Starting phenix.real_space_refine on Fri Aug 9 07:07:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e00_27811/08_2024/8e00_27811_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e00_27811/08_2024/8e00_27811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e00_27811/08_2024/8e00_27811.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e00_27811/08_2024/8e00_27811.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e00_27811/08_2024/8e00_27811_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e00_27811/08_2024/8e00_27811_neut.cif" } resolution = 3.6 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= 0.003 sd= 0.091 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: 5 Type Number sf(0) Gaussians P 11 5.49 5 S 118 5.16 5 C 15867 2.51 5 N 4165 2.21 5 O 4633 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1854": "OD1" <-> "OD2" Residue "A GLU 1910": "OE1" <-> "OE2" Residue "A PHE 1987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2139": "OD1" <-> "OD2" Residue "A PHE 2244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 465": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24794 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 19069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2363, 19069 Classifications: {'peptide': 2363} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 64, 'TRANS': 2298} Chain breaks: 10 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2773 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain breaks: 4 Chain: "C" Number of atoms: 2832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2832 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 15, 'TRANS': 334} Chain breaks: 2 Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 120 Unusual residues: {'ADP': 1, 'ATP': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 14.38, per 1000 atoms: 0.58 Number of scatterers: 24794 At special positions: 0 Unit cell: (159.82, 113.97, 195.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 118 16.00 P 11 15.00 O 4633 8.00 N 4165 7.00 C 15867 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.11 Conformation dependent library (CDL) restraints added in 4.7 seconds 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5818 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 30 sheets defined 51.4% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'A' and resid 1449 through 1459 Processing helix chain 'A' and resid 1464 through 1468 removed outlier: 3.538A pdb=" N ASN A1467 " --> pdb=" O ASP A1464 " (cutoff:3.500A) Processing helix chain 'A' and resid 1469 through 1479 Processing helix chain 'A' and resid 1516 through 1522 Processing helix chain 'A' and resid 1523 through 1533 removed outlier: 3.638A pdb=" N GLN A1533 " --> pdb=" O ARG A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1534 through 1540 Processing helix chain 'A' and resid 1541 through 1551 Processing helix chain 'A' and resid 1556 through 1561 removed outlier: 3.548A pdb=" N LYS A1560 " --> pdb=" O ASP A1556 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1566 Processing helix chain 'A' and resid 1603 through 1633 Processing helix chain 'A' and resid 1635 through 1639 Processing helix chain 'A' and resid 1644 through 1665 Processing helix chain 'A' and resid 1669 through 1688 removed outlier: 4.080A pdb=" N ASN A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1717 Processing helix chain 'A' and resid 1720 through 1731 removed outlier: 3.798A pdb=" N LYS A1730 " --> pdb=" O LEU A1726 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A1731 " --> pdb=" O LEU A1727 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1788 removed outlier: 3.964A pdb=" N GLN A1788 " --> pdb=" O ASP A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1813 Processing helix chain 'A' and resid 1827 through 1842 Processing helix chain 'A' and resid 1850 through 1853 Processing helix chain 'A' and resid 1854 through 1861 Processing helix chain 'A' and resid 1861 through 1875 Processing helix chain 'A' and resid 1909 through 1914 Processing helix chain 'A' and resid 1925 through 1937 Processing helix chain 'A' and resid 1941 through 1960 Processing helix chain 'A' and resid 1969 through 1981 removed outlier: 3.588A pdb=" N SER A1981 " --> pdb=" O LEU A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1983 through 1988 Processing helix chain 'A' and resid 1990 through 2003 removed outlier: 3.616A pdb=" N VAL A1994 " --> pdb=" O GLY A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 2004 through 2006 No H-bonds generated for 'chain 'A' and resid 2004 through 2006' Processing helix chain 'A' and resid 2007 through 2022 Processing helix chain 'A' and resid 2031 through 2046 Processing helix chain 'A' and resid 2050 through 2064 Processing helix chain 'A' and resid 2079 through 2096 Processing helix chain 'A' and resid 2110 through 2115 Processing helix chain 'A' and resid 2128 through 2140 Processing helix chain 'A' and resid 2159 through 2164 removed outlier: 3.702A pdb=" N GLU A2164 " --> pdb=" O PRO A2160 " (cutoff:3.500A) Processing helix chain 'A' and resid 2166 through 2171 Processing helix chain 'A' and resid 2203 through 2208 Processing helix chain 'A' and resid 2221 through 2237 removed outlier: 3.629A pdb=" N LEU A2237 " --> pdb=" O SER A2233 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2257 Processing helix chain 'A' and resid 2258 through 2270 removed outlier: 3.729A pdb=" N LEU A2262 " --> pdb=" O ASP A2258 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) Processing helix chain 'A' and resid 2279 through 2282 Processing helix chain 'A' and resid 2283 through 2298 removed outlier: 3.574A pdb=" N ALA A2287 " --> pdb=" O LYS A2283 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A2298 " --> pdb=" O LEU A2294 " (cutoff:3.500A) Processing helix chain 'A' and resid 2299 through 2302 Processing helix chain 'A' and resid 2306 through 2328 Processing helix chain 'A' and resid 2331 through 2347 removed outlier: 3.576A pdb=" N GLY A2347 " --> pdb=" O ASN A2343 " (cutoff:3.500A) Processing helix chain 'A' and resid 2372 through 2374 No H-bonds generated for 'chain 'A' and resid 2372 through 2374' Processing helix chain 'A' and resid 2381 through 2387 Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2423 through 2434 removed outlier: 3.981A pdb=" N ASN A2434 " --> pdb=" O ASN A2430 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2458 removed outlier: 3.542A pdb=" N ILE A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A2458 " --> pdb=" O ILE A2454 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2513 Processing helix chain 'A' and resid 2547 through 2552 Processing helix chain 'A' and resid 2563 through 2579 Processing helix chain 'A' and resid 2580 through 2581 No H-bonds generated for 'chain 'A' and resid 2580 through 2581' Processing helix chain 'A' and resid 2582 through 2587 removed outlier: 5.163A pdb=" N SER A2587 " --> pdb=" O GLU A2584 " (cutoff:3.500A) Processing helix chain 'A' and resid 2588 through 2607 Processing helix chain 'A' and resid 2618 through 2635 removed outlier: 4.391A pdb=" N LEU A2622 " --> pdb=" O SER A2618 " (cutoff:3.500A) Processing helix chain 'A' and resid 2640 through 2657 Processing helix chain 'A' and resid 2662 through 2681 Processing helix chain 'A' and resid 2708 through 2727 Processing helix chain 'A' and resid 2735 through 2750 Processing helix chain 'A' and resid 2765 through 2777 Processing helix chain 'A' and resid 2791 through 2809 Processing helix chain 'A' and resid 2820 through 2822 No H-bonds generated for 'chain 'A' and resid 2820 through 2822' Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 4.034A pdb=" N LEU A2828 " --> pdb=" O GLU A2824 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A2833 " --> pdb=" O GLU A2829 " (cutoff:3.500A) Processing helix chain 'A' and resid 2840 through 2845 removed outlier: 4.302A pdb=" N GLN A2845 " --> pdb=" O ASP A2842 " (cutoff:3.500A) Processing helix chain 'A' and resid 2846 through 2863 Processing helix chain 'A' and resid 2869 through 2884 Processing helix chain 'A' and resid 2896 through 2905 Processing helix chain 'A' and resid 2905 through 2910 Processing helix chain 'A' and resid 2921 through 2933 Processing helix chain 'A' and resid 2934 through 2936 No H-bonds generated for 'chain 'A' and resid 2934 through 2936' Processing helix chain 'A' and resid 2949 through 2953 Processing helix chain 'A' and resid 2960 through 2981 removed outlier: 3.547A pdb=" N ALA A2964 " --> pdb=" O THR A2960 " (cutoff:3.500A) Processing helix chain 'A' and resid 2989 through 3058 removed outlier: 4.316A pdb=" N LYS A3036 " --> pdb=" O ASN A3032 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR A3037 " --> pdb=" O GLU A3033 " (cutoff:3.500A) Processing helix chain 'A' and resid 3265 through 3299 Processing helix chain 'A' and resid 3299 