Starting phenix.real_space_refine on Fri Sep 19 00:31:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dmw_47019/09_2025/9dmw_47019.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dmw_47019/09_2025/9dmw_47019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dmw_47019/09_2025/9dmw_47019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dmw_47019/09_2025/9dmw_47019.map" model { file = "/net/cci-nas-00/data/ceres_data/9dmw_47019/09_2025/9dmw_47019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dmw_47019/09_2025/9dmw_47019.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 1 5.21 5 S 95 5.16 5 C 13602 2.51 5 N 3578 2.21 5 O 3927 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21212 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 17980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2308, 17980 Classifications: {'peptide': 2308} Incomplete info: {'truncation_to_alanine': 187} Link IDs: {'PTRANS': 64, 'TRANS': 2243} Chain breaks: 17 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 678 Unresolved non-hydrogen angles: 831 Unresolved non-hydrogen dihedrals: 553 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 8, 'ASN:plan1': 12, 'TRP:plan': 2, 'GLU:plan': 41, 'PHE:plan': 4, 'TYR:plan': 1, 'ASP:plan': 21, 'ARG:plan': 12, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 409 Chain: "C" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2746 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 16, 'TRANS': 330} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'ARG%COO:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 373 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'HIS:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 5, 'ASP:plan': 4, 'TYR:plan': 2, 'GLN:plan1': 3, 'TRP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 113 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 113 Unusual residues: {' MG': 1, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.11, per 1000 atoms: 0.24 Number of scatterers: 21212 At special positions: 0 Unit cell: (110.2, 155.44, 174, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 95 16.00 P 9 15.00 Mg 1 11.99 O 3927 8.00 N 3578 7.00 C 13602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 851.1 milliseconds Enol-peptide restraints added in 1.7 microseconds 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5202 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 24 sheets defined 53.8% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 1443 through 1461 Processing helix chain 'A' and resid 1473 through 1488 Processing helix chain 'A' and resid 1512 through 1523 Processing helix chain 'A' and resid 1523 through 1534 removed outlier: 4.035A pdb=" N PHE A1534 " --> pdb=" O GLN A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1539 removed outlier: 3.737A pdb=" N PHE A1539 " --> pdb=" O ARG A1536 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1551 removed outlier: 3.523A pdb=" N SER A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1562 through 1567 removed outlier: 3.520A pdb=" N PHE A1566 " --> pdb=" O MET A1562 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1632 removed outlier: 3.589A pdb=" N TRP A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1665 Processing helix chain 'A' and resid 1669 through 1690 Processing helix chain 'A' and resid 1692 through 1717 removed outlier: 3.980A pdb=" N GLU A1704 " --> pdb=" O ALA A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1731 Processing helix chain 'A' and resid 1772 through 1788 removed outlier: 4.127A pdb=" N GLN A1788 " --> pdb=" O ASP A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1814 Processing helix chain 'A' and resid 1830 through 1842 Processing helix chain 'A' and resid 1849 through 1853 removed outlier: 3.588A pdb=" N ARG A1852 " --> pdb=" O GLU A1849 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU A1853 " --> pdb=" O PHE A1850 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1849 through 1853' Processing helix chain 'A' and resid 1854 through 1874 Processing helix chain 'A' and resid 1909 through 1914 Processing helix chain 'A' and resid 1925 through 1938 removed outlier: 3.519A pdb=" N ILE A1929 " --> pdb=" O GLN A1925 " (cutoff:3.500A) Processing helix chain 'A' and resid 1942 through 1959 Processing helix chain 'A' and resid 1969 through 1980 Processing helix chain 'A' and resid 1983 through 1988 Processing helix chain 'A' and resid 1990 through 2003 removed outlier: 4.020A 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 2008 through 2022 Processing helix chain 'A' and resid 2031 through 2045 removed outlier: 3.522A pdb=" N VAL A2035 " --> pdb=" O SER A2031 " (cutoff:3.500A) Processing helix chain 'A' and resid 2050 through 2065 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 2139 Processing helix chain 'A' and resid 2144 through 2147 No H-bonds generated for 'chain 'A' and resid 2144 through 2147' Processing helix chain 'A' and resid 2159 through 2166 Processing helix chain 'A' and resid 2203 through 2210 removed outlier: 3.523A pdb=" N ILE A2207 " --> pdb=" O THR A2203 " (cutoff:3.500A) Processing helix chain 'A' and resid 2221 through 2236 Processing helix chain 'A' and resid 2246 through 2256 Processing helix chain 'A' and resid 2258 through 2270 removed outlier: 3.898A 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: 4.055A pdb=" N GLN A2289 " --> pdb=" O GLU A2285 " (cutoff:3.500A) Processing helix chain 'A' and resid 2299 through 2302 Processing helix chain 'A' and resid 2306 through 2327 removed outlier: 3.524A pdb=" N ALA A2327 " --> pdb=" O LEU A2323 " (cutoff:3.500A) Processing helix chain 'A' and resid 2331 through 2346 Processing helix chain 'A' and resid 2370 through 2374 removed outlier: 3.717A pdb=" N SER A2373 " --> pdb=" O SER A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2381 through 2387 removed outlier: 3.713A pdb=" N VAL A2385 " --> pdb=" O ALA A2382 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET A2386 " --> pdb=" O HIS A2383 " (cutoff:3.500A) Processing helix chain 'A' and resid 2394 through 2409 Processing helix chain 'A' and resid 2423 through 2434 removed outlier: 3.563A pdb=" N ASN A2434 " --> pdb=" O ASN A2430 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2460 removed outlier: 4.040A pdb=" N ILE A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) Processing helix chain 'A' and resid 2501 through 2512 Processing helix chain 'A' and resid 2547 through 2552 removed outlier: 3.790A pdb=" N THR A2551 " --> pdb=" O SER A2547 " (cutoff:3.500A) Processing helix chain 'A' and resid 2563 through 2580 Processing helix chain 'A' and resid 2582 through 2587 removed outlier: 3.569A pdb=" N PHE A2585 " --> pdb=" O VAL A2582 " (cutoff:3.500A) removed outlier: 5.436A 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: 3.910A pdb=" N LEU A2622 " --> pdb=" O SER A2618 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR A2635 " --> pdb=" O THR A2631 " (cutoff:3.500A) Processing helix chain 'A' and resid 2640 through 2657 removed outlier: 3.574A pdb=" N ALA A2657 " --> pdb=" O TRP A2653 " (cutoff:3.500A) 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 2749 Processing helix chain 'A' and resid 2766 through 2777 Processing helix chain 'A' and resid 2791 through 2808 removed outlier: 3.663A pdb=" N PHE A2795 " --> pdb=" O ASN A2791 " (cutoff:3.500A) Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 4.059A pdb=" N LEU A2828 " --> pdb=" O GLU A2824 " (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 2904 Processing helix chain 'A' and resid 2905 through 2910 removed outlier: 4.298A pdb=" N ASN A2910 " --> pdb=" O PRO A2906 " (cutoff:3.500A) Processing helix chain 'A' and resid 2921 through 2934 removed outlier: 3.584A pdb=" N ASP A2934 " --> pdb=" O ASN A2930 " (cutoff:3.500A) Processing