Starting phenix.real_space_refine on Thu Jul 25 05:19:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqy_17828/07_2024/8pqy_17828_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqy_17828/07_2024/8pqy_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqy_17828/07_2024/8pqy_17828.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqy_17828/07_2024/8pqy_17828.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqy_17828/07_2024/8pqy_17828_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqy_17828/07_2024/8pqy_17828_neut.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 Residue "A ASP 1525": "OD1" <-> "OD2" Residue "A GLU 1610": "OE1" <-> "OE2" Residue "A PHE 1866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1980": "OE1" <-> "OE2" Residue "A GLU 2578": "OE1" <-> "OE2" Residue "A GLU 2775": "OE1" <-> "OE2" Residue "A PHE 2776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2912": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3066": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3100": "OE1" <-> "OE2" Residue "A PHE 3109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3131": "OD1" <-> "OD2" Residue "A PHE 3823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 90": "OD1" <-> "OD2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 141": "OD1" <-> "OD2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "C PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C ASP 205": "OD1" <-> "OD2" Residue "C TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 287": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 14.71, 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 - 3.50 Amino acid : False - 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: 10.33 Conformation dependent library (CDL) restraints added in 4.5 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: 4.26 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: 18.41 Time building geometry restraints manager: 11.46 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: 94.93 - 103.85: 411 103.85 - 112.78: 15481 112.78 - 121.71: 16472 121.71 - 130.64: 6182 130.64 - 139.56: 183 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 2.440 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 2.440 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 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: 1.060 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: 1.050 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 79.750 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.950 ------------------------------------------------------------------------------- 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= 0.262 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 *********************** 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 fitting. rotamer outliers: 11 poor density : 172 time to evaluate : 3.319 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: 0.4418 time to fit residues: 127.2730 Evaluate side-chains 162 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 159 time to evaluate : 3.015 ------------------------------------------------------------------------------- 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: 6.9990 chunk 266 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 275 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 204 optimal weight: 8.9990 chunk 318 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1481 GLN A1667 ASN A2134 GLN ** A2471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2560 HIS ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2730 HIS A2964 HIS ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 28526 Z= 0.263 Angle : 0.613 11.726 38729 Z= 0.310 Chirality : 0.041 0.153 4398 Planarity : 0.005 0.095 4930 Dihedral : 6.774 142.888 3862 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.39 % Favored : 96.58 % Rotamer: Outliers : 2.75 % Allowed : 22.16 % Favored : 75.09 % 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: -0.49 (0.14), residues: 3482 helix: 0.54 (0.12), residues: 1665 sheet: -0.65 (0.23), residues: 505 loop : -1.21 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 261 HIS 0.007 0.001 HIS A2588 PHE 0.017 0.002 PHE A2912 TYR 0.023 0.002 TYR A3836 ARG 0.007 0.000 ARG A2358 *********************** 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 244 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 161 time to evaluate : 2.964 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: 0.9164 (tpp-160) cc_final: 0.8910 (tpt-90) REVERT: A 1892 MET cc_start: 0.7932 (mmt) cc_final: 0.7518 (mmt) REVERT: A 1960 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7507 (t80) REVERT: A 2358 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6273 (ttp-110) REVERT: A 2438 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7087 (tm-30) REVERT: A 2538 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8326 (pt0) REVERT: A 2994 MET cc_start: 0.7970 (ppp) cc_final: 0.7710 (ptm) REVERT: A 3043 MET cc_start: 0.5515 (mmm) cc_final: 0.5117 (mmt) REVERT: A 3199 MET cc_start: 0.7675 (mmm) cc_final: 0.7441 (tpt) REVERT: A 3653 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.8793 (p) REVERT: A 3825 TYR cc_start: 0.7430 (OUTLIER) cc_final: 0.6195 (p90) REVERT: A 3875 MET cc_start: 0.8517 (tpp) cc_final: 0.7969 (ttm) REVERT: A 4004 MET cc_start: 0.6754 (mmp) cc_final: 0.6542 (mmp) REVERT: A 4419 MET cc_start: 0.7845 (tpp) cc_final: 0.7640 (tpp) REVERT: C 92 LYS cc_start: 0.7980 (tptt) cc_final: 0.7762 (tptp) REVERT: C 311 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7120 (tt) REVERT: C 322 MET cc_start: 0.7671 (tpp) cc_final: 0.7333 (tpp) outliers start: 83 outliers final: 39 residues processed: 231 average time/residue: 0.3998 time to fit residues: 150.1283 Evaluate side-chains 199 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 153 time to evaluate : 3.420 ------------------------------------------------------------------------------- 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 1703 THR Chi-restraints excluded: chain A residue 1722 THR 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 2159 SER 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 2835 ASP Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2912 PHE 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 3555 ASN Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3653 VAL 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 4223 LEU 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 127 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 311 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 177 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 265 optimal weight: 0.9980 chunk 217 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 319 optimal weight: 6.9990 chunk 344 optimal weight: 9.9990 chunk 284 optimal weight: 8.9990 chunk 316 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 256 optimal weight: 10.