through 3319 removed outlier: 4.578A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3334 Processing helix chain 'A' and resid 3335 through 3337 No H-bonds generated for 'chain 'A' and resid 3335 through 3337' Processing helix chain 'A' and resid 3338 through 3356 Processing helix chain 'A' and resid 3365 through 3371 Processing helix chain 'A' and resid 3372 through 3382 Processing helix chain 'A' and resid 3387 through 3399 Processing helix chain 'A' and resid 3412 through 3423 removed outlier: 4.069A pdb=" N THR A3416 " --> pdb=" O SER A3412 " (cutoff:3.500A) Processing helix chain 'A' and resid 3435 through 3447 Processing helix chain 'A' and resid 3454 through 3458 Processing helix chain 'A' and resid 3459 through 3461 No H-bonds generated for 'chain 'A' and resid 3459 through 3461' Processing helix chain 'A' and resid 3462 through 3467 removed outlier: 3.507A pdb=" N ILE A3466 " --> pdb=" O ILE A3462 " (cutoff:3.500A) Processing helix chain 'A' and resid 3506 through 3511 Processing helix chain 'A' and resid 3521 through 3538 Processing helix chain 'A' and resid 3538 through 3572 removed outlier: 3.548A pdb=" N GLN A3542 " --> pdb=" O ASN A3538 " (cutoff:3.500A) Processing helix chain 'A' and resid 3580 through 3606 removed outlier: 3.912A pdb=" N GLU A3606 " --> pdb=" O SER A3602 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3617 removed outlier: 4.010A pdb=" N PHE A3611 " --> pdb=" O PHE A3607 " (cutoff:3.500A) Processing helix chain 'A' and resid 3618 through 3637 Processing helix chain 'A' and resid 3645 through 3659 removed outlier: 3.628A pdb=" N PHE A3649 " --> pdb=" O SER A3645 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) Processing helix chain 'A' and resid 3670 through 3687 Processing helix chain 'A' and resid 3688 through 3690 No H-bonds generated for 'chain 'A' and resid 3688 through 3690' Processing helix chain 'A' and resid 3691 through 3711 removed outlier: 4.198A pdb=" N ASP A3709 " --> pdb=" O LEU A3705 " (cutoff:3.500A) Processing helix chain 'A' and resid 3712 through 3727 Processing helix chain 'A' and resid 3742 through 3753 Processing helix chain 'A' and resid 3755 through 3768 removed outlier: 4.227A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS A3764 " --> pdb=" O LEU A3760 " (cutoff:3.500A) Processing helix chain 'A' and resid 3773 through 3780 Processing helix chain 'A' and resid 3796 through 3807 Processing helix chain 'A' and resid 3818 through 3835 removed outlier: 3.644A pdb=" N LYS A3833 " --> pdb=" O ILE A3829 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3846 Processing helix chain 'A' and resid 3847 through 3852 Processing helix chain 'A' and resid 3853 through 3866 removed outlier: 4.236A pdb=" N GLU A3860 " --> pdb=" O HIS A3856 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A3866 " --> pdb=" O THR A3862 " (cutoff:3.500A) Processing helix chain 'A' and resid 3885 through 3891 Processing helix chain 'A' and resid 3902 through 3914 removed outlier: 3.721A pdb=" N GLN A3914 " --> pdb=" O LEU A3910 " (cutoff:3.500A) Processing helix chain 'A' and resid 3923 through 3943 Processing helix chain 'A' and resid 3957 through 3974 removed outlier: 3.548A pdb=" N PHE A3961 " --> pdb=" O ASN A3957 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR A3974 " --> pdb=" O ASN A3970 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3992 Processing helix chain 'A' and resid 3994 through 3998 Processing helix chain 'A' and resid 4000 through 4015 Processing helix chain 'A' and resid 4037 through 4051 Processing helix chain 'A' and resid 4057 through 4062 Processing helix chain 'A' and resid 4066 through 4091 removed outlier: 4.139A pdb=" N ASP A4072 " --> pdb=" O GLU A4068 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYR A4073 " --> pdb=" O SER A4069 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'C' and resid 362 through 369 Processing sheet with id=AA1, first strand: chain 'A' and resid 1569 through 1574 removed outlier: 9.628A pdb=" N SER A1578 " --> pdb=" O GLU A1594 " (cutoff:3.500A) removed outlier: 10.876A pdb=" N GLU A1594 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N THR A1580 " --> pdb=" O LEU A1592 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1733 through 1736 Processing sheet with id=AA3, first strand: chain 'A' and resid 1817 through 1821 removed outlier: 6.605A pdb=" N GLY A1792 " --> pdb=" O ILE A1896 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N