Starting phenix.real_space_refine on Wed Jul 24 03:29:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqv_17825/07_2024/8pqv_17825.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqv_17825/07_2024/8pqv_17825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqv_17825/07_2024/8pqv_17825.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqv_17825/07_2024/8pqv_17825.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqv_17825/07_2024/8pqv_17825.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pqv_17825/07_2024/8pqv_17825.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 121 5.16 5 C 15366 2.51 5 N 4163 2.21 5 O 4472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1499": "OE1" <-> "OE2" Residue "A GLU 1723": "OE1" <-> "OE2" Residue "A GLU 1934": "OE1" <-> "OE2" Residue "A ASP 1937": "OD1" <-> "OD2" Residue "A GLU 2117": "OE1" <-> "OE2" Residue "A ASP 2320": "OD1" <-> "OD2" Residue "A GLU 2391": "OE1" <-> "OE2" Residue "A ASP 2835": "OD1" <-> "OD2" Residue "A ASP 2847": "OD1" <-> "OD2" Residue "A TYR 2901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2904": "OE1" <-> "OE2" Residue "A TYR 3176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3506": "OD1" <-> "OD2" Residue "A PHE 3583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3683": "OD1" <-> "OD2" Residue "A PHE 3698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3816": "OE1" <-> "OE2" Residue "A PHE 4017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4482": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 24122 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 24122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2996, 24122 Classifications: {'peptide': 2996} Link IDs: {'PCIS': 3, 'PTRANS': 129, 'TRANS': 2863} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Time building chain proxies: 12.96, per 1000 atoms: 0.54 Number of scatterers: 24122 At special positions: 0 Unit cell: (162.027, 131.316, 133.434, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 121 16.00 O 4472 8.00 N 4163 7.00 C 15366 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: 9.71 Conformation dependent library (CDL) restraints added in 4.8 seconds 5968 Ramachandran restraints generated. 2984 Oldfield, 0 Emsley, 2984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5702 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 20 sheets defined 61.1% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'A' and resid 1327 through 1348 removed outlier: 3.882A pdb=" N GLY A1331 " --> pdb=" O GLN A1327 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS A1338 " --> pdb=" O SER A1334 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL A1339 " --> pdb=" O GLU A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1372 Processing helix chain 'A' and resid 1380 through 1396 removed outlier: 3.843A pdb=" N GLU A1384 " --> pdb=" O TYR A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1404 Processing helix chain 'A' and resid 1409 through 1421 Processing helix chain 'A' and resid 1430 through 1437 removed outlier: 3.795A pdb=" N ILE A1434 " --> pdb=" O THR A1430 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL A1437 " --> pdb=" O GLN A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1472 removed outlier: 3.963A pdb=" N VAL A1446 " --> pdb=" O ASN A1442 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A1472 " --> pdb=" O GLU A1468 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1508 removed outlier: 3.638A pdb=" N LEU A1493 " --> pdb=" O GLY A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1552 removed outlier: 4.536A pdb=" N VAL A1536 " --> pdb=" O ALA A1532 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TRP A1544 " --> pdb=" O VAL A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1561 removed outlier: 3.705A pdb=" N LEU A1560 " --> pdb=" O ASP A1556 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1585 removed outlier: 3.929A pdb=" N SER A1585 " --> pdb=" O LYS A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1592 Processing helix chain 'A' and resid 1596 through 1626 Processing helix chain 'A' and resid 1627 through 1632 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1647 through 1652 removed outlier: 4.271A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1658 removed outlier: 3.684A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1728 removed outlier: 4.243A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE A1727 " --> pdb=" O GLU A1723 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1770 removed outlier: 3.632A pdb=" N GLY A1770 " --> pdb=" O LEU A1766 " (cutoff:3.500A) Processing helix chain 'A' and resid 1775 through 1796 Processing helix chain 'A' and resid 1801 through 1828 removed outlier: 3.846A pdb=" N HIS A1817 " --> pdb=" O THR A1813 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 Processing helix chain 'A' and resid 1940 through 1952 Processing helix chain 'A' and resid 1959 through 1963 removed outlier: 3.694A pdb=" N LEU A1963 " --> pdb=" O PHE A1960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1964 through 1985 removed outlier: 3.786A pdb=" N HIS A1985 " --> pdb=" O ALA A1981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 1993 removed outlier: 3.824A pdb=" N LYS A1992 " --> pdb=" O ASN A1989 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR A1993 " --> pdb=" O TYR A1990 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1989 through 1993' Processing helix chain 'A' and resid 2045 through 2056 Processing helix chain 'A' and resid 2061 through 2080 removed outlier: 4.040A pdb=" N LEU A2065 " --> pdb=" O THR A2061 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A2066 " --> pdb=" O ALA A2062 " (cutoff:3.500A) Proline residue: A2071 - end of helix removed outlier: 3.771A pdb=" N LYS A2074 " --> pdb=" O VAL A2070 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2118 Processing helix chain 'A' and resid 2123 through 2130 Processing helix chain 'A' and resid 2133 through 2146 Processing helix chain 'A' and resid 2147 through 2149 No H-bonds generated for 'chain 'A' and resid 2147 through 2149' Processing helix chain 'A' and resid 2153 through 2165 Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2217 removed outlier: 3.617A pdb=" N VAL A2204 " --> pdb=" O GLY A2200 " (cutoff:3.500A) Processing helix chain 'A' and resid 2229 through 2245 removed outlier: 4.409A pdb=" N TRP A2234 " --> pdb=" O LYS A2230 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ARG A2235 " --> pdb=" O SER A2231 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG A2243 " --> pdb=" O LYS A2239 " (cutoff:3.500A) Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 removed outlier: 3.594A pdb=" N SER A2290 " --> pdb=" O LYS A2286 " (cutoff:3.500A) Processing helix chain 'A' and resid 2293 through 2297 Processing helix chain 'A' and resid 2315 through 2320 Processing helix chain 'A' and resid 2352 through 2357 Processing helix chain 'A' and resid 2365 through 2369 Processing helix chain 'A' and resid 2370 through 2383 removed outlier: 3.648A pdb=" N ILE A2374 " --> pdb=" O SER A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2410 through 2424 removed outlier: 3.655A pdb=" N GLN A2414 " --> pdb=" O SER A2410 " (cutoff:3.500A) Processing helix chain 'A' and resid 2432 through 2441 Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.600A pdb=" N CYS A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2504 removed outlier: 3.658A 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 2571 through 2585 Processing helix chain 'A' and resid 2600 through 2612 removed outlier: 3.776A pdb=" N LEU A2612 " --> pdb=" O ALA A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.475A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2690 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2739 through 2756 removed outlier: 4.247A pdb=" N SER A2743 " --> pdb=" O PRO A2739 " (cutoff:3.500A) Processing helix chain 'A' and resid 2766 through 2784 removed outlier: 3.704A pdb=" N ALA A2771 " --> pdb=" O GLU A2767 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A2772 " --> pdb=" O PRO A2768 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR A2777 " --> pdb=" O MET A2773 " (cutoff:3.500A) Processing helix chain 'A' and resid 2795 through 2810 removed outlier: 3.720A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 removed outlier: 3.569A pdb=" N LEU A2821 " --> pdb=" O PRO A2817 " (cutoff:3.500A) Processing helix chain 'A' and resid 2835 through 2837 No H-bonds generated for 'chain 'A' and resid 2835 through 2837' Processing helix chain 'A' and resid 2839 through 2858 removed outlier: 3.619A pdb=" N ASP A2851 " --> pdb=" O ASP A2847 " (cutoff:3.500A) Processing helix chain 'A' and resid 2862 through 2867 removed outlier: 3.823A pdb=" N ALA A2866 " --> pdb=" O ASP A2862 " (cutoff:3.500A) Processing helix chain 'A' and resid 2886 through 2902 removed outlier: 3.901A pdb=" N GLU A2902 " --> pdb=" O LYS A2898 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2928 removed outlier: 3.625A pdb=" N LEU A2916 " --> pdb=" O PHE A2912 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A2917 " --> pdb=" O ASN A2913 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN A2928 " --> pdb=" O ARG A2924 " (cutoff:3.500A) Processing helix chain 'A' and resid 2945 through 2954 Processing helix chain 'A' and resid 2968 through 2985 Processing helix chain 'A' and resid 3003 through 3007 removed outlier: 4.494A pdb=" N GLU A3006 " --> pdb=" O GLY A3003 " (cutoff:3.500A) Processing helix chain 'A' and resid 3008 through 3014 Processing helix chain 'A' and resid 3023 through 3040 removed outlier: 4.216A pdb=" N ALA A3027 " --> pdb=" O GLY A3023 " (cutoff:3.500A) Processing helix chain 'A' and resid 3046 through 3062 removed outlier: 3.505A pdb=" N LEU A3050 " --> pdb=" O SER A3046 " (cutoff:3.500A) Processing helix chain 'A' and resid 3082 through 3089 removed outlier: 3.794A pdb=" N CYS A3089 " --> pdb=" O LEU A3085 " (cutoff:3.500A) Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3165 removed outlier: 3.626A pdb=" N HIS A3151 " --> pdb=" O CYS A3147 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 3219 removed outlier: 3.777A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3471 through 3516 removed outlier: 3.656A pdb=" N THR A3476 " --> pdb=" O VAL A3472 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A3480 " --> pdb=" O THR A3476 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A3481 " --> pdb=" O ALA A3477 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A3483 " --> pdb=" O LEU A3479 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ALA A3484 " --> pdb=" O LYS A3480 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLY A3505 " --> pdb=" O SER A3501 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N CYS A3507 " --> pdb=" O ILE A3503 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE A3513 " --> pdb=" O LEU A3509 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3554 removed outlier: 3.623A 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 3580 removed outlier: 3.733A pdb=" N LEU A3580 " --> pdb=" O ASN A3576 " (cutoff:3.500A) Processing helix chain 'A' and resid 3594 through 3604 removed outlier: 3.959A pdb=" N GLU A3598 " --> pdb=" O GLY A3594 " (cutoff:3.500A) Processing helix chain 'A' and resid 3605 through 3608 Processing helix chain 'A' and resid 3619 through 3630 Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3651 removed outlier: 3.528A pdb=" N ASN A3650 " --> pdb=" O ASN A3646 " (cutoff:3.500A) Processing helix chain 'A' and resid 3689 through 3694 removed outlier: 3.574A pdb=" N SER A3694 " --> pdb=" O PRO A3690 " (cutoff:3.500A) Processing helix chain 'A' and resid 3704 through 3721 Processing helix chain 'A' and resid 3721 through 3733 Processing helix chain 'A' and resid 3735 through 3751 removed outlier: 4.136A pdb=" N GLN A3739 " --> pdb=" O GLN A3735 " (cutoff:3.500A) Processing helix chain 'A' and resid 3766 through 3786 removed outlier: 3.931A pdb=" N LEU A3773 " --> pdb=" O THR A3769 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A3774 " --> pdb=" O LEU A3770 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A3776 " --> pdb=" O ASN A3772 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A3778 " --> pdb=" O LYS A3774 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A3785 " --> pdb=" O THR A3781 " (cutoff:3.500A) Processing helix chain 'A' and resid 3787 through 3801 removed outlier: 3.784A pdb=" N MET A3791 " --> pdb=" O THR A3787 " (cutoff:3.500A) Processing helix chain 'A' and resid 3801 through 3818 removed outlier: 3.716A pdb=" N SER A3805 " --> pdb=" O TYR A3801 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 3843 through 3847 removed outlier: 3.946A pdb=" N LYS A3847 " --> pdb=" O PRO A3844 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 Processing helix chain 'A' and resid 3879 through 3895 Processing helix chain 'A' and resid 3901 through 3910 Processing helix chain 'A' and resid 3911 through 3914 Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 removed outlier: 4.128A pdb=" N TRP A3960 " --> pdb=" O GLN A3956 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP A3962 " --> pdb=" O GLY A3958 " (cutoff:3.500A) Processing helix chain 'A' and resid 3965 through 3969 removed outlier: 3.666A pdb=" N GLN A3968 " --> pdb=" O SER A3965 " (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 4034 removed outlier: 3.727A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4063 removed outlier: 3.911A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 4.365A pdb=" N LYS A4089 " --> pdb=" O ASN A4085 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4101 No H-bonds generated for 'chain 'A' and resid 4099 through 4101' Processing helix chain 'A' and resid 4102 through 4115 removed outlier: 3.870A pdb=" N SER A4115 " --> pdb=" O LYS A4111 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4141 removed outlier: 3.968A pdb=" N LEU A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) Processing helix chain 'A' and resid 4152 through 4164 removed outlier: 3.576A pdb=" N ASN A4156 " --> pdb=" O GLY A4152 " (cutoff:3.500A) Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.652A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4174 through 4190 removed outlier: 4.556A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) Processing helix chain 'A' and resid 4192 through 4197 removed outlier: 3.968A pdb=" N ALA A4197 " --> pdb=" O LEU A4194 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4228 removed outlier: 3.665A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A4228 " --> pdb=" O ASP A4224 " (cutoff:3.500A) Processing helix chain 'A' and resid 4234 through 4238 removed outlier: 3.519A pdb=" N ILE A4238 " --> pdb=" O PRO A4235 " (cutoff:3.500A) Processing helix chain 'A' and resid 4239 through 4249 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4275 through 4279 Processing helix chain 'A' and resid 4301 through 4311 removed outlier: 3.718A pdb=" N PHE A4305 " --> pdb=" O ARG A4301 " (cutoff:3.500A) Processing helix chain 'A' and resid 4317 through 4321 Processing helix chain 'A' and resid 4325 through 4346 removed outlier: 3.808A pdb=" N ARG A4329 " --> pdb=" O ASN A4325 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR A4333 " --> pdb=" O ARG A4329 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS A4342 " --> pdb=" O ASP A4338 " (cutoff:3.500A) Processing helix chain 'A' and resid 4376 through 4391 removed outlier: 4.098A pdb=" N THR A4382 " --> pdb=" O ARG A4378 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A4391 " --> pdb=" O TRP A4387 " (cutoff:3.500A) Processing helix chain 'A' and resid 4407 through 4438 removed outlier: 3.894A pdb=" N ARG A4411 " --> pdb=" O ASP A4407 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N MET A4419 " --> pdb=" O ARG A4415 " (cutoff:3.500A) Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4475 through 4500 removed outlier: 3.554A pdb=" N GLY A4500 " --> pdb=" O ALA A4496 " (cutoff:3.500A) Processing helix chain 'A' and resid 4502 through 4507 removed outlier: 4.227A pdb=" N ASN A4506 " --> pdb=" O LYS A4502 " (cutoff:3.500A) Processing helix chain 'A' and resid 4517 through 4533 Processing sheet with id=AA1, first strand: chain 'A' and resid 1477 through 1480 Processing sheet with id=AA2, first strand: chain 'A' and resid 1663 through 1666 removed outlier: 3.697A pdb=" N SER A1663 " --> pdb=" O SER A1677 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.705A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.605A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.123A pdb=" N PHE A1686 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 removed outlier: 6.646A pdb=" N GLY A1901 " --> pdb=" O ARG A2037 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LEU A2039 " --> pdb=" O GLY A1901 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER A1903 " --> pdb=" O LEU A2039 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1931 removed outlier: 3.809A pdb=" N ASP A1958 " --> pdb=" O PHE A1930 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (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: 7.156A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE A2303 " --> pdb=" O GLU A2344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2324 through 2326 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: 7.062A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2639 through 2642 Processing sheet with id=AB3, first strand: chain 'A' and resid 2872 through 2873 removed outlier: 4.443A pdb=" N LEU A2872 " --> pdb=" O VAL A2884 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2957 through 2959 removed outlier: 6.619A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ILE A2990 " --> pdb=" O HIS A3063 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.412A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N THR A3681 " --> pdb=" O PRO A3587 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE A3589 " --> pdb=" O THR A3681 " (cutoff:3.500A) 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 4066 through 4070 removed outlier: 6.127A pdb=" N VAL A4041 " --> pdb=" O LEU A4126 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N MET A4128 " --> pdb=" O VAL A4041 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N MET A4043 " --> pdb=" O MET A4128 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4283 through 4288 removed outlier: 6.762A pdb=" N ILE A4294 " --> pdb=" O LEU A4284 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N CYS A4286 " --> pdb=" O LYS A4292 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LYS A4292 " --> pdb=" O CYS A4286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4539 through 4545 Processing sheet with id=AC1, first strand: chain 'A' and resid 4564 through 4565 Processing sheet with id=AC2, first strand: chain 'A' and resid 4568 through 4571 1331 hydrogen bonds defined for protein. 3885 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.75 Time building geometry restraints manager: 10.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6553 1.33 - 1.46: 5125 1.46 - 1.58: 12747 1.58 - 1.70: 3 1.70 - 1.83: 205 Bond restraints: 24633 Sorted by residual: bond pdb=" CA THR A3502 " pdb=" C THR A3502 " ideal model delta sigma weight residual 1.521 1.471 0.050 1.36e-02 5.41e+03 1.34e+01 bond pdb=" C MET A3500 " pdb=" N SER A3501 " ideal model delta sigma weight residual 1.335 1.298 0.037 1.30e-02 5.92e+03 8.05e+00 bond pdb=" CG LEU A3154 " pdb=" CD1 LEU A3154 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.46e+00 bond pdb=" CA SER A3501 " pdb=" C SER A3501 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.35e-02 5.49e+03 7.43e+00 bond pdb=" CG PRO A2480 " pdb=" CD PRO A2480 " ideal model delta sigma weight residual 1.503 1.413 0.090 3.40e-02 8.65e+02 6.98e+00 ... (remaining 24628 not shown) Histogram of bond angle deviations from ideal: 94.44 - 102.92: 145 102.92 - 111.41: 10217 111.41 - 119.89: 11943 119.89 - 128.37: 10870 128.37 - 136.86: 203 Bond angle restraints: 33378 Sorted by residual: angle pdb=" CA PRO A3690 " pdb=" N PRO A3690 " pdb=" CD PRO A3690 " ideal model delta sigma weight residual 112.00 101.75 10.25 1.40e+00 5.10e-01 5.36e+01 angle pdb=" CA LYS A4418 " pdb=" CB LYS A4418 " pdb=" CG LYS A4418 " ideal model delta sigma weight residual 114.10 127.89 -13.79 2.00e+00 2.50e-01 4.75e+01 angle pdb=" CA PRO A2480 " pdb=" N PRO A2480 " pdb=" CD PRO A2480 " ideal model delta sigma weight residual 112.00 102.94 9.06 1.40e+00 5.10e-01 4.18e+01 angle pdb=" C ILE A3503 " pdb=" N ALA A3504 " pdb=" CA ALA A3504 " ideal model delta sigma weight residual 122.42 112.46 9.96 1.55e+00 4.16e-01 4.13e+01 angle pdb=" CA LEU A2002 " pdb=" CB LEU A2002 " pdb=" CG LEU A2002 " ideal model delta sigma weight residual 116.30 136.86 -20.56 3.50e+00 8.16e-02 3.45e+01 ... (remaining 33373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 12371 17.38 - 34.77: 1860 34.77 - 52.15: 546 52.15 - 69.54: 139 69.54 - 86.92: 35 Dihedral angle restraints: 14951 sinusoidal: 6178 harmonic: 8773 Sorted by residual: dihedral pdb=" CA PHE A1516 " pdb=" C PHE A1516 " pdb=" N GLU A1517 " pdb=" CA GLU A1517 " ideal model delta harmonic sigma weight residual -180.00 -152.62 -27.38 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA GLN A1541 " pdb=" C GLN A1541 " pdb=" N ARG A1542 " pdb=" CA ARG A1542 " ideal model delta harmonic sigma weight residual -180.00 -152.82 -27.18 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA ALA A1995 " pdb=" C ALA A1995 " pdb=" N PRO A1996 " pdb=" CA PRO A1996 " ideal model delta harmonic sigma weight residual -180.00 -153.93 -26.07 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 14948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 3528 0.099 - 0.198: 208 0.198 - 0.297: 11 0.297 - 0.396: 1 0.396 - 0.495: 1 Chirality restraints: 3749 Sorted by residual: chirality pdb=" CB VAL A4099 " pdb=" CA VAL A4099 " pdb=" CG1 VAL A4099 " pdb=" CG2 VAL A4099 " both_signs ideal model delta sigma weight residual False -2.63 -2.13 -0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" CB VAL A1426 " pdb=" CA VAL A1426 " pdb=" CG1 VAL A1426 " pdb=" CG2 VAL A1426 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CB ILE A2871 " pdb=" CA ILE A2871 " pdb=" CG1 ILE A2871 " pdb=" CG2 ILE A2871 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 3746 not shown) Planarity restraints: 4294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A3689 " -0.111 5.00e-02 4.00e+02 1.60e-01 4.11e+01 pdb=" N PRO A3690 " 0.277 5.00e-02 4.00e+02 pdb=" CA PRO A3690 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO A3690 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1995 " 0.080 5.00e-02 4.00e+02 1.22e-01 2.38e+01 pdb=" N PRO A1996 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO A1996 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO A1996 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A2795 " -0.054 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO A2796 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A2796 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A2796 " -0.045 5.00e-02 4.00e+02 ... (remaining 4291 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2579 2.75 - 3.29: 23109 3.29 - 3.83: 42016 3.83 - 4.36: 45667 4.36 - 4.90: 79303 Nonbonded interactions: 192674 Sorted by model distance: nonbonded pdb=" O THR A3502 " pdb=" N ALA A3504 " model vdw 2.216 2.520 nonbonded pdb=" O GLU A2775 " pdb=" OG1 THR A2778 " model vdw 2.262 2.440 nonbonded pdb=" OG1 THR A2644 " pdb=" O GLY A2647 " model vdw 2.280 2.440 nonbonded pdb=" O TRP A3489 " pdb=" OG1 THR A3492 " model vdw 2.293 2.440 nonbonded pdb=" OG1 THR A3010 " pdb=" O GLU A3016 " model vdw 2.295 2.440 ... (remaining 192669 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 70.900 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 24633 Z= 0.303 Angle : 0.884 20.556 33378 Z= 0.452 Chirality : 0.050 0.495 3749 Planarity : 0.008 0.160 4294 Dihedral : 18.619 86.921 9249 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.98 % Favored : 96.92 % Rotamer: Outliers : 0.53 % Allowed : 28.21 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.14), residues: 2984 helix: -0.71 (0.11), residues: 1681 sheet: -0.80 (0.32), residues: 249 loop : -0.90 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A1424 HIS 0.007 0.001 HIS A3535 PHE 0.054 0.002 PHE A4412 TYR 0.019 0.002 TYR A3825 ARG 0.018 0.001 ARG A3007 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5968 Ramachandran restraints generated. 2984 Oldfield, 0 Emsley, 2984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5968 Ramachandran restraints generated. 2984 Oldfield, 0 Emsley, 2984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 172 time to evaluate : 2.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2361 MET cc_start: 0.8343 (mtp) cc_final: 0.8031 (mtm) REVERT: A 3029 LEU cc_start: 0.7276 (tp) cc_final: 0.6749 (pp) REVERT: A 3885 MET cc_start: 0.8935 (mmm) cc_final: 0.8630 (tpp) outliers start: 14 outliers final: 5 residues processed: 183 average time/residue: 0.3498 time to fit residues: 108.0191 Evaluate side-chains 167 residues out of total 2666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 162 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1958 ASP Chi-restraints excluded: chain A residue 2170 TYR Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 3502 THR Chi-restraints excluded: chain A residue 3703 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 252 optimal weight: 0.0050 chunk 226 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 152 optimal weight: 0.0470 chunk 121 optimal weight: 0.4980 chunk 234 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 142 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 271 optimal weight: 6.9990 overall best weight: 0.7094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1465 GLN ** A2964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3155 HIS ** A3214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 24633 Z= 0.142 Angle : 0.496 10.182 33378 Z= 0.254 Chirality : 0.038 0.170 3749 Planarity : 0.005 0.119 4294 Dihedral : 4.546 40.816 3260 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.74 % Favored : 98.19 % Rotamer: Outliers : 2.21 % Allowed : 26.82 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.25 (0.15), residues: 2984 helix: 0.74 (0.12), residues: 1712 sheet: -0.65 (0.33), residues: 238 loop : -0.42 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A4478 HIS 0.002 0.001 HIS A3155 PHE 0.012 0.001 PHE A4412 TYR 0.014 0.001 TYR A1546 ARG 0.003 0.000 ARG A1543 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5968 Ramachandran restraints generated. 2984 Oldfield, 0 Emsley, 2984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5968 Ramachandran restraints generated. 2984 Oldfield, 0 Emsley, 2984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 171 time to evaluate : 2.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1941 MET cc_start: 0.7040 (tpp) cc_final: 0.6758 (tpp) REVERT: A 1966 ARG cc_start: 0.8021 (tmm160) cc_final: 0.7592 (tmm160) REVERT: A 2685 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8249 (tm-30) REVERT: A 2797 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.5414 (mmt180) REVERT: A 3029 LEU cc_start: 0.7643 (tp) cc_final: 0.7224 (pp) REVERT: A 3094 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.6654 (m-10) REVERT: A 3500 MET cc_start: 0.7286 (mmm) cc_final: 0.6925 (mmm) REVERT: A 3526 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7770 (tm-30) REVERT: A 3691 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7939 (t0) REVERT: A 3824 LEU cc_start: 0.8640 (tp) cc_final: 0.8341 (tp) REVERT: A 3875 MET cc_start: 0.7192 (ttt) cc_final: 0.6867 (ttp) REVERT: A 4343 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8015 (ttm) outliers start: 59 outliers final: 25 residues processed: 217 average time/residue: 0.3459 time to fit residues: 122.8715 Evaluate side-chains 190 residues out of total 2666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 159 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1958 ASP Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2170 TYR Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2339 VAL Chi-restraints excluded: chain A residue 2342 MET Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2685 GLN Chi-restraints excluded: chain A residue 2797 ARG Chi-restraints excluded: chain A residue 2853 VAL Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3526 GLN Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3691 ASP Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3827 TYR Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 3999 ASP Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4057 ASP Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4343 MET Chi-restraints excluded: chain A residue 4346 MET Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4468 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 150 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 225 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 272 optimal weight: 7.9990 chunk 293 optimal weight: 10.0000 chunk 242 optimal weight: 7.9990 chunk 269 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1528 ASN A2781 GLN ** A2964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3047 HIS A3155 HIS ** A3214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3837 HIS ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 24633 Z= 0.234 Angle : 0.530 7.768 33378 Z= 0.271 Chirality : 0.039 0.154 3749 Planarity : 0.004 0.116 4294 Dihedral : 4.373 45.503 3256 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.65 % Favored : 97.32 % Rotamer: Outliers : 3.68 % Allowed : 26.07 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.86 (0.16), residues: 2984 helix: 1.31 (0.13), residues: 1715 sheet: -0.83 (0.31), residues: 266 loop : -0.17 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A4478 HIS 0.005 0.001 HIS A4187 PHE 0.024 0.001 PHE A4412 TYR 0.016 0.001 TYR A2472 ARG 0.003 0.000 ARG A3191 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5968 Ramachandran restraints generated. 2984 Oldfield, 0 Emsley, 2984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5968 Ramachandran restraints generated. 2984 Oldfield, 0 Emsley, 2984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 163 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1763 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8705 (tt0) REVERT: A 1967 MET cc_start: 0.7476 (mmt) cc_final: 0.7110 (mmm) REVERT: A 2018 MET cc_start: 0.8408 (mmm) cc_final: 0.7785 (mmm) REVERT: A 2220 LEU cc_start: 0.8970 (pt) cc_final: 0.8667 (pp) REVERT: A 2346 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7409 (tm-30) REVERT: A 2427 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7411 (m-10) REVERT: A 2510 MET cc_start: 0.7883 (mtt) cc_final: 0.7626 (mtt) REVERT: A 2685 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8331 (tm-30) REVERT: A 3029 LEU cc_start: 0.7737 (tp) cc_final: 0.7281 (pp) REVERT: A 3094 PHE cc_start: 0.7105 (OUTLIER) cc_final: 0.6682 (m-10) REVERT: A 4109 LEU cc_start: 0.9301 (tp) cc_final: 0.8988 (tt) REVERT: A 4212 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8404 (mt) outliers start: 98 outliers final: 54 residues processed: 244 average time/residue: 0.3142 time to fit residues: 129.4623 Evaluate side-chains 216 residues out of total 2666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 156 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1763 GLU Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1958 ASP Chi-restraints excluded: chain A residue 2170 TYR Chi-restraints excluded: chain A residue 2308 ASP Chi-restraints excluded: chain A residue 2338 ASN Chi-restraints excluded: chain A residue 2342 MET Chi-restraints excluded: chain A residue 2346 GLN Chi-restraints excluded: chain A residue 2388 ASP Chi-restraints excluded: chain A residue 2427 PHE Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2466 CYS Chi-restraints excluded: chain A residue 2487 GLU Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2559 THR Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2685 GLN Chi-restraints excluded: chain A residue 2871 ILE Chi-restraints excluded: chain A residue 2885 ASP Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 2995 ASP Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3169 MET Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3203 VAL Chi-restraints excluded: chain A residue 3205 LEU Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3570 ASP Chi-restraints excluded: chain A residue 3597 THR Chi-restraints excluded: chain A residue 3653 VAL Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3849 VAL Chi-restraints excluded: chain A residue 3896 VAL Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 4013 LEU Chi-restraints excluded: chain A residue 4025 LEU Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4212 LEU Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4337 VAL Chi-restraints excluded: chain A residue 4346 MET Chi-restraints excluded: chain A residue 4377 MET Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4427 VAL Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4605 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 268 optimal weight: 8.9990 chunk 204 optimal weight: 7.9990 chunk 141 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 182 optimal weight: 7.9990 chunk 272 optimal weight: 1.9990 chunk 289 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 258 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1502 ASN ** A2964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3155 HIS ** A3214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 24633 Z= 0.173 Angle : 0.488 11.084 33378 Z= 0.246 Chirality : 0.038 0.211 3749 Planarity : 0.004 0.112 4294 Dihedral : 4.215 47.332 3256 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.41 % Favored : 97.55 % Rotamer: Outliers : 3.45 % Allowed : 26.44 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.16), residues: 2984 helix: 1.65 (0.13), residues: 1712 sheet: -0.65 (0.32), residues: 253 loop : -0.07 (0.20), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A4478 HIS 0.003 0.001 HIS A4187 PHE 0.020 0.001 PHE A4412 TYR 0.014 0.001 TYR A2748 ARG 0.002 0.000 ARG A2720 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5968 Ramachandran restraints generated. 2984 Oldfield, 0 Emsley, 2984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5968 Ramachandran restraints generated. 2984 Oldfield, 0 Emsley, 2984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 166 time to evaluate : 2.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2003 ASN cc_start: 0.8192 (m-40) cc_final: 0.7746 (t0) REVERT: A 2018 MET cc_start: 0.8349 (mmm) cc_final: 0.7697 (mmm) REVERT: A 2346 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7622 (tm-30) REVERT: A 2427 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7389 (m-10) REVERT: A 2510 MET cc_start: 0.7904 (mtt) cc_final: 0.7626 (mtt) REVERT: A 2685 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8294 (tm-30) REVERT: A 3007 ARG cc_start: 0.7779 (ttm-80) cc_final: 0.7468 (ttm-80) REVERT: A 3029 LEU cc_start: 0.7674 (tp) cc_final: 0.7238 (pp) REVERT: A 3030 MET cc_start: 0.7238 (mmp) cc_final: 0.6996 (mmp) REVERT: A 3094 PHE cc_start: 0.7016 (OUTLIER) cc_final: 0.6548 (m-10) REVERT: A 3579 MET cc_start: 0.8067 (mmt) cc_final: 0.7715 (mmt) REVERT: A 4109 LEU cc_start: 0.9291 (tp) cc_final: 0.8998 (tt) REVERT: A 4212 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8377 (mt) outliers start: 92 outliers final: 55 residues processed: 244 average time/residue: 0.3365 time to fit residues: 136.1222 Evaluate side-chains 221 residues out of total 2666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 161 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1958 ASP Chi-restraints excluded: chain A residue 2170 TYR Chi-restraints excluded: chain A residue 2297 LYS Chi-restraints excluded: chain A residue 2308 ASP Chi-restraints excluded: chain A residue 2342 MET Chi-restraints excluded: chain A residue 2346 GLN Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2412 MET Chi-restraints excluded: chain A residue 2427 PHE Chi-restraints excluded: chain A residue 2466 CYS Chi-restraints excluded: chain A residue 2487 GLU Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2559 THR Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2657 LYS Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2685 GLN Chi-restraints excluded: chain A residue 2853 VAL Chi-restraints excluded: chain A residue 2885 ASP Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3474 ARG Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3546 ASP Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3597 THR Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3670 ASP Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3725 ASP Chi-restraints excluded: chain A residue 3849 VAL Chi-restraints excluded: chain A residue 3879 ASP Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 4025 LEU Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4057 ASP Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4183 LEU Chi-restraints excluded: chain A residue 4212 LEU Chi-restraints excluded: chain A residue 4330 VAL Chi-restraints excluded: chain A residue 4343 MET Chi-restraints excluded: chain A residue 4346 MET Chi-restraints excluded: chain A residue 4435 VAL Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4605 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 240 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 119 optimal weight: 0.0020 chunk 246 optimal weight: 10.0000 chunk 199 optimal weight: 0.0050 chunk 0 optimal weight: 30.0000 chunk 147 optimal weight: 6.9990 chunk 259 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.6008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1502 ASN ** A2964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 24633 Z= 0.164 Angle : 0.491 10.871 33378 Z= 0.245 Chirality : 0.038 0.203 3749 Planarity : 0.004 0.110 4294 Dihedral : 4.123 48.068 3256 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.82 % Favored : 97.15 % Rotamer: Outliers : 3.11 % Allowed : 26.78 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.16), residues: 2984 helix: 1.80 (0.13), residues: 1712 sheet: -0.49 (0.32), residues: 263 loop : -0.02 (0.21), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A4478 HIS 0.010 0.001 HIS A3155 PHE 0.020 0.001 PHE A4412 TYR 0.015 0.001 TYR A2748 ARG 0.002 0.000 ARG A4428 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5968 Ramachandran restraints generated. 2984 Oldfield, 0 Emsley, 2984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5968 Ramachandran restraints generated. 2984 Oldfield, 0 Emsley, 2984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 167 time to evaluate : 2.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2003 ASN cc_start: 0.8152 (m-40) cc_final: 0.7708 (t0) REVERT: A 2018 MET cc_start: 0.8320 (mmm) cc_final: 0.7697 (mmm) REVERT: A 2065 LEU cc_start: 0.8454 (tp) cc_final: 0.8221 (tp) REVERT: A 2139 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8308 (tt0) REVERT: A 2346 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: A 2427 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7361 (m-10) REVERT: A 2481 MET cc_start: 0.7800 (tpp) cc_final: 0.7478 (tpp) REVERT: A 2510 MET cc_start: 0.7909 (mtt) cc_final: 0.7613 (mtt) REVERT: A 2685 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8288 (tm-30) REVERT: A 3029 LEU cc_start: 0.7612 (tp) cc_final: 0.7202 (pp) REVERT: A 3030 MET cc_start: 0.7252 (mmp) cc_final: 0.6995 (mmp) REVERT: A 3094 PHE cc_start: 0.7007 (OUTLIER) cc_final: 0.6550 (m-10) REVERT: A 3155 HIS cc_start: 0.8331 (OUTLIER) cc_final: 0.7139 (t-90) REVERT: A 3824 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8532 (tp) REVERT: A 3875 MET cc_start: 0.7447 (ttp) cc_final: 0.7041 (ttt) REVERT: A 3923 ARG cc_start: 0.5569 (OUTLIER) cc_final: 0.4993 (tpm170) REVERT: A 4063 ASN cc_start: 0.8394 (t0) cc_final: 0.8164 (t0) REVERT: A 4109 LEU cc_start: 0.9295 (tp) cc_final: 0.9005 (tt) REVERT: A 4212 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8352 (mt) REVERT: A 4252 TYR cc_start: 0.8413 (m-80) cc_final: 0.8205 (m-80) outliers start: 83 outliers final: 61 residues processed: 237 average time/residue: 0.3433 time to fit residues: 133.9977 Evaluate side-chains 231 residues out of total 2666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 161 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1405 SER Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 2139 GLN Chi-restraints excluded: chain A residue 2170 TYR Chi-restraints excluded: chain A residue 2308 ASP Chi-restraints excluded: chain A residue 2342 MET Chi-restraints excluded: chain A residue 2346 GLN Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2388 ASP Chi-restraints excluded: chain A residue 2427 PHE Chi-restraints excluded: chain A residue 2466 CYS Chi-restraints excluded: chain A residue 2487 GLU Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2559 THR Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2685 GLN Chi-restraints excluded: chain A residue 2810 LEU Chi-restraints excluded: chain A residue 2853 VAL Chi-restraints excluded: chain A residue 2885 ASP Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 2995 ASP Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3203 VAL Chi-restraints excluded: chain A residue 3205 LEU Chi-restraints excluded: chain A residue 3474 ARG Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3546 ASP Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3597 THR Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3756 VAL Chi-restraints excluded: chain A residue 3824 LEU Chi-restraints excluded: chain A residue 3849 VAL Chi-restraints excluded: chain A residue 3879 ASP Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 3923 ARG Chi-restraints excluded: chain A residue 4025 LEU Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4057 ASP Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4078 ASN Chi-restraints excluded: chain A residue 4112 LYS Chi-restraints excluded: chain A residue 4183 LEU Chi-restraints excluded: chain A residue 4212 LEU Chi-restraints excluded: chain A residue 4330 VAL Chi-restraints excluded: chain A residue 4343 MET Chi-restraints excluded: chain A residue 4346 MET Chi-restraints excluded: chain A residue 4377 MET Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4435 VAL Chi-restraints excluded: chain A residue 4605 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 97 optimal weight: 8.9990 chunk 260 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 169 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 289 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 151 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1502 ASN A2476 HIS ** A2964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3155 HIS ** A3214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 24633 Z= 0.227 Angle : 0.526 10.645 33378 Z= 0.265 Chirality : 0.039 0.168 3749 Planarity : 0.004 0.109 4294 Dihedral : 4.165 52.167 3254 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.02 % Favored : 96.95 % Rotamer: Outliers : 4.05 % Allowed : 26.52 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.16), residues: 2984 helix: 1.82 (0.13), residues: 1712 sheet: -0.62 (0.33), residues: 240 loop : 0.04 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A4478 HIS 0.004 0.001 HIS A4187 PHE 0.019 0.001 PHE A4412 TYR 0.014 0.001 TYR A2748 ARG 0.006 0.000 ARG A3759 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5968 Ramachandran restraints generated. 2984 Oldfield, 0 Emsley, 2984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5968 Ramachandran restraints generated. 2984 Oldfield, 0 Emsley, 2984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 161 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1345 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7697 (pm20) REVERT: A 2002 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7558 (tt) REVERT: A 2003 ASN cc_start: 0.8205 (m-40) cc_final: 0.7766 (t0) REVERT: A 2018 MET cc_start: 0.8351 (mmm) cc_final: 0.7705 (mmm) REVERT: A 2139 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8342 (tt0) REVERT: A 2170 TYR cc_start: 0.7665 (OUTLIER) cc_final: 0.7313 (p90) REVERT: A 2346 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7770 (tt0) REVERT: A 2427 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7460 (m-10) REVERT: A 2510 MET cc_start: 0.7835 (mtt) cc_final: 0.7635 (mtt) REVERT: A 2685 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8343 (tm-30) REVERT: A 3029 LEU cc_start: 0.7741 (tp) cc_final: 0.7303 (pp) REVERT: A 3030 MET cc_start: 0.7426 (mmp) cc_final: 0.6776 (mmp) REVERT: A 3094 PHE cc_start: 0.7069 (OUTLIER) cc_final: 0.6623 (m-10) REVERT: A 3824 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8592 (tp) REVERT: A 3923 ARG cc_start: 0.5632 (OUTLIER) cc_final: 0.5050 (tpm170) REVERT: A 3968 GLN cc_start: 0.9282 (OUTLIER) cc_final: 0.8985 (mp10) REVERT: A 4063 ASN cc_start: 0.8434 (t0) cc_final: 0.8046 (t0) REVERT: A 4109 LEU cc_start: 0.9297 (tp) cc_final: 0.8998 (tt) REVERT: A 4157 MET cc_start: 0.8839 (mmm) cc_final: 0.8504 (mmm) REVERT: A 4212 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8336 (mt) REVERT: A 4252 TYR cc_start: 0.8475 (m-80) cc_final: 0.8258 (m-80) REVERT: A 4346 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7725 (mmp) REVERT: A 4597 ASN cc_start: 0.7486 (m-40) cc_final: 0.6594 (p0) outliers start: 108 outliers final: 78 residues processed: 246 average time/residue: 0.3297 time to fit residues: 134.4768 Evaluate side-chains 250 residues out of total 2666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 159 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1345 GLN Chi-restraints excluded: chain A residue 1405 SER Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1958 ASP Chi-restraints excluded: chain A residue 2002 LEU Chi-restraints excluded: chain A residue 2009 SER Chi-restraints excluded: chain A residue 2139 GLN Chi-restraints excluded: chain A residue 2170 TYR Chi-restraints excluded: chain A residue 2308 ASP Chi-restraints excluded: chain A residue 2318 VAL Chi-restraints excluded: chain A residue 2338 ASN Chi-restraints excluded: chain A residue 2342 MET Chi-restraints excluded: chain A residue 2346 GLN Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2388 ASP Chi-restraints excluded: chain A residue 2427 PHE Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2466 CYS Chi-restraints excluded: chain A residue 2487 GLU Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2559 THR Chi-restraints excluded: chain A residue 2562 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2646 ASN Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2685 GLN Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 2810 LEU Chi-restraints excluded: chain A residue 2853 VAL Chi-restraints excluded: chain A residue 2871 ILE Chi-restraints excluded: chain A residue 2885 ASP Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 2994 MET Chi-restraints excluded: chain A residue 2995 ASP Chi-restraints excluded: chain A residue 3010 THR Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3126 MET Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3203 VAL Chi-restraints excluded: chain A residue 3205 LEU Chi-restraints excluded: chain A residue 3474 ARG Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3546 ASP Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3570 ASP Chi-restraints excluded: chain A residue 3597 THR Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3670 ASP Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3725 ASP Chi-restraints excluded: chain A residue 3824 LEU Chi-restraints excluded: chain A residue 3849 VAL Chi-restraints excluded: chain A residue 3879 ASP Chi-restraints excluded: chain A residue 3896 VAL Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 3923 ARG Chi-restraints excluded: chain A residue 3968 GLN Chi-restraints excluded: chain A residue 4013 LEU Chi-restraints excluded: chain A residue 4025 LEU Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4057 ASP Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4078 ASN Chi-restraints excluded: chain A residue 4183 LEU Chi-restraints excluded: chain A residue 4212 LEU Chi-restraints excluded: chain A residue 4343 MET Chi-restraints excluded: chain A residue 4346 MET Chi-restraints excluded: chain A residue 4377 MET Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4404 ASN Chi-restraints excluded: chain A residue 4435 VAL Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4605 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 278 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 164 optimal weight: 6.9990 chunk 211 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 243 optimal weight: 7.9990 chunk 161 optimal weight: 8.9990 chunk 288 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 133 optimal weight: 0.0670 overall best weight: 3.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1502 ASN ** A2964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3155 HIS ** A3214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 24633 Z= 0.234 Angle : 0.533 10.023 33378 Z= 0.267 Chirality : 0.039 0.156 3749 Planarity : 0.004 0.106 4294 Dihedral : 4.207 55.645 3254 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.82 % Favored : 97.15 % Rotamer: Outliers : 4.31 % Allowed : 26.48 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.16), residues: 2984 helix: 1.84 (0.13), residues: 1715 sheet: -0.57 (0.33), residues: 240 loop : -0.01 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1701 HIS 0.004 0.001 HIS A4187 PHE 0.016 0.001 PHE A4412 TYR 0.015 0.001 TYR A2748 ARG 0.011 0.000 ARG A3007 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5968 Ramachandran restraints generated. 2984 Oldfield, 0 Emsley, 2984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5968 Ramachandran restraints generated. 2984 Oldfield, 0 Emsley, 2984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 162 time to evaluate : 2.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1345 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7672 (pm20) REVERT: A 2002 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7555 (tt) REVERT: A 2003 ASN cc_start: 0.8213 (m-40) cc_final: 0.7782 (t0) REVERT: A 2139 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8339 (tt0) REVERT: A 2170 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.7300 (p90) REVERT: A 2346 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: A 2427 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.7497 (m-10) REVERT: A 2510 MET cc_start: 0.7857 (mtt) cc_final: 0.7653 (mtt) REVERT: A 2685 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8373 (tm-30) REVERT: A 3029 LEU cc_start: 0.7745 (tp) cc_final: 0.7301 (pp) REVERT: A 3030 MET cc_start: 0.7622 (mmp) cc_final: 0.6817 (mmp) REVERT: A 3094 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.6749 (m-10) REVERT: A 3923 ARG cc_start: 0.5604 (OUTLIER) cc_final: 0.5034 (tpm170) REVERT: A 3968 GLN cc_start: 0.9289 (OUTLIER) cc_final: 0.9000 (mp10) REVERT: A 4063 ASN cc_start: 0.8476 (t0) cc_final: 0.8090 (t0) REVERT: A 4109 LEU cc_start: 0.9305 (tp) cc_final: 0.9010 (tt) REVERT: A 4157 MET cc_start: 0.8836 (mmm) cc_final: 0.8490 (mmm) REVERT: A 4212 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8277 (mt) REVERT: A 4346 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7667 (mmp) REVERT: A 4597 ASN cc_start: 0.7541 (m-40) cc_final: 0.6661 (p0) outliers start: 115 outliers final: 87 residues processed: 257 average time/residue: 0.3286 time to fit residues: 141.4922 Evaluate side-chains 259 residues out of total 2666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 160 time to evaluate : 2.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1345 GLN Chi-restraints excluded: chain A residue 1405 SER Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1958 ASP Chi-restraints excluded: chain A residue 2002 LEU Chi-restraints excluded: chain A residue 2009 SER Chi-restraints excluded: chain A residue 2139 GLN Chi-restraints excluded: chain A residue 2141 VAL Chi-restraints excluded: chain A residue 2170 TYR Chi-restraints excluded: chain A residue 2308 ASP Chi-restraints excluded: chain A residue 2318 VAL Chi-restraints excluded: chain A residue 2342 MET Chi-restraints excluded: chain A residue 2346 GLN Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2388 ASP Chi-restraints excluded: chain A residue 2392 ASP Chi-restraints excluded: chain A residue 2427 PHE Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2466 CYS Chi-restraints excluded: chain A residue 2487 GLU Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2559 THR Chi-restraints excluded: chain A residue 2562 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2609 LEU Chi-restraints excluded: chain A residue 2646 ASN Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2685 GLN Chi-restraints excluded: chain A residue 2803 VAL Chi-restraints excluded: chain A residue 2810 LEU Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2853 VAL Chi-restraints excluded: chain A residue 2871 ILE Chi-restraints excluded: chain A residue 2885 ASP Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 2994 MET Chi-restraints excluded: chain A residue 2995 ASP Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3126 MET Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3203 VAL Chi-restraints excluded: chain A residue 3205 LEU Chi-restraints excluded: chain A residue 3474 ARG Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3546 ASP Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3570 ASP Chi-restraints excluded: chain A residue 3597 THR Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3670 ASP Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3725 ASP Chi-restraints excluded: chain A residue 3849 VAL Chi-restraints excluded: chain A residue 3879 ASP Chi-restraints excluded: chain A residue 3896 VAL Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 3923 ARG Chi-restraints excluded: chain A residue 3968 GLN Chi-restraints excluded: chain A residue 4013 LEU Chi-restraints excluded: chain A residue 4025 LEU Chi-restraints excluded: chain A residue 4028 THR Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4057 ASP Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4071 ILE Chi-restraints excluded: chain A residue 4078 ASN Chi-restraints excluded: chain A residue 4162 SER Chi-restraints excluded: chain A residue 4183 LEU Chi-restraints excluded: chain A residue 4212 LEU Chi-restraints excluded: chain A residue 4330 VAL Chi-restraints excluded: chain A residue 4343 MET Chi-restraints excluded: chain A residue 4346 MET Chi-restraints excluded: chain A residue 4377 MET Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4404 ASN Chi-restraints excluded: chain A residue 4435 VAL Chi-restraints excluded: chain A residue 4437 VAL Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4605 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 178 optimal weight: 0.0370 chunk 115 optimal weight: 6.9990 chunk 172 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 226 optimal weight: 0.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1502 ASN ** A2964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 24633 Z= 0.148 Angle : 0.509 13.202 33378 Z= 0.249 Chirality : 0.038 0.214 3749 Planarity : 0.004 0.104 4294 Dihedral : 4.081 56.199 3254 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.45 % Favored : 97.52 % Rotamer: Outliers : 3.08 % Allowed : 27.98 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.16), residues: 2984 helix: 2.01 (0.13), residues: 1710 sheet: -0.38 (0.33), residues: 245 loop : 0.05 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1701 HIS 0.021 0.001 HIS A3155 PHE 0.020 0.001 PHE A4412 TYR 0.016 0.001 TYR A2748 ARG 0.008 0.000 ARG A3007 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5968 Ramachandran restraints generated. 2984 Oldfield, 0 Emsley, 2984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5968 Ramachandran restraints generated. 2984 Oldfield, 0 Emsley, 2984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 171 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1345 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7703 (pm20) REVERT: A 1488 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7014 (ttp80) REVERT: A 2002 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7612 (tt) REVERT: A 2003 ASN cc_start: 0.8186 (m-40) cc_final: 0.7807 (t0) REVERT: A 2145 MET cc_start: 0.8909 (mmt) cc_final: 0.8521 (mmt) REVERT: A 2170 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.7259 (p90) REVERT: A 2346 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: A 2427 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.7455 (m-10) REVERT: A 2481 MET cc_start: 0.8060 (tpp) cc_final: 0.7678 (tpp) REVERT: A 2510 MET cc_start: 0.7839 (mtt) cc_final: 0.7624 (mtt) REVERT: A 2685 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8343 (tm-30) REVERT: A 3029 LEU cc_start: 0.7609 (tp) cc_final: 0.7217 (pp) REVERT: A 3030 MET cc_start: 0.7618 (mmp) cc_final: 0.6793 (mmp) REVERT: A 3068 MET cc_start: 0.6796 (mmt) cc_final: 0.6513 (mmt) REVERT: A 3094 PHE cc_start: 0.7028 (OUTLIER) cc_final: 0.6621 (m-10) REVERT: A 3824 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8498 (tp) REVERT: A 3968 GLN cc_start: 0.9262 (OUTLIER) cc_final: 0.9001 (mp10) REVERT: A 4063 ASN cc_start: 0.8459 (t0) cc_final: 0.8071 (t0) REVERT: A 4109 LEU cc_start: 0.9298 (tp) cc_final: 0.9013 (tt) REVERT: A 4157 MET cc_start: 0.8790 (mmm) cc_final: 0.8442 (mmm) REVERT: A 4212 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8314 (mt) REVERT: A 4346 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7631 (mmp) REVERT: A 4597 ASN cc_start: 0.7486 (m-40) cc_final: 0.6615 (p0) outliers start: 82 outliers final: 61 residues processed: 235 average time/residue: 0.3393 time to fit residues: 133.4797 Evaluate side-chains 234 residues out of total 2666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 161 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1345 GLN Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain A residue 1488 ARG Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 2002 LEU Chi-restraints excluded: chain A residue 2009 SER Chi-restraints excluded: chain A residue 2170 TYR Chi-restraints excluded: chain A residue 2308 ASP Chi-restraints excluded: chain A residue 2318 VAL Chi-restraints excluded: chain A residue 2338 ASN Chi-restraints excluded: chain A residue 2342 MET Chi-restraints excluded: chain A residue 2346 GLN Chi-restraints excluded: chain A residue 2388 ASP Chi-restraints excluded: chain A residue 2427 PHE Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2466 CYS Chi-restraints excluded: chain A residue 2487 GLU Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2559 THR Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2603 MET Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2685 GLN Chi-restraints excluded: chain A residue 2810 LEU Chi-restraints excluded: chain A residue 2885 ASP Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 2994 MET Chi-restraints excluded: chain A residue 2995 ASP Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3126 MET Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3205 LEU Chi-restraints excluded: chain A residue 3474 ARG Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3524 MET Chi-restraints excluded: chain A residue 3546 ASP Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3597 THR Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3670 ASP Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3725 ASP Chi-restraints excluded: chain A residue 3824 LEU Chi-restraints excluded: chain A residue 3849 VAL Chi-restraints excluded: chain A residue 3879 ASP Chi-restraints excluded: chain A residue 3896 VAL Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 3968 GLN Chi-restraints excluded: chain A residue 4025 LEU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4057 ASP Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4078 ASN Chi-restraints excluded: chain A residue 4162 SER Chi-restraints excluded: chain A residue 4183 LEU Chi-restraints excluded: chain A residue 4212 LEU Chi-restraints excluded: chain A residue 4330 VAL Chi-restraints excluded: chain A residue 4343 MET Chi-restraints excluded: chain A residue 4346 MET Chi-restraints excluded: chain A residue 4398 LEU Chi-restraints excluded: chain A residue 4435 VAL Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4605 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 262 optimal weight: 2.9990 chunk 276 optimal weight: 5.9990 chunk 251 optimal weight: 9.9990 chunk 268 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 210 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 253 optimal weight: 0.9980 chunk 267 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1502 ASN A3155 HIS ** A3214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4062 GLN ** A4174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 24633 Z= 0.240 Angle : 0.557 12.254 33378 Z= 0.276 Chirality : 0.040 0.216 3749 Planarity : 0.004 0.104 4294 Dihedral : 4.171 59.357 3254 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.98 % Favored : 96.95 % Rotamer: Outliers : 3.60 % Allowed : 27.64 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.16), residues: 2984 helix: 1.96 (0.13), residues: 1711 sheet: -0.53 (0.33), residues: 242 loop : 0.04 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A4478 HIS 0.004 0.001 HIS A4187 PHE 0.023 0.001 PHE A2784 TYR 0.014 0.001 TYR A2748 ARG 0.014 0.000 ARG A3007 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5968 Ramachandran restraints generated. 2984 Oldfield, 0 Emsley, 2984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5968 Ramachandran restraints generated. 2984 Oldfield, 0 Emsley, 2984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 160 time to evaluate : 2.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1345 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7698 (pm20) REVERT: A 1488 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7055 (ttp80) REVERT: A 2002 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7571 (tt) REVERT: A 2003 ASN cc_start: 0.8203 (m-40) cc_final: 0.7791 (t0) REVERT: A 2145 MET cc_start: 0.8918 (mmt) cc_final: 0.8520 (mmt) REVERT: A 2170 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.7366 (p90) REVERT: A 2346 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7890 (tt0) REVERT: A 2427 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7518 (m-10) REVERT: A 2481 MET cc_start: 0.8097 (tpp) cc_final: 0.7635 (tpp) REVERT: A 2510 MET cc_start: 0.7810 (mtt) cc_final: 0.7593 (mtt) REVERT: A 2685 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8368 (tm-30) REVERT: A 3029 LEU cc_start: 0.7704 (tp) cc_final: 0.7266 (pp) REVERT: A 3030 MET cc_start: 0.7749 (mmp) cc_final: 0.6910 (mmp) REVERT: A 3094 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6715 (m-10) REVERT: A 3824 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8573 (tp) REVERT: A 3923 ARG cc_start: 0.5588 (OUTLIER) cc_final: 0.5007 (tpm170) REVERT: A 3968 GLN cc_start: 0.9295 (OUTLIER) cc_final: 0.9012 (mp10) REVERT: A 4063 ASN cc_start: 0.8540 (t0) cc_final: 0.8227 (t0) REVERT: A 4109 LEU cc_start: 0.9314 (tp) cc_final: 0.9020 (tt) REVERT: A 4157 MET cc_start: 0.8836 (mmm) cc_final: 0.8490 (mmm) REVERT: A 4212 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8274 (mt) REVERT: A 4346 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7647 (mmp) REVERT: A 4597 ASN cc_start: 0.7477 (m-40) cc_final: 0.6703 (p0) outliers start: 96 outliers final: 78 residues processed: 237 average time/residue: 0.3412 time to fit residues: 134.3984 Evaluate side-chains 250 residues out of total 2666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 159 time to evaluate : 3.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1345 GLN Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain A residue 1488 ARG Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1826 ILE Chi-restraints excluded: chain A residue 1958 ASP Chi-restraints excluded: chain A residue 1967 MET Chi-restraints excluded: chain A residue 2002 LEU Chi-restraints excluded: chain A residue 2009 SER Chi-restraints excluded: chain A residue 2162 SER Chi-restraints excluded: chain A residue 2170 TYR Chi-restraints excluded: chain A residue 2308 ASP Chi-restraints excluded: chain A residue 2310 GLU Chi-restraints excluded: chain A residue 2318 VAL Chi-restraints excluded: chain A residue 2338 ASN Chi-restraints excluded: chain A residue 2342 MET Chi-restraints excluded: chain A residue 2346 GLN Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2388 ASP Chi-restraints excluded: chain A residue 2392 ASP Chi-restraints excluded: chain A residue 2427 PHE Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2466 CYS Chi-restraints excluded: chain A residue 2487 GLU Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2559 THR Chi-restraints excluded: chain A residue 2562 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2646 ASN Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2685 GLN Chi-restraints excluded: chain A residue 2810 LEU Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2885 ASP Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 2994 MET Chi-restraints excluded: chain A residue 2995 ASP Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3126 MET Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3205 LEU Chi-restraints excluded: chain A residue 3474 ARG Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3546 ASP Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3570 ASP Chi-restraints excluded: chain A residue 3597 THR Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3670 ASP Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3725 ASP Chi-restraints excluded: chain A residue 3824 LEU Chi-restraints excluded: chain A residue 3849 VAL Chi-restraints excluded: chain A residue 3879 ASP Chi-restraints excluded: chain A residue 3896 VAL Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 3923 ARG Chi-restraints excluded: chain A residue 3968 GLN Chi-restraints excluded: chain A residue 4025 LEU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4057 ASP Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4078 ASN Chi-restraints excluded: chain A residue 4162 SER Chi-restraints excluded: chain A residue 4183 LEU Chi-restraints excluded: chain A residue 4212 LEU Chi-restraints excluded: chain A residue 4330 VAL Chi-restraints excluded: chain A residue 4343 MET Chi-restraints excluded: chain A residue 4346 MET Chi-restraints excluded: chain A residue 4404 ASN Chi-restraints excluded: chain A residue 4427 VAL Chi-restraints excluded: chain A residue 4435 VAL Chi-restraints excluded: chain A residue 4441 LYS Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4605 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 176 optimal weight: 9.9990 chunk 283 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 chunk 197 optimal weight: 0.8980 chunk 297 optimal weight: 0.2980 chunk 274 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1502 ASN ** A3214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4062 GLN ** A4174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 24633 Z= 0.149 Angle : 0.519 11.869 33378 Z= 0.254 Chirality : 0.039 0.244 3749 Planarity : 0.004 0.102 4294 Dihedral : 4.033 59.996 3254 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.41 % Favored : 97.55 % Rotamer: Outliers : 3.08 % Allowed : 28.17 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.16), residues: 2984 helix: 2.13 (0.13), residues: 1711 sheet: -0.29 (0.34), residues: 238 loop : 0.09 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1424 HIS 0.003 0.001 HIS A2964 PHE 0.019 0.001 PHE A4412 TYR 0.016 0.001 TYR A2748 ARG 0.014 0.000 ARG A3007 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5968 Ramachandran restraints generated. 2984 Oldfield, 0 Emsley, 2984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5968 Ramachandran restraints generated. 2984 Oldfield, 0 Emsley, 2984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 169 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1345 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7691 (pm20) REVERT: A 1488 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.7139 (ttp80) REVERT: A 2002 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7655 (tt) REVERT: A 2003 ASN cc_start: 0.8178 (m-40) cc_final: 0.7827 (t0) REVERT: A 2139 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8349 (tt0) REVERT: A 2145 MET cc_start: 0.8918 (mmt) cc_final: 0.8529 (mmt) REVERT: A 2170 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.7420 (p90) REVERT: A 2346 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: A 2481 MET cc_start: 0.8107 (tpp) cc_final: 0.7586 (tpp) REVERT: A 2510 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7626 (mtt) REVERT: A 3029 LEU cc_start: 0.7609 (tp) cc_final: 0.7225 (pp) REVERT: A 3030 MET cc_start: 0.7684 (mmp) cc_final: 0.6804 (mmp) REVERT: A 3094 PHE cc_start: 0.7002 (OUTLIER) cc_final: 0.6593 (m-10) REVERT: A 3968 GLN cc_start: 0.9270 (OUTLIER) cc_final: 0.9019 (mp10) REVERT: A 4063 ASN cc_start: 0.8474 (t0) cc_final: 0.8147 (t0) REVERT: A 4109 LEU cc_start: 0.9299 (tp) cc_final: 0.9008 (tt) REVERT: A 4212 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8322 (mt) REVERT: A 4346 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7663 (mmp) REVERT: A 4398 LEU cc_start: 0.4056 (OUTLIER) cc_final: 0.3533 (mp) REVERT: A 4597 ASN cc_start: 0.7414 (m-40) cc_final: 0.6624 (p0) outliers start: 82 outliers final: 64 residues processed: 234 average time/residue: 0.3561 time to fit residues: 139.8634 Evaluate side-chains 235 residues out of total 2666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 159 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1345 GLN Chi-restraints excluded: chain A residue 1377 LEU Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain A residue 1488 ARG Chi-restraints excluded: chain A residue 1515 VAL Chi-restraints excluded: chain A residue 1607 LEU Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1785 VAL Chi-restraints excluded: chain A residue 1796 VAL Chi-restraints excluded: chain A residue 1808 LEU Chi-restraints excluded: chain A residue 1958 ASP Chi-restraints excluded: chain A residue 2002 LEU Chi-restraints excluded: chain A residue 2009 SER Chi-restraints excluded: chain A residue 2139 GLN Chi-restraints excluded: chain A residue 2170 TYR Chi-restraints excluded: chain A residue 2308 ASP Chi-restraints excluded: chain A residue 2310 GLU Chi-restraints excluded: chain A residue 2318 VAL Chi-restraints excluded: chain A residue 2338 ASN Chi-restraints excluded: chain A residue 2342 MET Chi-restraints excluded: chain A residue 2346 GLN Chi-restraints excluded: chain A residue 2388 ASP Chi-restraints excluded: chain A residue 2457 SER Chi-restraints excluded: chain A residue 2466 CYS Chi-restraints excluded: chain A residue 2487 GLU Chi-restraints excluded: chain A residue 2510 MET Chi-restraints excluded: chain A residue 2522 THR Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2559 THR Chi-restraints excluded: chain A residue 2562 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2821 LEU Chi-restraints excluded: chain A residue 2885 ASP Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 2994 MET Chi-restraints excluded: chain A residue 2995 ASP Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3114 ASP Chi-restraints excluded: chain A residue 3126 MET Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3205 LEU Chi-restraints excluded: chain A residue 3474 ARG Chi-restraints excluded: chain A residue 3478 LEU Chi-restraints excluded: chain A residue 3546 ASP Chi-restraints excluded: chain A residue 3557 ASP Chi-restraints excluded: chain A residue 3563 GLN Chi-restraints excluded: chain A residue 3597 THR Chi-restraints excluded: chain A residue 3656 THR Chi-restraints excluded: chain A residue 3670 ASP Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3849 VAL Chi-restraints excluded: chain A residue 3879 ASP Chi-restraints excluded: chain A residue 3896 VAL Chi-restraints excluded: chain A residue 3921 THR Chi-restraints excluded: chain A residue 3968 GLN Chi-restraints excluded: chain A residue 4025 LEU Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4057 ASP Chi-restraints excluded: chain A residue 4058 LEU Chi-restraints excluded: chain A residue 4078 ASN Chi-restraints excluded: chain A residue 4162 SER Chi-restraints excluded: chain A residue 4212 LEU Chi-restraints excluded: chain A residue 4330 VAL Chi-restraints excluded: chain A residue 4343 MET Chi-restraints excluded: chain A residue 4346 MET Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4398 LEU Chi-restraints excluded: chain A residue 4401 THR Chi-restraints excluded: chain A residue 4404 ASN Chi-restraints excluded: chain A residue 4435 VAL Chi-restraints excluded: chain A residue 4441 LYS Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4605 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 188 optimal weight: 2.9990 chunk 252 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 218 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 65 optimal weight: 0.1980 chunk 237 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 243 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1502 ASN ** A2685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4062 GLN ** A4174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.060491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.051073 restraints weight = 113987.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.052325 restraints weight = 65460.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.053157 restraints weight = 44355.419| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24633 Z= 0.169 Angle : 0.529 11.613 33378 Z= 0.259 Chirality : 0.039 0.297 3749 Planarity : 0.004 0.102 4294 Dihedral : 4.007 58.612 3254 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.71 % Favored : 97.25 % Rotamer: Outliers : 3.30 % Allowed : 27.87 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.16), residues: 2984 helix: 2.14 (0.13), residues: 1712 sheet: -0.28 (0.34), residues: 238 loop : 0.10 (0.20), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A4478 HIS 0.003 0.001 HIS A2964 PHE 0.021 0.001 PHE A4412 TYR 0.016 0.001 TYR A2748 ARG 0.005 0.000 ARG A3759 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3880.64 seconds wall clock time: 71 minutes 8.16 seconds (4268.16 seconds total)