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1595 GLN A1755 GLN A1921 HIS ** A2471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2560 HIS A2707 GLN ** A3878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4389 HIS B 381 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28526 Z= 0.228 Angle : 0.579 13.560 38729 Z= 0.289 Chirality : 0.041 0.150 4398 Planarity : 0.004 0.059 4930 Dihedral : 6.476 137.160 3855 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.39 % Favored : 96.58 % Rotamer: Outliers : 3.64 % Allowed : 22.39 % Favored : 73.96 % 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: -0.01 (0.14), residues: 3482 helix: 1.08 (0.12), residues: 1675 sheet: -0.68 (0.23), residues: 505 loop : -1.10 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 261 HIS 0.004 0.001 HIS A2964 PHE 0.015 0.001 PHE A2776 TYR 0.020 0.002 TYR A3836 ARG 0.020 0.000 ARG A1488 *********************** 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 266 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 156 time to evaluate : 2.990 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: 0.9172 (tpp-160) cc_final: 0.8902 (tpt-90) REVERT: A 1892 MET cc_start: 0.7872 (mmt) cc_final: 0.7655 (mmt) REVERT: A 1960 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7516 (t80) REVERT: A 2189 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7326 (ttm) REVERT: A 2358 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.6872 (ttp-170) REVERT: A 2384 SER cc_start: 0.6722 (OUTLIER) cc_final: 0.6506 (p) REVERT: A 2538 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8316 (pt0) REVERT: A 2671 MET cc_start: 0.7951 (tmm) cc_final: 0.7685 (tmm) REVERT: A 3008 MET cc_start: 0.8390 (mmm) cc_final: 0.8015 (mmm) REVERT: A 3199 MET cc_start: 0.7546 (mmm) cc_final: 0.7289 (tpt) REVERT: A 3825 TYR cc_start: 0.7515 (OUTLIER) cc_final: 0.6524 (p90) REVERT: A 3836 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.7712 (t80) REVERT: A 3875 MET cc_start: 0.8512 (tpp) cc_final: 0.8065 (ttm) REVERT: A 3999 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7597 (p0) REVERT: B 218 MET cc_start: 0.7095 (tpp) cc_final: 0.6745 (tpp) REVERT: B 261 TRP cc_start: 0.6583 (OUTLIER) cc_final: 0.5160 (m100) REVERT: C 322 MET cc_start: 0.7776 (tpp) cc_final: 0.7361 (tpp) outliers start: 110 outliers final: 61 residues processed: 256 average time/residue: 0.3925 time to fit residues: 165.6554 Evaluate side-chains 220 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 150 time to evaluate : 2.928 ------------------------------------------------------------------------------- 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 1703 THR Chi-restraints excluded: chain A residue 1722 THR Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 1861 MET 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 2079 GLN Chi-restraints excluded: chain A residue 2146 VAL Chi-restraints excluded: chain A residue 2159 SER 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 2358 ARG Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2468 ASN Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2538 GLU Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2646 ASN Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2861 ILE 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 3495 THR Chi-restraints excluded: chain A residue 3555 ASN 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 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 3999 ASP Chi-restraints excluded: chain A residue 4223 LEU 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 4516 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 266 LYS Chi-restraints excluded: chain C residue 381 HIS Chi-restraints excluded: chain C residue 399 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 315 optimal weight: 7.9990 chunk 240 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 35 optimal weight: 0.2980 chunk 152 optimal weight: 6.9990 chunk 214 optimal weight: 9.9990 chunk 320 optimal weight: 1.9990 chunk 339 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 chunk 303 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2482 GLN A2560 HIS A3038 GLN ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3735 GLN A3878 GLN ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4335 GLN A4389 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28526 Z= 0.183 Angle : 0.548 14.028 38729 Z= 0.272 Chirality : 0.040 0.146 4398 Planarity : 0.004 0.053 4930 Dihedral : 6.300 137.705 3855 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.33 % Favored : 96.64 % Rotamer: Outliers : 3.71 % Allowed : 23.39 % Favored : 72.90 % 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: 0.30 (0.14), residues: 3482 helix: 1.44 (0.13), residues: 1672 sheet: -0.69 (0.22), residues: 505 loop : -1.01 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 261 HIS 0.003 0.001 HIS A3852 PHE 0.016 0.001 PHE A2776 TYR 0.019 0.001 TYR A3836 ARG 0.003 0.000 ARG C 113 *********************** 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 269 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 157 time to evaluate : 3.478 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: 0.9194 (tpp-160) cc_final: 0.8909 (tpt-90) REVERT: A 1894 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7487 (mm110) REVERT: A 1960 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7406 (t80) REVERT: A 1982 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7228 (mm) REVERT: A 2189 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7333 (ttm) REVERT: A 2358 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6891 (ttp-170) REVERT: A 2384 SER cc_start: 0.6682 (OUTLIER) cc_final: 0.6481 (p) REVERT: A 2461 MET cc_start: 0.8392 (mmm) cc_final: 0.7979 (mmm) REVERT: A 2487 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7616 (tm-30) REVERT: A 2538 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8313 (pt0) REVERT: A 2615 MET cc_start: 0.7193 (mmm) cc_final: 0.6809 (mtp) REVERT: A 2671 MET cc_start: 0.8118 (tmm) cc_final: 0.7485 (tmm) REVERT: A 2920 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7321 (mm) REVERT: A 3008 MET cc_start: 0.8206 (mmm) cc_final: 0.7932 (mmm) REVERT: A 3199 MET cc_start: 0.7538 (mmm) cc_final: 0.7305 (tpt) REVERT: A 3825 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.6557 (p90) REVERT: A 3836 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.7676 (t80) REVERT: A 3875 MET cc_start: 0.8538 (tpp) cc_final: 0.8171 (ttm) REVERT: A 4419 MET cc_start: 0.7812 (tpp) cc_final: 0.7595 (tpp) REVERT: B 218 MET cc_start: 0.7228 (tpp) cc_final: 0.6923 (tpp) REVERT: B 261 TRP cc_start: 0.6585 (OUTLIER) cc_final: 0.5050 (m100) REVERT: B 332 MET cc_start: 0.5990 (tmm) cc_final: 0.5622 (tmm) REVERT: C 311 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6881 (tt) REVERT: C 322 MET cc_start: 0.7682 (tpp) cc_final: 0.7302 (tpp) outliers start: 112 outliers final: 70 residues processed: 257 average time/residue: 0.3996 time to fit residues: 171.1343 Evaluate side-chains 236 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 154 time to evaluate : 3.201 ------------------------------------------------------------------------------- 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 1722 THR Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1797 LEU 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 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 2004 LYS Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2146 VAL Chi-restraints excluded: chain A residue 2159 SER 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 2348 LEU Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2371 THR Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2468 ASN Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2528 THR Chi-restraints excluded: chain A residue 2538 GLU Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2646 ASN 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 2835 ASP Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2920 LEU 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 3131 ASP Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3213 ASP Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3555 ASN Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3662 ILE 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 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 4004 MET Chi-restraints excluded: chain A residue 4084 ILE Chi-restraints excluded: chain A residue 4162 SER Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4391 ILE Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 SER 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 C residue 129 ASP Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 254 ASN 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 282 optimal weight: 7.9990 chunk 192 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 252 optimal weight: 20.0000 chunk 139 optimal weight: 0.1980 chunk 289 optimal weight: 9.9990 chunk 234 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 173 optimal weight: 5.9990 chunk 304 optimal weight: 30.0000 chunk 85 optimal weight: 5.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2560 HIS ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4389 HIS A4566 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28526 Z= 0.229 Angle : 0.567 14.044 38729 Z= 0.282 Chirality : 0.041 0.146 4398 Planarity : 0.004 0.052 4930 Dihedral : 6.260 138.573 3855 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.24 % Rotamer: Outliers : 4.34 % Allowed : 23.35 % Favored : 72.31 % 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: 0.35 (0.14), residues: 3482 helix: 1.52 (0.13), residues: 1671 sheet: -0.78 (0.22), residues: 517 loop : -1.01 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 261 HIS 0.009 0.001 HIS B 206 PHE 0.016 0.001 PHE A2776 TYR 0.019 0.001 TYR A3836 ARG 0.006 0.000 ARG A1543 *********************** 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 289 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 158 time to evaluate : 3.288 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: 0.9200 (tpp-160) cc_final: 0.8927 (tpt-90) REVERT: A 1894 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7489 (mm110) REVERT: A 1960 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7371 (t80) REVERT: A 1982 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7290 (mm) REVERT: A 2189 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7450 (ttm) REVERT: A 2358 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6928 (ttp-170) REVERT: A 2384 SER cc_start: 0.6764 (OUTLIER) cc_final: 0.6552 (p) REVERT: A 2487 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7663 (tm-30) REVERT: A 2538 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8331 (pt0) REVERT: A 2671 MET cc_start: 0.8068 (tmm) cc_final: 0.7447 (tmm) REVERT: A 3747 LYS cc_start: 0.9209 (tmtt) cc_final: 0.8888 (mmtt) REVERT: A 3825 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.6622 (p90) REVERT: A 3875 MET cc_start: 0.8578 (tpp) cc_final: 0.8104 (ttm) REVERT: A 4455 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7600 (mm) REVERT: B 261 TRP cc_start: 0.6637 (OUTLIER) cc_final: 0.5073 (m100) REVERT: B 332 MET cc_start: 0.6039 (tmm) cc_final: 0.5609 (tmm) REVERT: C 164 LEU cc_start: 0.8541 (tp) cc_final: 0.8066 (tt) REVERT: C 311 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.6873 (tt) REVERT: C 322 MET cc_start: 0.7705 (tpp) cc_final: 0.7323 (tpp) outliers start: 131 outliers final: 87 residues processed: 280 average time/residue: 0.3908 time to fit residues: 179.6700 Evaluate side-chains 250 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 152 time to evaluate : 3.