LEU A1898 " --> pdb=" O GLY A1792 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE A1794 " --> pdb=" O LEU A1898 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLY A1791 " --> pdb=" O ARG A1917 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N PHE A1919 " --> pdb=" O GLY A1791 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N CYS A1793 " --> pdb=" O PHE A1919 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1878 through 1881 Processing sheet with id=AA5, first strand: chain 'A' and resid 2098 through 2104 removed outlier: 6.529A pdb=" N LEU A2070 " --> pdb=" O PHE A2194 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N THR A2196 " --> pdb=" O LEU A2070 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LEU A2072 " --> pdb=" O THR A2196 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA A2069 " --> pdb=" O GLY A2211 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU A2213 " --> pdb=" O ALA A2069 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE A2071 " --> pdb=" O LEU A2213 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N PHE A2215 " --> pdb=" O ILE A2071 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A2073 " --> pdb=" O PHE A2215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2117 through 2119 Processing sheet with id=AA7, first strand: chain 'A' and resid 2175 through 2177 Processing sheet with id=AA8, first strand: chain 'A' and resid 2357 through 2360 Processing sheet with id=AA9, first strand: chain 'A' and resid 2438 through 2441 removed outlier: 6.494A pdb=" N LEU A2482 " --> pdb=" O HIS A2530 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL A2532 " --> pdb=" O LEU A2482 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LEU A2484 " --> pdb=" O VAL A2532 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ALA A2534 " --> pdb=" O LEU A2484 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2462 through 2465 removed outlier: 6.759A pdb=" N LEU A2471 " --> pdb=" O THR A2525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2696 through 2697 Processing sheet with id=AB3, first strand: chain 'A' and resid 2780 through 2782 removed outlier: 6.057A pdb=" N LYS A2780 " --> pdb=" O CYS A2814 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE A2816 " --> pdb=" O LYS A2780 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL A2782 " --> pdb=" O ILE A2816 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ASP A2818 " --> pdb=" O VAL A2782 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3426 through 3430 removed outlier: 6.341A pdb=" N VAL A3427 " --> pdb=" O ILE A3451 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLN A3453 " --> pdb=" O VAL A3427 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU A3429 " --> pdb=" O GLN A3453 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A3404 " --> pdb=" O ARG A3514 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N VAL A3516 " --> pdb=" O VAL A3404 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE A3406 " --> pdb=" O VAL A3516 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3478 through 3481 Processing sheet with id=AB6, first strand: chain 'A' and resid 3811 through 3815 removed outlier: 3.656A pdb=" N LYS A3872 " --> pdb=" O GLY A3837 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 4020 through 4021 Processing sheet with id=AB8, first strand: chain 'B' and resid 150 through 153 removed outlier: 4.000A pdb=" N LYS B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 158 through 163 removed outlier: 4.389A pdb=" N LYS B 178 " --> pdb=" O THR B 174 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 201 through 208 removed outlier: 4.476A pdb=" N LEU B 220 " --> pdb=" O TRP B 236 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN B 230 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE B 231 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER B 248 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B 233 " --> pdb=" O ILE B 246 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 256 through 264 removed outlier: 6.936A pdb=" N VAL B 279 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N THR B 292 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE B 281 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 300 through 306 removed outlier: 3.593A pdb=" N ILE B 311 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 319 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL B 332 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU B 321 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 340 through 346 removed outlier: 4.795A pdb=" N TYR B 372 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE B 382 " --> pdb=" O THR B 412 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR B 412 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE B 384 " --> pdb=" O VAL B 410 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 420 through 426 removed outlier: 3.688A pdb=" N ASP B 422 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS B 433 " --> pdb=" O ASP B 422 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ASP B 443 " --> pdb=" O CYS B 449 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N CYS B 449 " --> pdb=" O ASP B 443 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 150 through 153 removed outlier: 4.049A pdb=" N LYS C 488 " --> pdb=" O GLY C 484 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 158 through 163 removed outlier: 4.411A pdb=" N LYS C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 201 through 208 removed outlier: 3.501A pdb=" N SER C 203 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU C 220 " --> pdb=" O TRP C 236 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE C 231 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER C 248 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL C 233 " --> pdb=" O ILE C 246 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 256 through 264 removed outlier: 6.815A pdb=" N VAL C 279 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR C 292 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE C 281 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 300 through 306 removed outlier: 6.353A pdb=" N LEU C 319 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL C 332 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU C 321 " --> pdb=" O LEU C 330 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 340 through 345 removed outlier: 4.091A pdb=" N THR C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE C 382 " --> pdb=" O THR C 412 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR C 412 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE C 384 " --> pdb=" O VAL C 410 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 420 through 426 removed outlier: 3.566A pdb=" N ASP C 422 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL C 439 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL C 452 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N CYS C 441 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN C 448 " --> pdb=" O ASP C 443 " (cutoff:3.500A) 1361 hydrogen bonds defined for protein. 3933 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: 14.73 Time building geometry restraints manager: 11.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4063 1.29 - 1.43: 6559 1.43 - 1.56: 14506 1.56 - 1.70: 18 1.70 - 1.83: 181 Bond restraints: 25327 Sorted by residual: bond pdb=" C MET A2259 " pdb=" O MET A2259 " ideal model delta sigma weight residual 1.237 1.160 0.077 1.17e-02 7.31e+03 4.31e+01 bond pdb=" C VAL A3859 " pdb=" O VAL A3859 " ideal model delta sigma weight residual 1.237 1.183 0.054 1.17e-02 7.31e+03 2.16e+01 bond pdb=" CA SER A3832 " pdb=" CB SER A3832 " ideal model delta sigma weight residual 1.530 1.466 0.065 1.69e-02 3.50e+03 1.46e+01 bond pdb=" C GLU A3860 " pdb=" O GLU A3860 " ideal model delta sigma weight residual 1.237 1.282 -0.045 1.19e-02 7.06e+03 1.43e+01 bond pdb=" CA ALA A3886 " pdb=" CB ALA A3886 " ideal model delta sigma weight residual 1.534 1.494 0.040 1.18e-02 7.18e+03 1.17e+01 ... (remaining 25322 not shown) Histogram of bond angle deviations from ideal: 97.22 - 106.06: 478 106.06 - 114.89: 15385 114.89 - 123.72: 17594 123.72 - 132.56: 762 132.56 - 141.39: 65 Bond angle restraints: 34284 Sorted by residual: angle pdb=" N LYS A3863 " pdb=" CA LYS A3863 " pdb=" C LYS A3863 " ideal model delta sigma weight residual 111.28 97.93 13.35 1.09e+00 8.42e-01 1.50e+02 angle pdb=" C THR A3862 " pdb=" CA THR A3862 " pdb=" CB THR A3862 " ideal model delta sigma weight residual 109.72 124.20 -14.48 1.92e+00 2.71e-01 5.69e+01 angle pdb=" CA ASP A1454 " pdb=" C ASP A1454 " pdb=" O ASP A1454 " ideal model delta sigma weight residual 120.82 113.82 7.00 1.05e+00 9.07e-01 4.44e+01 angle pdb=" C ILE A3834 " pdb=" N GLU A3835 " pdb=" CA GLU A3835 " ideal