helix chain 'A' and resid 2960 through 2980 removed outlier: 3.750A pdb=" N ALA A2964 " --> pdb=" O THR A2960 " (cutoff:3.500A) Processing helix chain 'A' and resid 2989 through 3039 Processing helix chain 'A' and resid 3285 through 3318 removed outlier: 3.830A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3333 removed outlier: 3.577A pdb=" N ILE A3325 " --> pdb=" O ILE A3321 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A3326 " --> pdb=" O GLY A3322 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A3327 " --> pdb=" O ASN A3323 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR A3332 " --> pdb=" O SER A3328 " (cutoff:3.500A) 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 3381 Processing helix chain 'A' and resid 3387 through 3398 Processing helix chain 'A' and resid 3414 through 3423 Processing helix chain 'A' and resid 3424 through 3426 No H-bonds generated for 'chain 'A' and resid 3424 through 3426' Processing helix chain 'A' and resid 3435 through 3447 Processing helix chain 'A' and resid 3454 through 3458 removed outlier: 3.794A pdb=" N PHE A3458 " --> pdb=" O GLY A3455 " (cutoff:3.500A) 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 3468 Processing helix chain 'A' and resid 3506 through 3511 Processing helix chain 'A' and resid 3521 through 3538 removed outlier: 3.666A pdb=" N ASN A3538 " --> pdb=" O LEU A3534 " (cutoff:3.500A) Processing helix chain 'A' and resid 3538 through 3570 removed outlier: 3.792A pdb=" N GLN A3542 " --> pdb=" O ASN A3538 " (cutoff:3.500A) Processing helix chain 'A' and resid 3580 through 3606 removed outlier: 3.953A pdb=" N GLU A3606 " --> pdb=" O SER A3602 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3618 removed outlier: 3.597A pdb=" N PHE A3611 " --> pdb=" O PHE A3607 " (cutoff:3.500A) Processing helix chain 'A' and resid 3619 through 3639 removed outlier: 3.538A pdb=" N HIS A3639 " --> pdb=" O PHE A3635 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3659 removed outlier: 3.509A pdb=" N VAL A3656 " --> pdb=" O CYS A3652 " (cutoff:3.500A) removed outlier: 3.892A 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 3691 through 3711 Processing helix chain 'A' and resid 3712 through 3727 Processing helix chain 'A' and resid 3742 through 3753 removed outlier: 3.512A pdb=" N THR A3753 " --> pdb=" O ASP A3749 " (cutoff:3.500A) Processing helix chain 'A' and resid 3755 through 3767 removed outlier: 4.867A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.704A 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 3836 removed outlier: 4.118A pdb=" N ILE A3834 " --> pdb=" O SER A3830 " (cutoff:3.500A) Processing helix chain 'A' and resid 3847 through 3859 removed outlier: 4.447A pdb=" N HIS A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LYS A3857 " --> pdb=" O THR A3853 " (cutoff:3.500A) Processing helix chain 'A' and resid 3885 through 3891 Processing helix chain 'A' and resid 3903 through 3914 Processing helix chain 'A' and resid 3922 through 3944 removed outlier: 3.845A pdb=" N ARG A3944 " --> pdb=" O THR A3940 " (cutoff:3.500A) Processing helix chain 'A' and resid 3957 through 3974 removed outlier: 3.857A pdb=" N PHE A3961 " --> pdb=" O ASN A3957 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3992 Processing helix chain 'A' and resid 4000 through 4015 removed outlier: 3.520A pdb=" N LEU A4004 " --> pdb=" O GLU A4000 " (cutoff:3.500A) Processing helix chain 'A' and resid 4037 through 4052 removed outlier: 3.824A pdb=" N GLU A4041 " --> pdb=" O SER A4037 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR A4052 " --> pdb=" O ILE A4048 " (cutoff:3.500A) Processing helix chain 'A' and resid 4057 through 4062 Processing helix chain 'A' and resid 4066 through 4090 removed outlier: 3.605A pdb=" N ILE A4070 " --> pdb=" O PRO A4066 " (cutoff:3.500A) 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: 3.846A pdb=" N SER A1571 " --> pdb=" O ARG A1583 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A1573 " --> pdb=" O GLY A1581 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY A1581 " --> pdb=" O ILE A1573 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N SER A1578 " --> pdb=" O GLU A1594 " (cutoff:3.500A) removed outlier: 10.390A pdb=" N GLU A1594 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR A1580 " --> pdb=" O LEU A1592 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A1582 " --> pdb=" O LEU A1590 " (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 1896 through 1898 removed outlier: 6.909A pdb=" N GLY A1791 " --> pdb=" O ARG A1917 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE A1919 " --> pdb=" O GLY A1791 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N CYS A1793 " --> pdb=" O PHE A1919 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1817 through 1820 Processing sheet with id=AA5, first strand: chain 'A' and resid 1878 through 1881 Processing sheet with id=AA6, first strand: chain 'A' and resid 2098 through 2104 removed outlier: 6.368A pdb=" N ALA A2098 " --> pdb=" O ARG A2149 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TRP A2151 " --> pdb=" O ALA A2098 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL A2100 " --> pdb=" O TRP A2151 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL A2153 " --> pdb=" O VAL A2100 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR A2102 " --> pdb=" O VAL A2153 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ARG A2191 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE A2150 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N LEU A2193 " --> pdb=" O ILE A2150 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL A2152 " --> pdb=" O LEU A2193 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N GLU A2195 " --> pdb=" O VAL A2152 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE A2154 " --> pdb=" O GLU A2195 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU A2070 " --> pdb=" O PHE A2194 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N THR A2196 " --> pdb=" O LEU A2070 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU A2072 " --> pdb=" O THR A2196 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2483 through 2484 removed outlier: 6.861A pdb=" N ILE A2414 " --> pdb=" O GLY A2533 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N CYS A2535 " --> pdb=" O ILE A2414 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LEU A2416 " --> pdb=" O CYS A2535 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLY A2413 " --> pdb=" O ALA A2555 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU A2557 " --> pdb=" O GLY A2413 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE A2415 " --> pdb=" O LEU A2557 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2462 through 2464 Processing sheet with id=AA9, first strand: chain 'A' and resid 2696 through 2697 Processing sheet with id=AB1, first strand: chain 'A' and resid 2780 through 2782 removed outlier: 6.251A pdb=" N LYS A2780 " --> pdb=" O CYS A2814 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE A2816 " --> pdb=" O LYS A2780 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL A2782 " --> pdb=" O ILE A2816 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ASP A2818 " --> pdb=" O VAL A2782 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR A2813 " --> pdb=" O HIS A2886 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL A2888 " --> pdb=" O THR A2813 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU A2815 " --> pdb=" O VAL A2888 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR A2890 " --> pdb=" O LEU A2815 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE A2817 " --> pdb=" O THR A2890 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A2760 " --> pdb=" O ILE A2891 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N MET A2757 " --> pdb=" O ASN A2915 