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1615 LEU Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1703 THR Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1722 THR 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 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 2004 LYS Chi-restraints excluded: chain A residue 2103 VAL Chi-restraints excluded: chain A residue 2146 VAL Chi-restraints excluded: chain A residue 2159 SER 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 2348 LEU Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2371 THR Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2468 ASN Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2528 THR Chi-restraints excluded: chain A residue 2538 GLU Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2646 ASN 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 2835 ASP 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 3131 ASP Chi-restraints excluded: chain A residue 3213 ASP Chi-restraints excluded: chain A residue 3472 VAL Chi-restraints excluded: chain A residue 3495 THR Chi-restraints excluded: chain A residue 3555 ASN Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3615 LEU 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 3782 ARG Chi-restraints excluded: chain A residue 3802 LEU Chi-restraints excluded: chain A residue 3825 TYR 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 4004 MET Chi-restraints excluded: chain A residue 4009 VAL Chi-restraints excluded: chain A residue 4084 ILE 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 4321 LEU Chi-restraints excluded: chain A residue 4326 ASN 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 4522 THR Chi-restraints excluded: chain A residue 4604 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 SER 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 399 SER Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 254 ASN 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 399 SER 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 114 optimal weight: 5.9990 chunk 305 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 199 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 339 optimal weight: 6.9990 chunk 281 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 178 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1502 ASN ** A2471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3175 HIS ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4389 HIS B 256 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28526 Z= 0.290 Angle : 0.625 14.331 38729 Z= 0.311 Chirality : 0.042 0.221 4398 Planarity : 0.004 0.052 4930 Dihedral : 6.390 140.147 3855 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.34 % Favored : 95.63 % Rotamer: Outliers : 4.97 % Allowed : 22.95 % Favored : 72.08 % 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: 0.23 (0.14), residues: 3482 helix: 1.44 (0.13), residues: 1660 sheet: -0.81 (0.22), residues: 506 loop : -1.08 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A2234 HIS 0.005 0.001 HIS A2964 PHE 0.019 0.002 PHE A3109 TYR 0.026 0.002 TYR A3026 ARG 0.005 0.000 ARG A3525 *********************** 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 308 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 158 time to evaluate : 3.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1467 ARG cc_start: 0.9195 (tpp-160) cc_final: 0.8902 (tpt-90) REVERT: A 1894 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7600 (mm110) REVERT: A 1960 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7519 (t80) REVERT: A 1982 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7282 (mm) REVERT: A 2073 PHE cc_start: 0.6379 (OUTLIER) cc_final: 0.5646 (m-10) REVERT: A 2189 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7566 (ttm) REVERT: A 2358 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6908 (ttp-170) REVERT: A 2538 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8368 (pt0) REVERT: A 2545 TRP cc_start: 0.6663 (OUTLIER) cc_final: 0.6344 (m-10) REVERT: A 2671 MET cc_start: 0.7992 (tmm) cc_final: 0.7493 (tmm) REVERT: A 2960 GLN cc_start: 0.7856 (tp-100) cc_final: 0.7439 (tt0) REVERT: A 3068 MET cc_start: 0.7591 (ptp) cc_final: 0.7368 (ptp) REVERT: A 3747 LYS cc_start: 0.9220 (tmtt) cc_final: 0.8914 (mmtt) REVERT: A 3825 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.6554 (p90) REVERT: A 3875 MET cc_start: 0.8725 (tpp) cc_final: 0.8264 (ttm) REVERT: A 4128 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.6734 (pmm) REVERT: A 4419 MET cc_start: 0.7918 (tpp) cc_final: 0.7662 (tpp) REVERT: B 261 TRP cc_start: 0.6739 (OUTLIER) cc_final: 0.4997 (m100) REVERT: B 332 MET cc_start: 0.6108 (tmm) cc_final: 0.5675 (tmm) REVERT: C 164 LEU cc_start: 0.8628 (tp) cc_final: 0.8228 (tt) REVERT: C 311 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.6925 (tt) REVERT: C 322 MET cc_start: 0.7708 (tpp) cc_final: 0.7307 (tpp) outliers start: 150 outliers final: 109 residues processed: 295 average time/residue: 0.4097 time to fit residues: 197.1844 Evaluate side-chains 274 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 153 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1530 ILE Chi-restraints excluded: chain A residue 1615 LEU Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1703 THR Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1722 THR 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 1851 THR 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 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 2159 SER 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 2321 ASP Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2371 THR Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2468 ASN Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2538 GLU Chi-restraints excluded: chain A residue 2545 TRP Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2646 