model delta sigma weight residual 122.36 111.38 10.98 1.72e+00 3.38e-01 4.08e+01 angle pdb=" N LYS A3833 " pdb=" CA LYS A3833 " pdb=" C LYS A3833 " ideal model delta sigma weight residual 112.72 104.56 8.16 1.28e+00 6.10e-01 4.07e+01 ... (remaining 34279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 14959 35.61 - 71.23: 242 71.23 - 106.84: 12 106.84 - 142.45: 1 142.45 - 178.06: 2 Dihedral angle restraints: 15216 sinusoidal: 6270 harmonic: 8946 Sorted by residual: dihedral pdb=" C THR A3862 " pdb=" N THR A3862 " pdb=" CA THR A3862 " pdb=" CB THR A3862 " ideal model delta harmonic sigma weight residual -122.00 -140.78 18.78 0 2.50e+00 1.60e-01 5.64e+01 dihedral pdb=" O1B ADP A4203 " pdb=" O3A ADP A4203 " pdb=" PB ADP A4203 " pdb=" PA ADP A4203 " ideal model delta sinusoidal sigma weight residual -60.00 118.06 -178.06 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP A4203 " pdb=" O5' ADP A4203 " pdb=" PA ADP A4203 " pdb=" O2A ADP A4203 " ideal model delta sinusoidal sigma weight residual -60.00 100.40 -160.40 1 2.00e+01 2.50e-03 4.66e+01 ... (remaining 15213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 3753 0.124 - 0.247: 113 0.247 - 0.371: 10 0.371 - 0.494: 0 0.494 - 0.618: 1 Chirality restraints: 3877 Sorted by residual: chirality pdb=" CA THR A3862 " pdb=" N THR A3862 " pdb=" C THR A3862 " pdb=" CB THR A3862 " both_signs ideal model delta sigma weight residual False 2.53 1.91 0.62 2.00e-01 2.50e+01 9.55e+00 chirality pdb=" C3' ATP A4202 " pdb=" C2' ATP A4202 " pdb=" C4' ATP A4202 " pdb=" O3' ATP A4202 " both_signs ideal model delta sigma weight residual False -2.63 -2.98 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C2' ATP A4204 " pdb=" C1' ATP A4204 " pdb=" C3' ATP A4204 " pdb=" O2' ATP A4204 " both_signs ideal model delta sigma weight residual False -2.68 -2.99 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 3874 not shown) Planarity restraints: 4296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A3856 " -0.027 2.00e-02 2.50e+03 5.24e-02 2.74e+01 pdb=" C HIS A3856 " 0.091 2.00e-02 2.50e+03 pdb=" O HIS A3856 " -0.033 2.00e-02 2.50e+03 pdb=" N LYS A3857 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A2257 " 0.026 2.00e-02 2.50e+03 5.20e-02 2.71e+01 pdb=" C PHE A2257 " -0.090 2.00e-02 2.50e+03 pdb=" O PHE A2257 " 0.034 2.00e-02 2.50e+03 pdb=" N ASP A2258 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 210 " -0.022 2.00e-02 2.50e+03 4.34e-02 1.88e+01 pdb=" C ASN C 210 " 0.075 2.00e-02 2.50e+03 pdb=" O ASN C 210 " -0.028 2.00e-02 2.50e+03 pdb=" N TYR C 211 " -0.025 2.00e-02 2.50e+03 ... (remaining 4293 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2111 2.74 - 3.28: 24802 3.28 - 3.82: 41578 3.82 - 4.36: 50293 4.36 - 4.90: 85705 Nonbonded interactions: 204489 Sorted by model distance: nonbonded pdb=" NZ LYS A2225 " pdb=" O3' ATP A4201 " model vdw 2.201 3.120 nonbonded pdb=" N GLU A2112 " pdb=" OE1 GLU A2112 " model vdw 2.207 3.120 nonbonded pdb=" N GLU C 253 " pdb=" OE1 GLU C 253 " model vdw 2.223 3.120 nonbonded pdb=" O GLY A3643 " pdb=" NH2 ARG A3894 " model vdw 2.242 3.120 nonbonded pdb=" OD2 ASP A2839 " pdb=" OH TYR A2874 " model vdw 2.244 3.040 ... (remaining 204484 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 139 through 213 or resid 216 through 350 or resid 355 thro \ ugh 400 or resid 405 through 494)) } 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: 3.580 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: 1.070 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 74.970 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 25327 Z= 0.284 Angle : 0.792 14.480 34284 Z= 0.460 Chirality : 0.052 0.618 3877 Planarity : 0.005 0.100 4296 Dihedral : 12.790 178.064 9398 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.76 % Favored : 98.21 % Rotamer: Outliers : 0.47 % Allowed : 4.55 % Favored : 94.98 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.15), residues: 3017 helix: 1.69 (0.13), residues: 1387 sheet: 0.69 (0.22), residues: 504 loop : -0.31 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 442 HIS 0.016 0.001 HIS A2400 PHE 0.025 0.002 PHE A1561 TYR 0.027 0.002 TYR C 219 ARG 0.013 0.001 ARG A2387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2049 MET cc_start: 0.6982 (tpp) cc_final: 0.6471 (tpp) REVERT: A 2259 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8860 (tpp) REVERT: B 304 ASP cc_start: 0.7618 (t0) cc_final: 0.7353 (t0) REVERT: C 365 TYR cc_start: 0.7600 (m-80) cc_final: 0.7363 (m-10) outliers start: 13 outliers final: 5 residues processed: 159 average time/residue: 0.3986 time to fit residues: 103.3133 Evaluate side-chains 116 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 3.