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N MET A2917 " --> pdb=" O MET A2757 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE A2759 " --> pdb=" O MET A2917 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 3427 through 3430 removed outlier: 6.281A pdb=" N VAL A3450 " --> pdb=" O PHE A3495 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N HIS A3497 " --> pdb=" O VAL A3450 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ILE A3452 " --> pdb=" O HIS A3497 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A3496 " --> pdb=" O PRO A3405 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3478 through 3481 removed outlier: 3.766A pdb=" N VAL A3479 " --> pdb=" O VAL A3486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A3486 " --> pdb=" O VAL A3479 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A3481 " --> pdb=" O HIS A3484 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS A3484 " --> pdb=" O ILE A3481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 3786 through 3788 removed outlier: 6.223A pdb=" N THR A3787 " --> pdb=" O VAL A3895 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 3813 through 3814 Processing sheet with id=AB6, first strand: chain 'C' and resid 150 through 153 removed outlier: 3.790A pdb=" N CYS C 150 " --> pdb=" O VAL C 491 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 491 " --> pdb=" O CYS C 150 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL C 481 " --> pdb=" O ASP C 465 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP C 465 " --> pdb=" O VAL C 481 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 161 through 163 removed outlier: 3.513A pdb=" N PHE C 171 " --> pdb=" O LYS C 162 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 178 through 179 Processing sheet with id=AB9, first strand: chain 'C' and resid 201 through 208 removed outlier: 6.855A pdb=" N ALA C 225 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N MET C 204 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL C 223 " --> pdb=" O MET C 204 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL C 206 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL C 221 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEU C 220 " --> pdb=" O TRP C 236 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS C 232 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL C 233 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 237 " --> pdb=" O LYS C 242 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS C 242 " --> pdb=" O VAL C 237 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 256 through 263 removed outlier: 3.713A pdb=" N ILE C 281 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LYS C 291 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ASP C 283 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER C 289 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 300 through 306 removed outlier: 6.798A pdb=" N GLY C 313 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE C 303 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE C 311 " --> pdb=" O ILE C 303 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL C 305 " --> pdb=" O TYR C 309 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TYR C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG C 320 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER C 331 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N HIS C 323 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLY C 329 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 340 through 346 removed outlier: 4.614A pdb=" N TYR C 372 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER C 377 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE C 382 " --> pdb=" O THR C 412 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR C 412 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE C 384 " --> pdb=" O VAL C 410 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 423 through 426 removed outlier: 3.892A pdb=" N HIS C 451 " --> pdb=" O CYS C 441 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP C 443 " --> pdb=" O CYS C 449 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N CYS C 449 " --> pdb=" O ASP C 443 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 160 through 163 removed outlier: 3.764A pdb=" N SER B 160 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 201 through 207 removed outlier: 7.108A pdb=" N ALA B 225 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N MET B 204 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 223 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL B 206 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL B 221 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL B 233 " --> pdb=" O ILE B 246 " (cutoff:3.500A) 1133 hydrogen bonds defined for protein. 3327 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: 6.24 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6600 1.34 - 1.46: 4136 1.46 - 1.58: 10755 1.58 - 1.70: 11 1.70 - 1.82: 146 Bond restraints: 21648 Sorted by residual: bond pdb=" C TRP C 324 " pdb=" N PRO C 325 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.68e+00 bond pdb=" C GLU A2590 " pdb=" N PRO A2591 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.28e-02 6.10e+03 2.02e+00 bond pdb=" CB PHE A3638 " pdb=" CG PHE A3638 " ideal model delta sigma weight residual 1.502 1.535 -0.033 2.30e-02 1.89e+03 2.01e+00 bond pdb=" CG1 ILE A1936 " pdb=" CD1 ILE A1936 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.88e+00 bond pdb=" C ALA A3886 " pdb=" N PRO A3887 " ideal model delta sigma weight residual 1.335 1.350 -0.016 1.28e-02 6.10e+03 1.47e+00 ... (remaining 21643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 28656 1.95 - 3.91: 593 3.91 - 5.86: 107 5.86 - 7.81: 30 7.81 - 9.77: 8 Bond angle restraints: 29394 Sorted by residual: angle pdb=" C ASN C 265 " pdb=" N ASN C 266 " pdb=" CA ASN C 266 " ideal model delta sigma weight residual 121.54 130.02 -8.48 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C ASP C 316 " pdb=" N THR C 317 " pdb=" CA THR C 317 " ideal model delta sigma weight residual 122.08 128.12 -6.04 1.47e+00 4.63e-01 1.69e+01 angle pdb=" CA MET A1562 " pdb=" CB MET A1562 " pdb=" CG MET A1562 " ideal model delta sigma weight residual 114.10 121.32 -7.22 2.00e+00 2.50e-01 1.30e+01 angle pdb=" N ASP A3793 " pdb=" CA ASP A3793 " pdb=" CB ASP A3793 " ideal model delta sigma weight residual 113.65 108.93 4.72 1.47e+00 4.63e-01 1.03e+01 angle pdb=" N ILE A3844 " pdb=" CA ILE A3844 " pdb=" C ILE A3844 " ideal model delta sigma weight residual 112.29 109.38 2.91 9.40e-01 1.13e+00 9.59e+00 ... (remaining 29389 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.70: 12186 25.70 - 51.40: 633 51.40 - 77.10: 43 77.10 - 102.80: 15 102.80 - 128.50: 2 Dihedral angle restraints: 12879 sinusoidal: 4891 harmonic: 7988 Sorted by residual: dihedral pdb=" C2' ADP A4102 " pdb=" C1' ADP A4102 " pdb=" N9 ADP A4102 " pdb=" C4 ADP A4102 " ideal model delta sinusoidal sigma weight residual 91.55 -139.95 -128.50 1 2.00e+01 2.50e-03 3.89e+01 dihedral pdb=" O2A ADP A4104 " pdb=" O3A ADP A4104 " pdb=" PA ADP A4104 " pdb=" PB ADP A4104 " ideal model delta sinusoidal sigma weight residual -60.00 63.98 -123.98 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" CA GLU A2956 " pdb=" C GLU A2956 " pdb=" N PRO A2957 " pdb=" CA PRO A2957 " ideal model delta harmonic sigma weight residual -180.00 -156.28 -23.72 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 12876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2427 0.044 - 0.088: 721 0.088 - 0.132: 232 0.132 - 0.175: 27 0.175 - 0.219: 3 Chirality restraints: 3410 Sorted by residual: chirality pdb=" CB ILE A3329 " pdb=" CA ILE A3329 " pdb=" CG1 ILE A3329 " pdb=" CG2 ILE A3329 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ASN C 266 " pdb=" N ASN C 266 " pdb=" C ASN C 266 " pdb=" CB ASN C 266 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" CB VAL A3444 " pdb=" CA VAL A3444 " pdb=" CG1 VAL A3444 " pdb=" CG2 VAL A3444 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.04e-01 ... (remaining 3407 not shown) Planarity restraints: 3691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A2404 " 0.014 2.00e-02 2.50e+03 3.25e-02 1.85e+01 pdb=" CG PHE A2404 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE A2404 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 PHE A2404 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 PHE A2404 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A2404 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A2404 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A3313 " -0.017 2.00e-02 2.50e+03 2.28e-02 9.09e+00 pdb=" CG PHE A3313 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE A3313 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A3313 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A3313 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A3313 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A3313 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 294 " 0.045 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO C 295 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 295 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 295 " 0.037 5.00e-02 4.00e+02 ... (remaining 3688 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 380 2.69 - 3.24: 19678 3.24 - 3.79: 33995 3.79 - 4.35: 41863 4.35 - 4.90: 70134 Nonbonded interactions: 166050 Sorted by model distance: nonbonded pdb=" O2B ADP A4104 " pdb="MG MG A4105 " model vdw 2.135 2.170 nonbonded pdb=" O3B ADP A4104 " pdb="MG MG A4105 " model vdw 2.144 2.170 nonbonded pdb=" NZ LYS A2424 " pdb="MG MG A4105 " model vdw 2.196 2.250 nonbonded pdb=" OG SER C 160 " pdb=" O THR C 202 " model vdw 2.270 3.040 nonbonded pdb=" O TYR A3683 " pdb=" OG SER A3687 " model vdw 2.277 3.040 ... (remaining 166045 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 ========== 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: 2.980 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: 0.260 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.020 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 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 : 0.003 0.054 21648 Z= 0.150 Angle : 0.702 9.766 29394 Z= 0.353 Chirality : 0.046 0.219 3410 Planarity : 0.005 0.068 3691 Dihedral : 14.813 128.501 7677 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.15), residues: 2681 helix: 0.38 (0.13), residues: 1372 sheet: -0.01 (0.28), residues: 380 loop : -1.73 (0.18), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A3365 TYR 0.021 0.001 TYR A3330 PHE 0.068 0.002 PHE A2404 TRP 0.035 0.001 TRP C 262 HIS 0.005 0.001 HIS A2383 Details of bonding type rmsd covalent geometry : bond 0.00314 (21648) covalent geometry : angle 0.70172 (29394) hydrogen bonds : bond 0.13880 ( 1133) hydrogen bonds : angle 6.13770 ( 3327) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1655 MET cc_start: 0.7998 (tpt) cc_final: 0.7581 (tpp) REVERT: A 1867 GLN cc_start: 0.8377 (pp30) cc_final: 0.8071 (pp30) REVERT: A 1868 ILE cc_start: 0.8152 (pt) cc_final: 0.7694 (pt) REVERT: A 2173 ASN cc_start: 0.6876 (m-40) cc_final: 0.6457 (t0) REVERT: A 2508 GLN cc_start: 0.8665 (tt0) cc_final: 0.8168 (tp40) REVERT: A 2510 MET cc_start: 0.7077 (ptm) cc_final: 0.6866 (ptp) REVERT: A 2655 ILE cc_start: 0.9231 (tp) cc_final: 0.8763 (tp) REVERT: A 3491 ASP cc_start: 0.7474 (t0) cc_final: 0.7242 (t70) REVERT: A 4090 GLN cc_start: 0.7546 (pp30) cc_final: 0.6948 (pp30) REVERT: C 204 MET cc_start: 0.8446 (mtt) cc_final: 0.8211 (mtt) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.1415 time to fit residues: 68.9780 Evaluate side-chains 214 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1751 GLN A1870 ASN A2931 ASN A3948 HIS C 263 GLN C 269 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.148012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.121522 restraints weight = 38640.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.122653 restraints weight = 25826.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.123733 restraints weight = 21041.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.124706 restraints weight = 17555.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.124758 restraints weight = 16221.070| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 21648 Z= 0.198 Angle : 0.617 12.795 29394 Z= 0.314 Chirality : 0.043 0.207 3410 Planarity : 0.004 0.057 3691 Dihedral : 6.245 125.768 2954 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.76 % Allowed : 9.96 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.16), residues: 2681 helix: 1.36 (0.14), residues: 1377 sheet: -0.28 (0.28), residues: 373 loop : -1.56 (0.18), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A2044 TYR 0.029 0.002 TYR A3746 PHE 0.019 0.002 PHE A2346 TRP 0.017 0.001 TRP A2084 HIS 0.006 0.001 HIS A2228 Details of bonding type rmsd covalent geometry : bond 0.00469 (21648) covalent geometry : angle 0.61740 (29394) hydrogen bonds : bond 0.04068 ( 1133) hydrogen bonds : angle 4.57833 ( 3327) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1539 PHE cc_start: 0.6371 (m-80) cc_final: 0.6164 (m-10) REVERT: A 1867 GLN cc_start: 0.8421 (pp30) cc_final: 0.8033 (pp30) REVERT: A 2173 ASN cc_start: 0.7171 (m-40) cc_final: 0.6715 (t0) REVERT: A 2222 ILE cc_start: 0.8152 (mm) cc_final: 0.7518 (mm) REVERT: A 2417 CYS cc_start: 0.7875 (t) cc_final: 0.7553 (t) REVERT: A 2655 ILE cc_start: 0.9060 (tp) cc_final: 0.8577 (tp) REVERT: A 3313 PHE cc_start: 0.6348 (OUTLIER) cc_final: 0.5971 (t80) REVERT: A 4090 GLN cc_start: 0.7563 (pp30) cc_final: 0.6940 (tm-30) REVERT: C 155 GLU cc_start: 0.7998 (pm20) cc_final: 0.7437 (pm20) REVERT: C 162 LYS cc_start: 0.7680 (mmtt) cc_final: 0.7088 (mmmt) REVERT: C 266 ASN cc_start: 0.6854 (OUTLIER) cc_final: 0.6328 (p0) outliers start: 39 outliers final: 26 residues processed: 250 average time/residue: 0.1143 time to fit residues: 49.0030 Evaluate side-chains 227 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1718 CYS Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1960 CYS Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2105 ASP Chi-restraints excluded: chain A residue 2134 LEU Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2446 SER Chi-restraints excluded: chain A residue 2482 LEU Chi-restraints excluded: chain A residue 2483 VAL Chi-restraints excluded: chain A residue 2547 SER Chi-restraints excluded: chain A residue 2908 LEU Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 3019 VAL Chi-restraints excluded: chain A residue 3313 PHE Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3652 CYS Chi-restraints excluded: chain A residue 3943 THR Chi-restraints excluded: chain A residue 4011 CYS Chi-restraints excluded: chain A residue 4049 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 263 GLN Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 269 HIS Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 452 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 152 optimal weight: 0.6980 chunk 241 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 245 optimal weight: 3.9990 chunk 165 optimal weight: 0.0980 chunk 124 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1878 HIS A2508 GLN A3843 ASN C 263 GLN C 269 HIS C 367 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.151063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.125335 restraints weight = 38541.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.126565 restraints weight = 25899.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.127661 restraints weight = 20630.