: 1.42 (0.12), residues: 1685 sheet: -0.91 (0.22), residues: 508 loop : -1.04 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 261 HIS 0.006 0.001 HIS A2857 PHE 0.014 0.001 PHE A3823 TYR 0.020 0.001 TYR A3836 ARG 0.005 0.000 ARG A1529 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 1488) hydrogen bonds : angle 4.24961 ( 4353) covalent geometry : bond 0.00319 (28526) covalent geometry : angle 0.58568 (38729) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 159 time to evaluate : 3.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1467 ARG cc_start: 0.9147 (tpp-160) cc_final: 0.8846 (tpt-90) REVERT: A 1826 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8618 (tt) REVERT: A 1894 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7701 (mm110) REVERT: A 1960 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7365 (t80) REVERT: A 1982 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7378 (mm) REVERT: A 2073 PHE cc_start: 0.6390 (OUTLIER) cc_final: 0.5644 (m-10) REVERT: A 2189 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7340 (ttm) REVERT: A 2358 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6783 (ttp-170) REVERT: A 2461 MET cc_start: 0.8393 (mmm) cc_final: 0.7990 (mmm) REVERT: A 2545 TRP cc_start: 0.6710 (OUTLIER) cc_final: 0.6409 (m-10) REVERT: A 2671 MET cc_start: 0.8091 (tmm) cc_final: 0.7503 (tmm) REVERT: A 3155 HIS cc_start: 0.7867 (OUTLIER) cc_final: 0.7579 (t-90) REVERT: A 3199 MET cc_start: 0.7519 (mmm) cc_final: 0.7282 (tpt) REVERT: A 3747 LYS cc_start: 0.9218 (tmtt) cc_final: 0.8948 (mmtt) REVERT: A 3825 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.6650 (p90) REVERT: A 3875 MET cc_start: 0.8722 (tpp) cc_final: 0.8083 (ttm) REVERT: A 4097 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7864 (mtmm) REVERT: A 4419 MET cc_start: 0.7696 (tpp) cc_final: 0.7457 (tpp) REVERT: A 4455 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7596 (mm) REVERT: B 261 TRP cc_start: 0.6735 (OUTLIER) cc_final: 0.4983 (m100) REVERT: C 164 LEU cc_start: 0.8566 (tp) cc_final: 0.8146 (tt) REVERT: C 218 MET cc_start: 0.7679 (tpp) cc_final: 0.7250 (tpp) REVERT: C 311 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6648 (tt) REVERT: C 322 MET cc_start: 0.7869 (tpp) cc_final: 0.7430 (tpp) outliers start: 122 outliers final: 79 residues processed: 273 average time/residue: 0.3963 time to fit residues: 175.7047 Evaluate side-chains 241 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 148 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1615 LEU Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1861 MET Chi-restraints excluded: chain A residue 1894 GLN Chi-restraints excluded: chain A residue 1932 CYS Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 1971 VAL Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2002 LEU Chi-restraints excluded: chain A residue 2073 PHE Chi-restraints excluded: chain A residue 2111 ILE Chi-restraints excluded: chain A residue 2146 VAL Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2545 TRP Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2681 SER Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 3058 VAL Chi-restraints excluded: chain A residue 3099 THR Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3213 ASP Chi-restraints excluded: chain A residue 3223 ARG Chi-restraints excluded: chain A residue 3472 VAL Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3662 ILE Chi-restraints excluded: chain A residue 3672 SER Chi-restraints excluded: chain A residue 3687 GLU Chi-restraints excluded: chain A residue 3768 THR Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3837 HIS Chi-restraints excluded: chain A residue 3858 ILE Chi-restraints excluded: chain A residue 3882 THR Chi-restraints excluded: chain A residue 3887 LEU Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3936 VAL Chi-restraints excluded: chain A residue 4009 VAL Chi-restraints excluded: chain A residue 4084 ILE Chi-restraints excluded: chain A residue 4097 LYS Chi-restraints excluded: chain A residue 4162 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4268 PHE Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4391 ILE Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 381 HIS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 400 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 278 optimal weight: 5.9990 chunk 65 optimal weight: 0.4980 chunk 138 optimal weight: 9.9990 chunk 213 optimal weight: 8.9990 chunk 318 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4316 GLN A4389 HIS B 206 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.057186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.049439 restraints weight = 187487.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.050513 restraints weight = 103407.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.051335 restraints weight = 69103.374| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28526 Z= 0.129 Angle : 0.585 13.798 38729 Z= 0.289 Chirality : 0.041 0.167 4398 Planarity : 0.004 0.053 4930 Dihedral : 6.355 136.298 3855 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.62 % Favored : 96.35 % Rotamer: Outliers : 3.64 % Allowed : 22.89 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: 0.34 (0.14), residues: 3482 helix: 1.52 (0.13), residues: 1685 sheet: -0.83 (0.22), residues: 507 loop : -1.03 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 261 HIS 0.007 0.001 HIS B 206 PHE 0.015 0.001 PHE A3823 TYR 0.018 0.001 TYR A3836 ARG 0.005 0.000 ARG A1529 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 1488) hydrogen bonds : angle 4.18422 ( 4353) covalent geometry : bond 0.00293 (28526) covalent geometry : angle 0.58460 (38729) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 158 time to evaluate : 3.367 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: A 1467 ARG cc_start: 0.9153 (tpp-160) cc_final: 0.8934 (tpt-90) REVERT: A 1826 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8539 (tt) REVERT: A 1894 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7680 (mm110) REVERT: A 1960 PHE cc_start: 0.7878 (OUTLIER) cc_final: 0.7383 (t80) REVERT: A 1982 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7413 (mm) REVERT: A 2073 PHE cc_start: 0.6384 (OUTLIER) cc_final: 0.5614 (m-10) REVERT: A 2358 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6851 (ttp-170) REVERT: A 2545 TRP cc_start: 0.6648 (OUTLIER) cc_final: 0.6417 (m-10) REVERT: A 3155 HIS cc_start: 0.7859 (OUTLIER) cc_final: 0.7578 (t-90) REVERT: A 3199 MET cc_start: 0.7485 (mmm) cc_final: 0.7269 (tpt) REVERT: A 3825 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.6629 (p90) REVERT: A 3875 MET cc_start: 0.8758 (tpp) cc_final: 0.8102 (ttm) REVERT: A 4419 MET cc_start: 0.7677 (tpp) cc_final: 0.7434 (tpp) REVERT: A 4455 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7608 (mm) REVERT: B 218 MET cc_start: 0.7206 (tpp) cc_final: 0.6791 (tpp) REVERT: B 261 TRP cc_start: 0.6726 (OUTLIER) cc_final: 0.4967 (m100) REVERT: B 332 MET cc_start: 0.6009 (tmm) cc_final: 0.5781 (tmm) REVERT: C 164 LEU cc_start: 0.8527 (tp) cc_final: 0.8153 (tt) REVERT: C 218 MET cc_start: 0.7718 (tpp) cc_final: 0.7494 (tpp) REVERT: C 311 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6717 (tt) REVERT: C 322 MET cc_start: 0.7800 (tpp) cc_final: 0.7399 (tpp) outliers start: 110 outliers final: 81 residues processed: 259 average time/residue: 0.3815 time to fit residues: 163.0936 Evaluate side-chains 245 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 152 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1615 LEU Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1894 GLN Chi-restraints excluded: chain A residue 1915 SER Chi-restraints excluded: chain A residue 1932 CYS Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 1971 VAL Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2002 LEU Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain A residue 2073 PHE Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2111 ILE Chi-restraints excluded: chain A residue 2146 VAL Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2191 LEU Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2545 TRP Chi-restraints excluded: chain A residue 2569 VAL Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2681 SER Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2945 THR Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 3058 VAL Chi-restraints excluded: chain A residue 3099 THR Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3213 ASP Chi-restraints excluded: chain A residue 3223 ARG Chi-restraints excluded: chain A residue 3472 VAL Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3662 ILE Chi-restraints excluded: chain A residue 3687 GLU Chi-restraints excluded: chain A residue 3768 THR Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3837 HIS Chi-restraints excluded: chain A residue 3858 ILE Chi-restraints excluded: chain A residue 3882 THR Chi-restraints excluded: chain A residue 3887 LEU Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3936 VAL Chi-restraints excluded: chain A residue 4009 VAL Chi-restraints excluded: chain A residue 4084 ILE Chi-restraints excluded: chain A residue 4133 LYS Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4268 PHE Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4339 MET Chi-restraints excluded: chain A residue 4391 ILE Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4511 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 135 TRP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 277 HIS Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 381 HIS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 400 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 223 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 197 optimal weight: 0.0980 chunk 35 optimal weight: 0.0370 chunk 84 optimal weight: 4.9990 chunk 254 optimal weight: 5.9990 chunk 334 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4316 GLN A4389 HIS C 402 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.057854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.050153 restraints weight = 188027.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.051251 restraints weight = 104121.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.052013 restraints weight = 69214.946| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28526 Z= 0.108 Angle : 0.566 14.564 38729 Z= 0.278 Chirality : 0.041 0.155 4398 Planarity : 0.004 0.053 4930 Dihedral : 6.180 136.238 3855 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.50 % Rotamer: Outliers : 2.91 % Allowed : 23.82 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: 0.52 (0.14), residues: 3482 helix: 1.68 (0.13), residues: 1686 sheet: -0.69 (0.22), residues: 499 loop : -0.99 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 261 HIS 0.012 0.001 HIS B 206 PHE 0.015 0.001 PHE A2776 TYR 0.016 0.001 TYR A3836 ARG 0.006 0.000 ARG A1485 Details of bonding type rmsd hydrogen bonds : bond 0.03348 ( 1488) hydrogen bonds : angle 4.05114 ( 4353) covalent geometry : bond 0.00241 (28526) covalent geometry : angle 0.56611 (38729) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 164 time to evaluate : 3.170 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: A 1960 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7460 (t80) REVERT: A 1982 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7370 (mm) REVERT: A 2073 PHE cc_start: 0.6408 (OUTLIER) cc_final: 0.5635 (m-10) REVERT: A 2358 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6835 (ttp-170) REVERT: A 2461 MET cc_start: 0.8304 (mmm) cc_final: 0.7946 (mmm) REVERT: A 2671 MET cc_start: 0.8531 (ttp) cc_final: 0.7323 (tmm) REVERT: A 3155 HIS cc_start: 0.7810 (OUTLIER) cc_final: 0.7549 (t-90) REVERT: A 3875 MET cc_start: 0.8782 (tpp) cc_final: 0.8320 (ttm) REVERT: A 4097 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7912 (mtmm) REVERT: A 4455 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7542 (mm) REVERT: B 218 MET cc_start: 0.7093 (tpp) cc_final: 0.6711 (tpp) REVERT: B 261 TRP cc_start: 0.6649 (OUTLIER) cc_final: 0.5056 (m100) REVERT: C 164 LEU cc_start: 0.8495 (tp) cc_final: 0.8124 (tt) REVERT: C 201 MET cc_start: 0.7200 (mpp) cc_final: 0.6995 (mpp) REVERT: C 218 MET cc_start: 0.7808 (tpp) cc_final: 0.7600 (tpp) REVERT: C 290 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.7181 (m-80) REVERT: C 311 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6238 (tt) REVERT: C 322 MET cc_start: 0.7842 (tpp) cc_final: 0.7295 (tpp) outliers start: 88 outliers final: 65 residues processed: 245 average time/residue: 0.3992 time to fit residues: 159.8483 Evaluate side-chains 230 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 155 time to evaluate : 3.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1615 LEU Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1861 MET Chi-restraints excluded: chain A residue 1915 SER Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 1963 LEU Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2002 LEU Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain A residue 2073 PHE Chi-restraints excluded: chain A residue 2146 VAL Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2681 SER Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2945 THR Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3213 ASP Chi-restraints excluded: chain A residue 3472 VAL Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3687 GLU Chi-restraints excluded: chain A residue 3768 THR Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3837 HIS Chi-restraints excluded: chain A residue 3858 ILE Chi-restraints excluded: chain A residue 3882 THR Chi-restraints excluded: chain A residue 3887 LEU Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3936 VAL Chi-restraints excluded: chain A residue 4084 ILE Chi-restraints excluded: chain A residue 4097 LYS Chi-restraints excluded: chain A residue 4133 LYS Chi-restraints excluded: chain A residue 4162 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4268 PHE Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4391 ILE Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 277 HIS Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 381 HIS Chi-restraints excluded: chain C residue 386 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 169 optimal weight: 1.9990 chunk 343 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 150 optimal weight: 0.6980 chunk 282 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2377 ASN ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4316 GLN A4389 HIS A4488 GLN B 189 HIS ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.058317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.050573 restraints weight = 187541.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.051691 restraints weight = 104466.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.052495 restraints weight = 69376.672| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28526 Z= 0.103 Angle : 0.566 14.982 38729 Z= 0.277 Chirality : 0.040 0.175 4398 Planarity : 0.004 0.052 4930 Dihedral : 6.054 135.996 3855 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.25 % Favored : 96.73 % Rotamer: Outliers : 2.75 % Allowed : 23.88 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: 0.66 (0.15), residues: 3482 helix: 1.78 (0.13), residues: 1689 sheet: -0.58 (0.23), residues: 499 loop : -0.92 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A2545 HIS 0.009 0.001 HIS B 206 PHE 0.046 0.001 PHE C 388 TYR 0.016 0.001 TYR C 225 ARG 0.005 0.000 ARG C 113 Details of bonding type rmsd hydrogen bonds : bond 0.03230 ( 1488) hydrogen bonds : angle 3.97154 ( 4353) covalent geometry : bond 0.00229 (28526) covalent geometry : angle 0.56594 (38729) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 163 time to evaluate : 3.097 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: A 1514 LYS cc_start: 0.7299 (mmtt) cc_final: 0.6950 (mmtt) REVERT: A 1960 PHE cc_start: 0.7844 (OUTLIER) cc_final: 0.7486 (t80) REVERT: A 2073 PHE cc_start: 0.6424 (OUTLIER) cc_final: 0.5606 (m-10) REVERT: A 2358 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.7000 (ttp-170) REVERT: A 2461 MET cc_start: 0.8264 (mmm) cc_final: 0.7862 (mmm) REVERT: A 2671 MET cc_start: 0.8551 (ttp) cc_final: 0.7894 (tpt) REVERT: A 3875 MET cc_start: 0.8754 (tpp) cc_final: 0.8239 (ttm) REVERT: A 4007 MET cc_start: 0.5831 (ptm) cc_final: 0.5387 (ptp) REVERT: A 4097 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7904 (mtmm) REVERT: A 4455 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7509 (mm) REVERT: B 218 MET cc_start: 0.7192 (tpp) cc_final: 0.6817 (tpp) REVERT: B 261 TRP cc_start: 0.6602 (OUTLIER) cc_final: 0.5044 (m100) REVERT: C 164 LEU cc_start: 0.8449 (tp) cc_final: 0.8110 (tt) REVERT: C 311 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6305 (tt) REVERT: C 322 MET cc_start: 0.7817 (tpp) cc_final: 0.7298 (tpp) outliers start: 83 outliers final: 65 residues processed: 240 average time/residue: 0.4029 time to fit residues: 156.4297 Evaluate side-chains 229 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 157 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1861 MET Chi-restraints excluded: chain A residue 1915 SER Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 1963 LEU Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain A residue 2073 PHE Chi-restraints excluded: chain A residue 2111 ILE Chi-restraints excluded: chain A residue 2146 VAL Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2945 THR Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3213 ASP Chi-restraints excluded: chain A residue 3472 VAL Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3687 GLU Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3887 LEU Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3936 VAL Chi-restraints excluded: chain A residue 4084 ILE Chi-restraints excluded: chain A residue 4097 LYS Chi-restraints excluded: chain A residue 4133 LYS Chi-restraints excluded: chain A residue 4162 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4230 ARG Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4268 PHE Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4455 LEU Chi-restraints excluded: chain A residue 4488 GLN Chi-restraints excluded: chain A residue 4511 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 277 HIS Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 381 HIS Chi-restraints excluded: chain C residue 386 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 294 optimal weight: 5.9990 chunk 160 optimal weight: 8.9990 chunk 155 optimal weight: 0.3980 chunk 74 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 142 optimal weight: 6.9990 chunk 229 optimal weight: 0.3980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4389 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.057437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.049728 restraints weight = 187839.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.050801 restraints weight = 103503.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.051600 restraints weight = 68552.435| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28526 Z= 0.140 Angle : 0.598 12.654 38729 Z= 0.293 Chirality : 0.041 0.168 4398 Planarity : 0.004 0.051 4930 Dihedral : 6.089 136.371 3855 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.85 % Favored : 96.12 % Rotamer: Outliers : 2.75 % Allowed : 23.78 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: 0.60 (0.15), residues: 3482 helix: 1.75 (0.13), residues: 1685 sheet: -0.60 (0.23), residues: 496 loop : -0.98 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP B 323 HIS 0.010 0.001 HIS B 206 PHE 0.037 0.001 PHE C 388 TYR 0.016 0.001 TYR A3836 ARG 0.011 0.000 ARG A2643 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 1488) hydrogen bonds : angle 4.04719 ( 4353) covalent geometry : bond 0.00321 (28526) covalent geometry : angle 0.59842 (38729) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6964 Ramachandran restraints generated. 3482 Oldfield, 0 Emsley, 3482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 158 time to evaluate : 3.156 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: A 1960 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.7394 (t80) REVERT: A 2073 PHE cc_start: 0.6453 (OUTLIER) cc_final: 0.5640 (m-10) REVERT: A 2358 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6948 (ttp-170) REVERT: A 2461 MET cc_start: 0.8397 (mmm) cc_final: 0.7976 (mmm) REVERT: A 2510 MET cc_start: 0.8081 (tpp) cc_final: 0.7878 (tpp) REVERT: A 3875 MET cc_start: 0.8768 (tpp) cc_final: 0.8173 (ttm) REVERT: A 4097 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7806 (mtmm) REVERT: B 218 MET cc_start: 0.7153 (tpp) cc_final: 0.6725 (tpp) REVERT: B 239 MET cc_start: 0.7431 (tmm) cc_final: 0.6826 (tmm) REVERT: B 261 TRP cc_start: 0.6693 (OUTLIER) cc_final: 0.5065 (m100) REVERT: C 164 LEU cc_start: 0.8519 (tp) cc_final: 0.8066 (tt) REVERT: C 201 MET cc_start: 0.7301 (mpp) cc_final: 0.7032 (mpp) REVERT: C 290 TYR cc_start: 0.7575 (OUTLIER) cc_final: 0.7227 (m-80) REVERT: C 311 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6649 (tt) REVERT: C 322 MET cc_start: 0.7794 (tpp) cc_final: 0.7475 (tpp) outliers start: 83 outliers final: 70 residues processed: 232 average time/residue: 0.4089 time to fit residues: 154.6257 Evaluate side-chains 232 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 155 time to evaluate : 3.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1530 ILE Chi-restraints excluded: chain A residue 1615 LEU Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1861 MET Chi-restraints excluded: chain A residue 1915 SER Chi-restraints excluded: chain A residue 1960 PHE Chi-restraints excluded: chain A residue 1963 LEU Chi-restraints excluded: chain A residue 2041 MET Chi-restraints excluded: chain A residue 2073 PHE Chi-restraints excluded: chain A residue 2111 ILE Chi-restraints excluded: chain A residue 2146 VAL Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2681 SER Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2945 THR Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3213 ASP Chi-restraints excluded: chain A residue 3472 VAL Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3687 GLU Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3825 TYR Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3858 ILE Chi-restraints excluded: chain A residue 3887 LEU Chi-restraints excluded: chain A residue 3915 VAL Chi-restraints excluded: chain A residue 3936 VAL Chi-restraints excluded: chain A residue 4084 ILE Chi-restraints excluded: chain A residue 4097 LYS Chi-restraints excluded: chain A residue 4133 LYS Chi-restraints excluded: chain A residue 4162 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4230 ARG Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4268 PHE Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4391 ILE Chi-restraints excluded: chain A residue 4511 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 135 TRP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 381 HIS Chi-restraints excluded: chain C residue 386 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 278 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 chunk 317 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 252 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 275 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4389 HIS B 347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.056631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.048989 restraints weight = 189601.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.050034 restraints weight = 105453.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.050820 restraints weight = 70352.864| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28526 Z= 0.179 Angle : 0.640 14.427 38729 Z= 0.314 Chirality : 0.042 0.170 4398 Planarity : 0.004 0.052 4930 Dihedral : 6.212 137.797 3855 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.11 % Favored : 95.86 % Rotamer: Outliers : 2.75 % Allowed : 24.01 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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 (0.14), residues: 3482 helix: 1.57 (0.13), residues: 1678 sheet: -0.78 (0.22), residues: 518 loop : -0.97 (0.18), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 323 HIS 0.011 0.001 HIS B 206 PHE 0.037 0.002 PHE C 388 TYR 0.018 0.002 TYR A3836 ARG 0.013 0.000 ARG A1467 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 1488) hydrogen bonds : angle 4.23462 ( 4353) covalent geometry : bond 0.00407 (28526) covalent geometry : angle 0.64037 (38729) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8475.71 seconds wall clock time: 149 minutes 46.20 seconds (8986.20 seconds total)