ASN Chi-restraints excluded: chain A residue 2676 THR 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 2835 ASP Chi-restraints excluded: chain A residue 2853 VAL Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2910 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 3058 VAL Chi-restraints excluded: chain A residue 3099 THR Chi-restraints excluded: chain A residue 3131 ASP 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 3495 THR Chi-restraints excluded: chain A residue 3533 SER Chi-restraints excluded: chain A residue 3555 ASN Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3615 LEU Chi-restraints excluded: chain A residue 3617 ASP 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 3782 ARG Chi-restraints excluded: chain A residue 3790 VAL 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 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 3928 THR Chi-restraints excluded: chain A residue 3936 VAL 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 4223 LEU Chi-restraints excluded: chain A residue 4230 ARG 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 4390 LEU Chi-restraints excluded: chain A residue 4391 ILE Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4604 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 211 SER 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 B residue 399 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 129 ASP 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 399 SER 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 327 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 285 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 338 optimal weight: 2.9990 chunk 211 optimal weight: 0.8980 chunk 206 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2560 HIS ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4389 HIS B 256 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28526 Z= 0.236 Angle : 0.588 14.351 38729 Z= 0.291 Chirality : 0.042 0.183 4398 Planarity : 0.004 0.055 4930 Dihedral : 6.332 141.115 3855 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.82 % Favored : 96.15 % Rotamer: Outliers : 4.54 % Allowed : 23.68 % Favored : 71.78 % 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: 0.33 (0.14), residues: 3482 helix: 1.54 (0.13), residues: 1664 sheet: -0.80 (0.22), residues: 505 loop : -1.06 (0.17), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 261 HIS 0.004 0.001 HIS A2857 PHE 0.013 0.001 PHE A3823 TYR 0.016 0.001 TYR A1546 ARG 0.005 0.000 ARG A1529 *********************** 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 298 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 161 time to evaluate : 3.335 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: 0.9211 (tpp-160) cc_final: 0.8965 (tpt-90) REVERT: A 1960 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.7580 (t80) REVERT: A 1982 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7328 (mm) REVERT: A 2073 PHE cc_start: 0.6369 (OUTLIER) cc_final: 0.5703 (m-10) REVERT: A 2189 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7515 (ttm) REVERT: A 2358 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6972 (ttp-170) REVERT: A 2487 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7518 (tm-30) REVERT: A 2538 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8369 (pt0) REVERT: A 2545 TRP cc_start: 0.6625 (OUTLIER) cc_final: 0.6376 (m-10) REVERT: A 2671 MET cc_start: 0.8076 (tmm) cc_final: 0.7568 (tmm) REVERT: A 2960 GLN cc_start: 0.7823 (tp-100) cc_final: 0.7451 (tt0) REVERT: A 3825 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.6647 (p90) REVERT: A 3875 MET cc_start: 0.8743 (tpp) cc_final: 0.8284 (ttm) REVERT: A 4097 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.7920 (mtmm) REVERT: A 4419 MET cc_start: 0.7877 (tpp) cc_final: 0.7621 (tpp) REVERT: B 261 TRP cc_start: 0.6749 (OUTLIER) cc_final: 0.5004 (m100) REVERT: B 332 MET cc_start: 0.6047 (tmm) cc_final: 0.5709 (tmm) REVERT: C 164 LEU cc_start: 0.8607 (tp) cc_final: 0.8201 (tt) REVERT: C 311 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.6881 (tt) REVERT: C 322 MET cc_start: 0.7696 (tpp) cc_final: 0.7346 (tpp) outliers start: 137 outliers final: 103 residues processed: 290 average time/residue: 0.4294 time to fit residues: 207.9298 Evaluate side-chains 262 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 148 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1540 VAL Chi-restraints excluded: chain A residue 1615 LEU Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1703 THR Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1722 THR 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 1861 MET 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 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 2159 SER 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 2321 ASP Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2371 THR 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 2538 GLU Chi-restraints excluded: chain A residue 2545 TRP Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2646 ASN Chi-restraints excluded: chain A residue 2681 SER Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2745 THR Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2910 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 3058 VAL Chi-restraints excluded: chain A residue 3099 THR Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3131 ASP 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 3495 THR Chi-restraints excluded: chain A residue 3533 SER Chi-restraints excluded: chain A residue 3555 ASN Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3609 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 3782 ARG Chi-restraints excluded: chain A residue 3790 VAL Chi-restraints excluded: chain A residue 3825 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 3928 THR 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 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 4321 LEU Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4391 ILE Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 207 ILE 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 B residue 399 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 135 TRP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 211 SER 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 399 SER 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 209 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 202 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 230 optimal weight: 6.9990 chunk 167 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 265 optimal weight: 4.