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.128360 restraints weight = 17258.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.128521 restraints weight = 16472.067| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21648 Z= 0.111 Angle : 0.521 8.664 29394 Z= 0.262 Chirality : 0.040 0.145 3410 Planarity : 0.003 0.062 3691 Dihedral : 6.063 126.442 2954 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.76 % Allowed : 13.47 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.16), residues: 2681 helix: 1.82 (0.14), residues: 1370 sheet: -0.17 (0.29), residues: 357 loop : -1.40 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2149 TYR 0.028 0.001 TYR A3746 PHE 0.015 0.001 PHE A2972 TRP 0.022 0.001 TRP C 299 HIS 0.007 0.001 HIS A1878 Details of bonding type rmsd covalent geometry : bond 0.00249 (21648) covalent geometry : angle 0.52082 (29394) hydrogen bonds : bond 0.03444 ( 1133) hydrogen bonds : angle 4.19496 ( 3327) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 224 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1655 MET cc_start: 0.8098 (tpt) cc_final: 0.7847 (tpp) REVERT: A 1867 GLN cc_start: 0.8446 (pp30) cc_final: 0.8032 (pp30) REVERT: A 2173 ASN cc_start: 0.7205 (m-40) cc_final: 0.6732 (t0) REVERT: A 2222 ILE cc_start: 0.8209 (mm) cc_final: 0.7604 (mm) REVERT: A 2572 GLU cc_start: 0.7574 (mm-30) cc_final: 0.6941 (mt-10) REVERT: A 2655 ILE cc_start: 0.9194 (tp) cc_final: 0.8683 (tp) REVERT: A 4090 GLN cc_start: 0.7600 (pp30) cc_final: 0.6953 (pp30) REVERT: C 263 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6785 (pm20) REVERT: C 266 ASN cc_start: 0.6730 (OUTLIER) cc_final: 0.6151 (p0) outliers start: 39 outliers final: 21 residues processed: 252 average time/residue: 0.1170 time to fit residues: 50.6416 Evaluate side-chains 229 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1478 PHE Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1636 ILE Chi-restraints excluded: chain A residue 1960 CYS Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2105 ASP Chi-restraints excluded: chain A residue 2134 LEU Chi-restraints excluded: chain A residue 2446 SER Chi-restraints excluded: chain A residue 2482 LEU Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3652 CYS Chi-restraints excluded: chain A residue 3672 ASP Chi-restraints excluded: chain A residue 4049 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 263 GLN Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 269 HIS Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 452 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 261 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 156 optimal weight: 0.7980 chunk 146 optimal weight: 0.4980 chunk 219 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 154 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1878 HIS ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.150438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.124610 restraints weight = 38291.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.125890 restraints weight = 25094.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.126970 restraints weight = 20827.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.127985 restraints weight = 16812.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.128009 restraints weight = 15363.374| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21648 Z= 0.119 Angle : 0.523 7.525 29394 Z= 0.262 Chirality : 0.041 0.172 3410 Planarity : 0.003 0.055 3691 Dihedral : 5.976 127.670 2954 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.03 % Allowed : 14.87 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.17), residues: 2681 helix: 1.97 (0.14), residues: 1372 sheet: -0.25 (0.29), residues: 358 loop : -1.32 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2149 TYR 0.028 0.001 TYR A3746 PHE 0.016 0.001 PHE A1850 TRP 0.035 0.001 TRP C 299 HIS 0.010 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00274 (21648) covalent geometry : angle 0.52276 (29394) hydrogen bonds : bond 0.03327 ( 1133) hydrogen bonds : angle 4.02537 ( 3327) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1655 MET cc_start: 0.8094 (tpt) cc_final: 0.7824 (tpp) REVERT: A 1867 GLN cc_start: 0.8490 (pp30) cc_final: 0.8067 (pp30) REVERT: A 2173 ASN cc_start: 0.7272 (m-40) cc_final: 0.6767 (t0) REVERT: A 2222 ILE cc_start: 0.8189 (mm) cc_final: 0.7645 (mm) REVERT: A 2417 CYS cc_start: 0.7943 (t) cc_final: 0.7620 (t) REVERT: A 2572 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7023 (mt-10) REVERT: A 2655 ILE cc_start: 0.9194 (tp) cc_final: 0.8633 (tp) REVERT: A 3478 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8022 (p) REVERT: A 4090 GLN cc_start: 0.7620 (pp30) cc_final: 0.6973 (pp30) REVERT: C 266 ASN cc_start: 0.6696 (OUTLIER) cc_final: 0.6097 (p0) outliers start: 45 outliers final: 30 residues processed: 248 average time/residue: 0.1268 time to fit residues: 53.8512 Evaluate side-chains 242 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1478 PHE Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1636 ILE Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1718 CYS Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1878 HIS Chi-restraints excluded: chain A residue 1960 CYS Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2105 ASP Chi-restraints excluded: chain A residue 2134 LEU Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2446 SER Chi-restraints excluded: chain A residue 2482 LEU Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2749 LEU Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3652 CYS Chi-restraints excluded: chain A residue 3702 MET Chi-restraints excluded: chain A residue 3943 THR Chi-restraints excluded: chain A residue 4049 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 269 HIS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 452 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 241 optimal weight: 0.7980 chunk 193 optimal weight: 2.9990 chunk 139 optimal weight: 0.0770 chunk 109 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 112 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 229 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1878 HIS ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.150729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.124902 restraints weight = 38100.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.126175 restraints weight = 25426.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.127201 restraints weight = 20752.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.127999 restraints weight = 17165.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.128102 restraints weight = 15981.444| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21648 Z= 0.112 Angle : 0.514 8.765 29394 Z= 0.257 Chirality : 0.040 0.159 3410 Planarity : 0.003 0.052 3691 Dihedral : 5.913 128.124 2954 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.34 % Allowed : 15.14 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.17), residues: 2681 helix: 2.08 (0.14), residues: 1373 sheet: -0.24 (0.29), residues: 356 loop : -1.26 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2149 TYR 0.028 0.001 TYR A3746 PHE 0.013 0.001 PHE A2404 TRP 0.018 0.001 TRP A2084 HIS 0.008 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00255 (21648) covalent geometry : angle 0.51383 (29394) hydrogen bonds : bond 0.03214 ( 1133) hydrogen bonds : angle 3.92163 ( 3327) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 216 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1867 GLN cc_start: 0.8470 (pp30) cc_final: 0.8056 (pp30) REVERT: A 2173 ASN cc_start: 0.7244 (m-40) cc_final: 0.6748 (t0) REVERT: A 2417 CYS cc_start: 0.7898 (t) cc_final: 0.7584 (t) REVERT: A 2572 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7035 (mt-10) REVERT: A 2655 ILE cc_start: 0.9120 (tp) cc_final: 0.8591 (tp) REVERT: A 3478 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8067 (p) REVERT: A 4090 GLN cc_start: 0.7664 (pp30) cc_final: 0.7034 (pp30) REVERT: C 266 ASN cc_start: 0.6611 (OUTLIER) cc_final: 0.6119 (p0) REVERT: C 334 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8139 (p) outliers start: 52 outliers final: 37 residues processed: 249 average time/residue: 0.1200 time to fit residues: 51.9098 Evaluate side-chains 249 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 209 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1478 PHE Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1636 ILE Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1718 CYS Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1854 ASP Chi-restraints excluded: chain A residue 1878 HIS Chi-restraints excluded: chain A residue 1960 CYS Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2134 LEU Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2334 SER Chi-restraints excluded: chain A residue 2446 SER Chi-restraints excluded: chain A residue 2482 LEU Chi-restraints excluded: chain A residue 2625 LEU Chi-restraints excluded: chain A residue 2749 LEU Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2936 VAL Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3652 CYS Chi-restraints excluded: chain A residue 3687 SER Chi-restraints excluded: chain A residue 3702 MET Chi-restraints excluded: chain A residue 3943 THR Chi-restraints excluded: chain A residue 4011 CYS Chi-restraints excluded: chain A residue 4049 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 269 HIS Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 452 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 108 optimal weight: 0.7980 chunk 209 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 249 optimal weight: 4.9990 chunk 196 optimal weight: 20.0000 chunk 230 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 35 optimal weight: 0.0370 chunk 63 optimal weight: 0.0050 chunk 25 optimal weight: 0.8980 overall best weight: 0.4872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1878 HIS A2508 GLN ** A3948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.151220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.125444 restraints weight = 38217.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.126595 restraints weight = 25791.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.127994 restraints weight = 21366.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.128831 restraints weight = 17361.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.128903 restraints weight = 14988.164| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 21648 Z= 0.104 Angle : 0.509 10.640 29394 Z= 0.254 Chirality : 0.040 0.150 3410 Planarity : 0.003 0.049 3691 Dihedral : 5.865 127.944 2954 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.34 % Allowed : 16.13 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.17), residues: 2681 helix: 2.14 (0.14), residues: 1378 sheet: -0.21 (0.29), residues: 355 loop : -1.22 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2149 TYR 0.027 0.001 TYR A3746 PHE 0.018 0.001 PHE A3638 TRP 0.018 0.001 TRP A2084 HIS 0.007 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00236 (21648) covalent geometry : angle 0.50907 (29394) hydrogen bonds : bond 0.03137 ( 1133) hydrogen bonds : angle 3.86015 ( 3327) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 217 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1867 GLN cc_start: 0.8458 (pp30) cc_final: 0.8052 (pp30) REVERT: A 2173 ASN cc_start: 0.7282 (m-40) cc_final: 0.6749 (t0) REVERT: A 2222 ILE cc_start: 0.8209 (mm) cc_final: 0.7676 (mm) REVERT: A 2417 CYS cc_start: 0.7746 (t) cc_final: 0.7322 (t) REVERT: A 2459 HIS cc_start: 0.7272 (m-70) cc_final: 0.6841 (m-70) REVERT: A 2572 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7108 (mt-10) REVERT: A 2655 ILE cc_start: 0.9116 (tp) cc_final: 0.8662 (tp) REVERT: A 3478 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8079 (p) REVERT: A 3760 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8327 (tp) REVERT: A 4090 GLN cc_start: 0.7653 (pp30) cc_final: 0.7025 (pp30) REVERT: C 266 ASN cc_start: 0.6649 (OUTLIER) cc_final: 0.6211 (p0) REVERT: C 334 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8128 (p) outliers start: 52 outliers final: 38 residues processed: 251 average time/residue: 0.1238 time to fit residues: 53.8490 Evaluate side-chains 249 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 207 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1478 PHE Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1636 ILE Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1718 CYS Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1854 ASP Chi-restraints excluded: chain A residue 1878 HIS Chi-restraints excluded: chain A residue 1960 CYS Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2134 LEU Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2334 SER Chi-restraints excluded: chain A residue 2446 SER Chi-restraints excluded: chain A residue 2482 LEU Chi-restraints excluded: chain A residue 2749 LEU Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2936 VAL Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3652 CYS Chi-restraints excluded: chain A residue 3687 SER Chi-restraints excluded: chain A residue 3702 MET Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3760 LEU Chi-restraints excluded: chain A residue 3848 LEU Chi-restraints excluded: chain A residue 4011 CYS Chi-restraints excluded: chain A residue 4049 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 269 HIS Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 452 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 130 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 114 optimal weight: 0.2980 chunk 71 optimal weight: 9.9990 chunk 256 optimal weight: 2.9990 chunk 48 optimal weight: 0.0270 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1878 HIS A3843 ASN A3845 GLN ** A3948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.150608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.124811 restraints weight = 38336.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.126036 restraints weight = 25475.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.127231 restraints weight = 20872.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.128178 restraints weight = 16892.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.128194 restraints weight = 15789.025| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21648 Z= 0.113 Angle : 0.515 8.407 29394 Z= 0.257 Chirality : 0.040 0.151 3410 Planarity : 0.003 0.049 3691 Dihedral : 5.837 127.056 2954 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.66 % Allowed : 16.49 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.17), residues: 2681 helix: 2.16 (0.14), residues: 1379 sheet: -0.29 (0.28), residues: 364 loop : -1.16 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2149 TYR 0.028 0.001 TYR A3746 PHE 0.013 0.001 PHE C 243 TRP 0.018 0.001 TRP A2084 HIS 0.006 0.001 HIS A2459 Details of bonding type rmsd covalent geometry : bond 0.00262 (21648) covalent geometry : angle 0.51538 (29394) hydrogen bonds : bond 0.03151 ( 1133) hydrogen bonds : angle 3.80695 ( 3327) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 219 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1867 GLN cc_start: 0.8468 (pp30) cc_final: 0.8061 (pp30) REVERT: A 2173 ASN cc_start: 0.7303 (m-40) cc_final: 0.6773 (t0) REVERT: A 2459 HIS cc_start: 0.7549 (m-70) cc_final: 0.7114 (m-70) REVERT: A 2508 GLN cc_start: 0.8635 (tt0) cc_final: 0.8231 (tp40) REVERT: A 2572 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7135 (mt-10) REVERT: A 2655 ILE cc_start: 0.9116 (tp) cc_final: 0.8664 (tp) REVERT: A 2949 ASN cc_start: 0.7472 (t0) cc_final: 0.7188 (t0) REVERT: A 3478 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8106 (p) REVERT: A 3760 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8376 (tp) REVERT: A 4090 GLN cc_start: 0.7656 (pp30) cc_final: 0.7028 (pp30) REVERT: C 266 ASN cc_start: 0.6668 (OUTLIER) cc_final: 0.6144 (p0) REVERT: C 334 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8232 (p) outliers start: 59 outliers final: 47 residues processed: 256 average time/residue: 0.1268 time to fit residues: 55.8999 Evaluate side-chains 263 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 212 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1478 PHE Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1636 ILE Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1718 CYS Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1854 ASP Chi-restraints excluded: chain A residue 1878 HIS Chi-restraints excluded: chain A residue 1956 LEU Chi-restraints excluded: chain A residue 1960 CYS Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2134 LEU Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2334 SER Chi-restraints excluded: chain A residue 2390 ILE Chi-restraints excluded: chain A residue 2446 SER Chi-restraints excluded: chain A residue 2482 LEU Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2749 LEU Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2936 VAL Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 2958 ILE Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3652 CYS Chi-restraints excluded: chain A residue 3687 SER Chi-restraints excluded: chain A residue 3702 MET Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3760 LEU Chi-restraints excluded: chain A residue 3848 LEU Chi-restraints excluded: chain A residue 3943 THR Chi-restraints excluded: chain A residue 4011 CYS Chi-restraints excluded: chain A residue 4049 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 269 HIS Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 452 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 189 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 187 optimal weight: 0.5980 chunk 142 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 chunk 139 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 167 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1878 HIS ** A3948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.150133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.124431 restraints weight = 38291.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.125584 restraints weight = 25467.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.126902 restraints weight = 20547.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.127844 restraints weight = 16654.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.127754 restraints weight = 15509.046| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21648 Z= 0.121 Angle : 0.535 11.614 29394 Z= 0.265 Chirality : 0.040 0.154 3410 Planarity : 0.003 0.048 3691 Dihedral : 5.835 126.287 2954 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.66 % Allowed : 17.08 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.17), residues: 2681 helix: 2.17 (0.14), residues: 1373 sheet: -0.35 (0.28), residues: 366 loop : -1.16 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2543 TYR 0.029 0.001 TYR A3746 PHE 0.038 0.001 PHE A3530 TRP 0.018 0.001 TRP A2084 HIS 0.008 0.001 HIS A1878 Details of bonding type rmsd covalent geometry : bond 0.00285 (21648) covalent geometry : angle 0.53512 (29394) hydrogen bonds : bond 0.03203 ( 1133) hydrogen bonds : angle 3.80966 ( 3327) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 213 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1867 GLN cc_start: 0.8465 (pp30) cc_final: 0.8061 (pp30) REVERT: A 2173 ASN cc_start: 0.7264 (m-40) cc_final: 0.6738 (t0) REVERT: A 2222 ILE cc_start: 0.8300 (mm) cc_final: 0.7758 (mm) REVERT: A 2459 HIS cc_start: 0.7532 (m-70) cc_final: 0.7075 (m-70) REVERT: A 2508 GLN cc_start: 0.8619 (tt0) cc_final: 0.8262 (tp40) REVERT: A 2572 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7168 (mt-10) REVERT: A 2655 ILE cc_start: 0.9103 (tp) cc_final: 0.8656 (tp) REVERT: A 3330 TYR cc_start: 0.7870 (OUTLIER) cc_final: 0.6891 (t80) REVERT: A 3478 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8136 (p) REVERT: A 4090 GLN cc_start: 0.7622 (pp30) cc_final: 0.7014 (pp30) REVERT: C 266 ASN cc_start: 0.6682 (OUTLIER) cc_final: 0.6237 (p0) REVERT: C 334 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8290 (p) outliers start: 59 outliers final: 44 residues processed: 254 average time/residue: 0.1259 time to fit residues: 55.1208 Evaluate side-chains 254 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 206 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1636 ILE Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1718 CYS Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1813 LEU Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1846 CYS Chi-restraints excluded: chain A residue 1854 ASP Chi-restraints excluded: chain A residue 1960 CYS Chi-restraints excluded: chain A residue 2134 LEU Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2334 SER Chi-restraints excluded: chain A residue 2390 ILE Chi-restraints excluded: chain A residue 2446 SER Chi-restraints excluded: chain A residue 2482 LEU Chi-restraints excluded: chain A residue 2618 SER Chi-restraints excluded: chain A residue 2749 LEU Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2936 VAL Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 2958 ILE Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3316 THR Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3652 CYS Chi-restraints excluded: chain A residue 3687 SER Chi-restraints excluded: chain A residue 3702 MET Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3848 LEU Chi-restraints excluded: chain A residue 3943 THR Chi-restraints excluded: chain A residue 4011 CYS Chi-restraints excluded: chain A residue 4049 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 452 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 196 optimal weight: 3.9990 chunk 97 optimal weight: 0.0980 chunk 184 optimal weight: 0.0670 chunk 87 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 156 optimal weight: 0.1980 chunk 217 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 259 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.151975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.126358 restraints weight = 38156.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.127473 restraints weight = 25441.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.128639 restraints weight = 21023.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.129628 restraints weight = 17330.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.129761 restraints weight = 15212.791| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21648 Z= 0.100 Angle : 0.529 11.348 29394 Z= 0.261 Chirality : 0.040 0.353 3410 Planarity : 0.003 0.048 3691 Dihedral : 5.754 126.023 2954 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.03 % Allowed : 18.07 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.17), residues: 2681 helix: 2.20 (0.14), residues: 1376 sheet: -0.34 (0.28), residues: 367 loop : -1.10 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2149 TYR 0.031 0.001 TYR A3746 PHE 0.034 0.001 PHE A3530 TRP 0.020 0.001 TRP A2084 HIS 0.006 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00224 (21648) covalent geometry : angle 0.52877 (29394) hydrogen bonds : bond 0.03040 ( 1133) hydrogen bonds : angle 3.73171 ( 3327) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 223 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1562 MET cc_start: 0.7888 (tmm) cc_final: 0.7610 (tmm) REVERT: A 1867 GLN cc_start: 0.8362 (pp30) cc_final: 0.7995 (pp30) REVERT: A 2173 ASN cc_start: 0.7402 (m-40) cc_final: 0.6918 (t0) REVERT: A 2222 ILE cc_start: 0.8213 (mm) cc_final: 0.7704 (mm) REVERT: A 2459 HIS cc_start: 0.7593 (m-70) cc_final: 0.7166 (m-70) REVERT: A 2508 GLN cc_start: 0.8533 (tt0) cc_final: 0.8292 (tp40) REVERT: A 2572 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7058 (mt-10) REVERT: A 2655 ILE cc_start: 0.9100 (tp) cc_final: 0.8640 (tp) REVERT: A 3330 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.7081 (t80) REVERT: A 3478 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8114 (p) REVERT: A 3843 ASN cc_start: 0.6690 (m110) cc_final: 0.6206 (p0) REVERT: A 4090 GLN cc_start: 0.7477 (pp30) cc_final: 0.6879 (pp30) REVERT: C 334 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8229 (p) outliers start: 45 outliers final: 36 residues processed: 252 average time/residue: 0.1291 time to fit residues: 55.5557 Evaluate side-chains 250 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1813 LEU Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1846 CYS Chi-restraints excluded: chain A residue 1854 ASP Chi-restraints excluded: chain A residue 1956 LEU Chi-restraints excluded: chain A residue 1960 CYS Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2134 LEU Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2334 SER Chi-restraints excluded: chain A residue 2390 ILE Chi-restraints excluded: chain A residue 2446 SER Chi-restraints excluded: chain A residue 2482 LEU Chi-restraints excluded: chain A residue 2749 LEU Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2936 VAL Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3525 ILE Chi-restraints excluded: chain A residue 3652 CYS Chi-restraints excluded: chain A residue 3687 SER Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3848 LEU Chi-restraints excluded: chain A residue 4049 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 452 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 11 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 175 optimal weight: 0.1980 chunk 16 optimal weight: 5.9990 chunk 239 optimal weight: 0.0570 chunk 114 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 1 optimal weight: 8.9990 chunk 146 optimal weight: 0.8980 chunk 262 optimal weight: 8.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1878 HIS ** A3948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.151712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.126028 restraints weight = 38291.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.127020 restraints weight = 26242.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.128530 restraints weight = 21625.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.129741 restraints weight = 16699.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.129700 restraints weight = 15337.349| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21648 Z= 0.108 Angle : 0.551 11.433 29394 Z= 0.271 Chirality : 0.041 0.342 3410 Planarity : 0.003 0.047 3691 Dihedral : 5.719 125.495 2954 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.16 % Allowed : 18.21 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.17), residues: 2681 helix: 2.19 (0.14), residues: 1377 sheet: -0.33 (0.28), residues: 367 loop : -1.08 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2149 TYR 0.030 0.001 TYR A3746 PHE 0.039 0.001 PHE A3530 TRP 0.019 0.001 TRP A2084 HIS 0.007 0.001 HIS C 347 Details of bonding type rmsd covalent geometry : bond 0.00251 (21648) covalent geometry : angle 0.55111 (29394) hydrogen bonds : bond 0.03107 ( 1133) hydrogen bonds : angle 3.75487 ( 3327) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 213 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1562 MET cc_start: 0.7882 (tmm) cc_final: 0.7620 (tmm) REVERT: A 1867 GLN cc_start: 0.8450 (pp30) cc_final: 0.8043 (pp30) REVERT: A 2173 ASN cc_start: 0.7460 (m-40) cc_final: 0.6918 (t0) REVERT: A 2222 ILE cc_start: 0.8246 (mm) cc_final: 0.7674 (mm) REVERT: A 2508 GLN cc_start: 0.8594 (tt0) cc_final: 0.8259 (tp40) REVERT: A 2572 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7140 (mt-10) REVERT: A 2655 ILE cc_start: 0.9043 (tp) cc_final: 0.8595 (tp) REVERT: A 3330 TYR cc_start: 0.7859 (OUTLIER) cc_final: 0.7030 (t80) REVERT: A 3478 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8138 (p) REVERT: A 3525 ILE cc_start: 0.6963 (OUTLIER) cc_final: 0.6626 (mt) REVERT: A 3843 ASN cc_start: 0.6832 (m110) cc_final: 0.6285 (p0) REVERT: A 4090 GLN cc_start: 0.7598 (pp30) cc_final: 0.6988 (pp30) REVERT: C 266 ASN cc_start: 0.6913 (OUTLIER) cc_final: 0.6502 (p0) REVERT: C 321 LEU cc_start: 0.8895 (tt) cc_final: 0.8528 (tt) REVERT: C 334 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8305 (p) outliers start: 48 outliers final: 40 residues processed: 245 average time/residue: 0.1250 time to fit residues: 52.6327 Evaluate side-chains 248 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 203 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1813 LEU Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1846 CYS Chi-restraints excluded: chain A residue 1854 ASP Chi-restraints excluded: chain A residue 1878 HIS Chi-restraints excluded: chain A residue 1956 LEU Chi-restraints excluded: chain A residue 1960 CYS Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2134 LEU Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2334 SER Chi-restraints excluded: chain A residue 2390 ILE Chi-restraints excluded: chain A residue 2446 SER Chi-restraints excluded: chain A residue 2482 LEU Chi-restraints excluded: chain A residue 2749 LEU Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2936 VAL Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 2958 ILE Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3371 VAL Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3525 ILE Chi-restraints excluded: chain A residue 3652 CYS Chi-restraints excluded: chain A residue 3687 SER Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3848 LEU Chi-restraints excluded: chain A residue 4049 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 452 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 79 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 252 optimal weight: 1.9990 chunk 254 optimal weight: 0.8980 chunk 246 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 59 optimal weight: 0.0050 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1878 HIS ** A3948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.151163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.125578 restraints weight = 38161.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.126777 restraints weight = 25377.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.127670 restraints weight = 21122.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.128675 restraints weight = 17904.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.128706 restraints weight = 15633.799| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21648 Z= 0.118 Angle : 0.560 13.155 29394 Z= 0.274 Chirality : 0.041 0.304 3410 Planarity : 0.003 0.048 3691 Dihedral : 5.720 125.036 2954 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.21 % Allowed : 18.48 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.17), residues: 2681 helix: 2.18 (0.14), residues: 1377 sheet: -0.35 (0.28), residues: 367 loop : -1.09 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2549 TYR 0.030 0.001 TYR A3746 PHE 0.026 0.001 PHE A3530 TRP 0.018 0.001 TRP A2084 HIS 0.006 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00278 (21648) covalent geometry : angle 0.55993 (29394) hydrogen bonds : bond 0.03136 ( 1133) hydrogen bonds : angle 3.75682 ( 3327) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3191.05 seconds wall clock time: 56 minutes 17.46 seconds (3377.46 seconds total)