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1615 ILE Chi-restraints excluded: chain A residue 2259 MET Chi-restraints excluded: chain A residue 2868 ASP Chi-restraints excluded: chain A residue 3748 TRP Chi-restraints excluded: chain A residue 3832 SER Chi-restraints excluded: chain A residue 3856 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 257 optimal weight: 3.9990 chunk 231 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 155 optimal weight: 20.0000 chunk 123 optimal weight: 1.9990 chunk 239 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 chunk 276 optimal weight: 7.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1899 ASN A2228 HIS A2553 HIS A3312 GLN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25327 Z= 0.212 Angle : 0.531 7.065 34284 Z= 0.287 Chirality : 0.043 0.154 3877 Planarity : 0.004 0.040 4296 Dihedral : 9.244 169.039 3384 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.00 % Allowed : 4.63 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.15), residues: 3017 helix: 2.41 (0.14), residues: 1389 sheet: 0.54 (0.22), residues: 514 loop : -0.20 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A2084 HIS 0.007 0.001 HIS A2400 PHE 0.018 0.002 PHE A2972 TYR 0.017 0.001 TYR A2571 ARG 0.006 0.001 ARG A2387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 125 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2043 GLN cc_start: 0.8049 (tp40) cc_final: 0.7463 (mt0) REVERT: A 2259 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8584 (tpp) REVERT: A 2272 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8605 (mm) REVERT: A 2302 PHE cc_start: 0.7878 (m-10) cc_final: 0.7473 (m-80) REVERT: A 2638 ARG cc_start: 0.7243 (tmm-80) cc_final: 0.6869 (ttp80) REVERT: A 3427 VAL cc_start: 0.8412 (t) cc_final: 0.8110 (m) REVERT: B 304 ASP cc_start: 0.7622 (t0) cc_final: 0.7310 (t0) REVERT: C 365 TYR cc_start: 0.7627 (m-80) cc_final: 0.7382 (m-80) outliers start: 28 outliers final: 11 residues processed: 148 average time/residue: 0.3361 time to fit residues: 84.4477 Evaluate side-chains 116 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 2.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 1712 ILE Chi-restraints excluded: chain A residue 2169 VAL Chi-restraints excluded: chain A residue 2175 ILE Chi-restraints excluded: chain A residue 2259 MET Chi-restraints excluded: chain A residue 2272 LEU Chi-restraints excluded: chain A residue 2339 ILE Chi-restraints excluded: chain A residue 2863 LEU Chi-restraints excluded: chain A residue 4024 VAL Chi-restraints excluded: chain A residue 4038 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 159 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 153 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 230 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 277 optimal weight: 9.9990 chunk 299 optimal weight: 8.9990 chunk 247 optimal weight: 10.0000 chunk 275 optimal weight: 0.5980 chunk 94 optimal weight: 7.9990 chunk 222 optimal weight: 5.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1867 GLN A3517 HIS B 176 HIS C 176 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 25327 Z= 0.459 Angle : 0.678 7.705 34284 Z= 0.357 Chirality : 0.047 0.202 3877 Planarity : 0.004 0.045 4296 Dihedral : 9.055 173.348 3375 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.54 % Allowed : 4.84 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.15), residues: 3017 helix: 2.10 (0.13), residues: 1399 sheet: 0.26 (0.22), residues: 531 loop : -0.64 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 299 HIS 0.009 0.002 HIS C 164 PHE 0.022 0.002 PHE B 182 TYR 0.023 0.002 TYR A2571 ARG 0.005 0.001 ARG A2659 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 103 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1544 ASP cc_start: 0.8135 (m-30) cc_final: 0.7914 (m-30) REVERT: A 1702 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8054 (mp) REVERT: A 2043 GLN cc_start: 0.8122 (tp40) cc_final: 0.7705 (mt0) REVERT: A 2259 MET cc_start: 0.8611 (mmm) cc_final: 0.8362 (tpp) REVERT: A 2272 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8680 (mm) REVERT: A 2302 PHE cc_start: 0.8238 (m-10) cc_final: 