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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** A2560 HIS ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4316 GLN A4325 ASN A4389 HIS A4506 ASN B 256 GLN B 275 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 28526 Z= 0.281 Angle : 0.628 14.587 38729 Z= 0.312 Chirality : 0.042 0.192 4398 Planarity : 0.004 0.054 4930 Dihedral : 6.367 142.423 3855 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.60 % Favored : 95.38 % Rotamer: Outliers : 4.87 % Allowed : 23.68 % Favored : 71.45 % 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: 0.19 (0.14), residues: 3482 helix: 1.44 (0.13), residues: 1664 sheet: -0.86 (0.22), residues: 513 loop : -1.14 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 261 HIS 0.005 0.001 HIS A2857 PHE 0.020 0.002 PHE A2776 TYR 0.019 0.002 TYR A2777 ARG 0.004 0.000 ARG A3474 *********************** 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 305 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 158 time to evaluate : 3.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1467 ARG cc_start: 0.9224 (tpp-160) cc_final: 0.8965 (tpt-90) REVERT: A 1982 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7279 (mm) REVERT: A 2012 MET cc_start: 0.8225 (mmm) cc_final: 0.6123 (tpt) REVERT: A 2073 PHE cc_start: 0.6396 (OUTLIER) cc_final: 0.5703 (m-10) REVERT: A 2189 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7501 (ttm) REVERT: A 2358 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.7002 (ttp-170) REVERT: A 2487 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7575 (tm-30) REVERT: A 2538 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8450 (pt0) REVERT: A 2545 TRP cc_start: 0.6654 (OUTLIER) cc_final: 0.6426 (m-10) REVERT: A 2671 MET cc_start: 0.8133 (tmm) cc_final: 0.7586 (tmm) REVERT: A 2960 GLN cc_start: 0.7922 (tp-100) cc_final: 0.7572 (tt0) REVERT: A 3747 LYS cc_start: 0.9250 (tmtt) cc_final: 0.8910 (mmtt) REVERT: A 3825 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.6639 (p90) REVERT: A 3875 MET cc_start: 0.8764 (tpp) cc_final: 0.8336 (ttm) REVERT: A 4097 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7900 (mtmm) REVERT: A 4128 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.6800 (pmm) REVERT: A 4419 MET cc_start: 0.7900 (tpp) cc_final: 0.7642 (tpp) REVERT: B 261 TRP cc_start: 0.6765 (OUTLIER) cc_final: 0.4866 (m100) REVERT: B 332 MET cc_start: 0.6333 (tmm) cc_final: 0.5965 (tmm) REVERT: C 164 LEU cc_start: 0.8612 (tp) cc_final: 0.8133 (tt) REVERT: C 311 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.6955 (tt) REVERT: C 322 MET cc_start: 0.7726 (tpp) cc_final: 0.7352 (tpp) outliers start: 147 outliers final: 120 residues processed: 296 average time/residue: 0.3943 time to fit residues: 191.9995 Evaluate side-chains 283 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 152 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1530 ILE Chi-restraints excluded: chain A residue 1540 VAL Chi-restraints excluded: chain A residue 1615 LEU Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1703 THR Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1722 THR 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 1851 THR Chi-restraints excluded: chain A residue 1861 MET Chi-restraints excluded: chain A residue 1915 SER Chi-restraints excluded: chain A residue 1932 CYS 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 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 2137 LEU Chi-restraints excluded: chain A residue 2146 VAL Chi-restraints excluded: chain A residue 2159 SER 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 2321 ASP Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2371 THR 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 2538 GLU Chi-restraints excluded: chain A residue 2545 TRP Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2646 ASN Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2681 SER Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2745 THR Chi-restraints excluded: chain A residue 2758 LEU Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2910 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 3002 SER Chi-restraints excluded: chain A residue 3046 SER Chi-restraints excluded: chain A residue 3058 VAL Chi-restraints excluded: chain A residue 3099 THR Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3131 ASP 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 3495 THR Chi-restraints excluded: chain A residue 3533 SER Chi-restraints excluded: chain A residue 3555 ASN Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3617 ASP 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 3782 ARG 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 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 3928 THR 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 4128 MET 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 4321 LEU Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4390 LEU 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 A residue 4604 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 275 HIS 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 114 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 135 TRP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 290 TYR 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 399 SER Chi-restraints excluded: chain C residue 400 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 307 optimal weight: 20.0000 chunk 324 optimal weight: 9.9990 chunk 295 optimal weight: 6.9990 chunk 315 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 137 optimal weight: 0.3980 chunk 247 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 284 optimal weight: 9.9990 chunk 298 optimal weight: 0.6980 chunk 314 optimal weight: 10.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- 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** A2554 GLN A2560 HIS ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4316 GLN A4389 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 28526 Z= 0.248 Angle : 0.612 14.720 38729 Z= 0.303 Chirality : 0.042 0.182 4398 Planarity : 0.004 0.054 4930 Dihedral : 6.313 142.386 3855 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.14 % Favored : 95.84 % Rotamer: Outliers : 4.64 % Allowed : 23.82 % Favored : 71.55 % 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: 0.26 (0.14), residues: 3482 helix: 1.53 (0.13), residues: 1656 sheet: -0.86 (0.22), residues: 513 loop : -1.12 (0.17), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 261 HIS 0.005 0.001 HIS A2857 PHE 0.020 0.001 PHE A2776 TYR 0.021 0.002 TYR A3026 ARG 0.010 0.000 ARG A2804 *********************** 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 295 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 155 time to evaluate : 3.191 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: 0.9227 (tpp-160) cc_final: 0.8953 (tpt-90) REVERT: A 1982 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7360 (mm) REVERT: A 2012 MET cc_start: 0.8307 (mmm) cc_final: 0.6076 (tpt) REVERT: A 2073 PHE cc_start: 0.6398 (OUTLIER) cc_final: 0.5712 (m-10) REVERT: A 2189 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7479 (ttm) REVERT: A 2358 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.7030 (ttp-170) REVERT: A 2671 MET cc_start: 0.8148 (tmm) cc_final: 0.7593 (tmm) REVERT: A 2804 ARG cc_start: 0.7887 (ptt90) cc_final: 0.7644 (ptt90) REVERT: A 2960 GLN cc_start: 0.7903 (tp-100) cc_final: 0.7654 (tt0) REVERT: A 3875 MET cc_start: 0.8770 (tpp) cc_final: 0.8367 (ttm) REVERT: A 4419 MET cc_start: 0.7887 (tpp) cc_final: 0.7627 (tpp) REVERT: B 171 ASP cc_start: 0.6022 (OUTLIER) cc_final: 0.5272 (p0) REVERT: B 218 MET cc_start: 0.7305 (tpp) cc_final: 0.6775 (tpp) REVERT: B 261 TRP cc_start: 0.6781 (OUTLIER) cc_final: 0.4844 (m100) REVERT: C 164 LEU cc_start: 0.8630 (tp) cc_final: 0.8158 (tt) REVERT: C 311 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.6864 (tt) REVERT: C 322 MET cc_start: 0.7714 (tpp) cc_final: 0.7376 (tpp) outliers start: 140 outliers final: 118 residues processed: 285 average time/residue: 0.4097 time to fit residues: 193.3719 Evaluate side-chains 278 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 153 time to evaluate : 3.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1530 ILE Chi-restraints excluded: chain A residue 1540 VAL Chi-restraints excluded: chain A residue 1615 LEU Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1703 THR Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1722 THR 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 1851 THR Chi-restraints excluded: chain A residue 1861 MET Chi-restraints excluded: chain A residue 1915 SER Chi-restraints excluded: chain A residue 1932 CYS Chi-restraints excluded: chain A residue 1963 LEU 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 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 2159 SER 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 2321 ASP Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2358 ARG Chi-restraints excluded: chain A residue 2371 THR Chi-restraints excluded: chain A residue 2384 SER Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2468 ASN Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2546 SER Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2646 ASN Chi-restraints excluded: chain A residue 2681 SER Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2745 THR Chi-restraints excluded: chain A residue 2758 LEU Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2910 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 3002 SER Chi-restraints excluded: chain A residue 3046 SER Chi-restraints excluded: chain A residue 3058 VAL Chi-restraints excluded: chain A residue 3099 THR Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3131 ASP 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 3495 THR Chi-restraints excluded: chain A residue 3533 SER Chi-restraints excluded: chain A residue 3555 ASN Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3617 ASP Chi-restraints excluded: chain A residue 3672 SER Chi-restraints excluded: chain A residue 3702 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 3790 VAL Chi-restraints excluded: chain A residue 3825 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 3928 THR 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 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 4321 LEU Chi-restraints excluded: chain A residue 4326 ASN Chi-restraints excluded: chain A residue 4390 LEU 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 92 LYS Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 207 ILE 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 B residue 399 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 135 TRP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 211 SER 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 399 SER Chi-restraints excluded: chain C residue 400 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 207 optimal weight: 5.9990 chunk 333 optimal weight: 8.9990 chunk 203 optimal weight: 5.9990 chunk 158 optimal weight: 0.0870 chunk 231 optimal weight: 4.9990 chunk 349 optimal weight: 6.9990 chunk 321 optimal weight: 9.9990 chunk 278 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 215 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 overall best weight: 2.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1481 GLN ** A1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2560 HIS ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4316 GLN A4389 HIS B 256 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28526 Z= 0.207 Angle : 0.600 14.695 38729 Z= 0.296 Chirality : 0.042 0.199 4398 Planarity : 0.004 0.053 4930 Dihedral : 6.213 142.333 3855 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.11 % Favored : 95.86 % Rotamer: Outliers : 3.97 % Allowed : 24.48 % Favored : 71.55 % 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: 0.39 (0.14), residues: 3482 helix: 1.64 (0.13), residues: 1653 sheet: -0.74 (0.22), residues: 502 loop : -1.08 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A2545 HIS 0.004 0.001 HIS C 117 PHE 0.021 0.001 PHE A2776 TYR 0.015 0.001 TYR A2777 ARG 0.008 0.000 ARG A2804 ********************** 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 281 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 161 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1467 ARG cc_start: 0.9216 (tpp-160) cc_final: 0.8927 (tpt-90) REVERT: A 1982 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7315 (mm) REVERT: A 2012 MET cc_start: 0.8290 (mmm) cc_final: 0.6065 (tpt) REVERT: A 2073 PHE cc_start: 0.6436 (OUTLIER) cc_final: 0.5728 (m-10) REVERT: A 2189 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7441 (ttm) REVERT: A 2358 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6797 (ttp-170) REVERT: A 2384 SER cc_start: 0.6745 (OUTLIER) cc_final: 0.6537 (p) REVERT: A 2671 MET cc_start: 0.8149 (tmm) cc_final: 0.7594 (tmm) REVERT: A 2804 ARG cc_start: 0.7976 (ptt90) cc_final: 0.7713 (ptt90) REVERT: A 2960 GLN cc_start: 0.7875 (tp-100) cc_final: 0.7613 (tt0) REVERT: A 3875 MET cc_start: 0.8754 (tpp) cc_final: 0.8321 (ttm) REVERT: A 4097 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.7946 (mtmm) REVERT: A 4419 MET cc_start: 0.7872 (tpp) cc_final: 0.7621 (tpp) REVERT: B 123 MET cc_start: 0.6146 (ppp) cc_final: 0.5880 (ppp) REVERT: B 218 MET cc_start: 0.7346 (tpp) cc_final: 0.6888 (tpp) REVERT: B 261 TRP cc_start: 0.6731 (OUTLIER) cc_final: 0.4833 (m100) REVERT: C 164 LEU cc_start: 0.8573 (tp) cc_final: 0.8084 (tt) REVERT: C 311 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.6819 (tt) REVERT: C 322 MET cc_start: 0.7678 (tpp) cc_final: 0.7392 (tpp) outliers start: 120 outliers final: 104 residues processed: 271 average time/residue: 0.4151 time to fit residues: 188.1859 Evaluate side-chains 268 residues out of total 3133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 156 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1530 ILE Chi-restraints excluded: chain A residue 1615 LEU Chi-restraints excluded: chain A residue 1634 ASP Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1703 THR Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1722 THR 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 1851 THR Chi-restraints excluded: chain A residue 1861 MET Chi-restraints excluded: chain A residue 1915 SER Chi-restraints excluded: chain A residue 1932 CYS Chi-restraints excluded: chain A residue 1963 LEU 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 2159 SER 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 2321 ASP 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 2468 ASN Chi-restraints excluded: chain A residue 2496 TYR Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2646 ASN Chi-restraints excluded: chain A residue 2681 SER Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2745 THR Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2835 ASP Chi-restraints excluded: chain A residue 2853 VAL Chi-restraints excluded: chain A residue 2861 ILE Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 2915 VAL Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 3002 SER Chi-restraints excluded: chain A residue 3046 SER Chi-restraints excluded: chain A residue 3058 VAL Chi-restraints excluded: chain A residue 3099 THR Chi-restraints excluded: chain A residue 3115 LEU Chi-restraints excluded: chain A residue 3131 ASP 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 3495 THR Chi-restraints excluded: chain A residue 3555 ASN Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3609 ILE Chi-restraints excluded: chain A residue 3702 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 3790 VAL Chi-restraints excluded: chain A residue 3825 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 3928 THR 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 4133 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 4270 GLU 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 A residue 4604 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 207 ILE 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 114 VAL Chi-restraints excluded: chain C residue 129 ASP 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 221 optimal weight: 0.0170 chunk 296 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 256 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 278 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 286 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.0570 overall best weight: 1.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1482 ASN ** A1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2560 HIS ** A3198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4389 HIS A4526 GLN C 402 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.057211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.049427 restraints weight = 188190.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.050556 restraints weight = 103467.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.051349 restraints weight = 68250.294| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28526 Z= 0.171 Angle : 0.579 14.329 38729 Z= 0.284 Chirality : 0.041 0.168 4398 Planarity : 0.004 0.051 4930 Dihedral : 6.051 141.883 3855 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.30 % Rotamer: Outliers : 3.28 % Allowed : 25.34 % Favored : 71.38 % 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: 0.57 (0.15), residues: 3482 helix: 1.78 (0.13), residues: 1661 sheet: -0.61 (0.23), residues: 480 loop : -1.03 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A2545 HIS 0.006 0.001 HIS C 379 PHE 0.040 0.001 PHE C 388 TYR 0.024 0.001 TYR A3026 ARG 0.008 0.000 ARG A2804 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4924.32 seconds wall clock time: 90 minutes 24.52 seconds (5424.52 seconds total)