0.7788 (m-80) REVERT: A 2917 MET cc_start: 0.9246 (mmm) cc_final: 0.8822 (mmm) REVERT: A 2938 MET cc_start: 0.8351 (mtt) cc_final: 0.8113 (mtm) REVERT: A 3345 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8467 (mmt) REVERT: A 3722 MET cc_start: 0.8788 (mmm) cc_final: 0.8493 (mmm) REVERT: A 3846 MET cc_start: 0.9201 (mmt) cc_final: 0.8889 (mmm) outliers start: 43 outliers final: 23 residues processed: 140 average time/residue: 0.3421 time to fit residues: 81.1970 Evaluate side-chains 117 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1615 ILE Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1741 LEU Chi-restraints excluded: chain A residue 1945 LEU Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2175 ILE Chi-restraints excluded: chain A residue 2272 LEU Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2681 LEU Chi-restraints excluded: chain A residue 2689 ILE Chi-restraints excluded: chain A residue 2863 LEU Chi-restraints excluded: chain A residue 2868 ASP Chi-restraints excluded: chain A residue 2948 VAL Chi-restraints excluded: chain A residue 3345 MET Chi-restraints excluded: chain A residue 3408 LEU Chi-restraints excluded: chain A residue 3710 ILE Chi-restraints excluded: chain A residue 3945 LEU Chi-restraints excluded: chain A residue 4024 VAL Chi-restraints excluded: chain A residue 4038 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 464 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 274 optimal weight: 0.6980 chunk 208 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 186 optimal weight: 10.0000 chunk 278 optimal weight: 0.5980 chunk 294 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 263 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 25327 Z= 0.157 Angle : 0.478 6.798 34284 Z= 0.254 Chirality : 0.041 0.150 3877 Planarity : 0.003 0.042 4296 Dihedral : 8.435 177.555 3372 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.00 % Allowed : 5.67 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.15), residues: 3017 helix: 2.59 (0.14), residues: 1404 sheet: 0.42 (0.22), residues: 521 loop : -0.54 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A2084 HIS 0.006 0.001 HIS A2400 PHE 0.015 0.001 PHE A2972 TYR 0.015 0.001 TYR A2571 ARG 0.003 0.000 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 3.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1702 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7905 (mp) REVERT: A 2043 GLN cc_start: 0.7986 (tp40) cc_final: 0.7569 (mt0) REVERT: A 2272 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8644 (mm) REVERT: A 2302 PHE cc_start: 0.8158 (m-10) cc_final: 0.7732 (m-80) REVERT: A 2518 THR cc_start: 0.7842 (p) cc_final: 0.7360 (t) REVERT: A 2867 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7724 (mm) REVERT: A 2917 MET cc_start: 0.9255 (mmm) cc_final: 0.8910 (mmm) REVERT: A 2938 MET cc_start: 0.8481 (mtt) cc_final: 0.8189 (mtm) REVERT: A 3345 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8373 (mmp) REVERT: A 3608 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.8423 (m-10) REVERT: A 3631 MET cc_start: 0.8513 (tmm) cc_final: 0.8084 (tmm) outliers start: 28 outliers final: 14 residues processed: 126 average time/residue: 0.3768 time to fit residues: 81.1960 Evaluate side-chains 114 residues out of total 2793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 3.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1615 ILE Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1945 LEU Chi-restraints excluded: chain A residue 2101 VAL Chi-restraints excluded: chain A residue 2272 LEU Chi-restraints excluded: chain A residue 2346 PHE Chi-restraints excluded: chain A residue 2361 ILE Chi-restraints excluded: chain A residue 2863 LEU Chi-restraints excluded: chain A residue 2867 LEU Chi-restraints excluded: chain A residue 3345 MET Chi-restraints excluded: chain A residue 3608 PHE Chi-restraints excluded: chain A residue 4038 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 211 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 245 optimal weight: 3.9990 chunk 167 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 219 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 251 optimal weight: 10.0000 chunk 203 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 150 optimal weight: 1.9990 chunk 264 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2834 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: