Starting phenix.real_space_refine on Fri Jun 20 04:34:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dld_46974/06_2025/9dld_46974.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dld_46974/06_2025/9dld_46974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dld_46974/06_2025/9dld_46974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dld_46974/06_2025/9dld_46974.map" model { file = "/net/cci-nas-00/data/ceres_data/9dld_46974/06_2025/9dld_46974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dld_46974/06_2025/9dld_46974.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 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 3 5.21 5 S 101 5.16 5 C 14739 2.51 5 N 3905 2.21 5 O 4239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22996 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 18072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2323, 18072 Classifications: {'peptide': 2323} Incomplete info: {'truncation_to_alanine': 198} Link IDs: {'PTRANS': 65, 'TRANS': 2257} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 715 Unresolved non-hydrogen angles: 881 Unresolved non-hydrogen dihedrals: 584 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 15, 'TRP:plan': 2, 'ASP:plan': 24, 'PHE:plan': 6, 'GLU:plan': 42, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 432 Chain: "C" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2771 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 16, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 2, 'HIS:plan': 1, 'ARG%COO:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "B" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2038 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 194} Link IDs: {'PTRANS': 11, 'TRANS': 319} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 692 Unresolved non-hydrogen angles: 890 Unresolved non-hydrogen dihedrals: 587 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 19, 'TYR:plan': 4, 'ASN:plan1': 11, 'TRP:plan': 6, 'HIS:plan': 9, 'PHE:plan': 8, 'GLU:plan': 6, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 378 Chain: "A" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 115 Unusual residues: {' MG': 3, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 13.74, per 1000 atoms: 0.60 Number of scatterers: 22996 At special positions: 0 Unit cell: (111.125, 150.241, 188.468, 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 101 16.00 P 9 15.00 Mg 3 11.99 O 4239 8.00 N 3905 7.00 C 14739 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: 5.53 Conformation dependent library (CDL) restraints added in 2.8 seconds 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5722 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 30 sheets defined 49.4% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.36 Creating SS restraints... Processing helix chain 'A' and resid 1443 through 1461 Processing helix chain 'A' and resid 1471 through 1488 Processing helix chain 'A' and resid 1512 through 1523 removed outlier: 3.610A pdb=" N LEU A1516 " --> pdb=" O THR A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1534 removed outlier: 3.738A pdb=" N PHE A1534 " --> pdb=" O GLN A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1539 Processing helix chain 'A' and resid 1541 through 1551 Processing helix chain 'A' and resid 1603 through 1632 removed outlier: 3.682A pdb=" N TRP A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1640 removed outlier: 4.081A pdb=" N VAL A1639 " --> pdb=" O ASP A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1665 Processing helix chain 'A' and resid 1669 through 1688 Processing helix chain 'A' and resid 1691 through 1717 removed outlier: 3.910A pdb=" N GLU A1704 " --> pdb=" O ALA A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1731 removed outlier: 3.569A pdb=" N ALA A1724 " --> pdb=" O THR A1720 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1788 removed outlier: 3.975A pdb=" N GLN A1788 " --> pdb=" O ASP A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1813 Processing helix chain 'A' and resid 1827 through 1842 Processing helix chain 'A' and resid 1854 through 1874 Processing helix chain 'A' and resid 1909 through 1914 Processing helix chain 'A' and resid 1925 through 1938 Processing helix chain 'A' and resid 1942 through 1960 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: 3.564A pdb=" N VAL A1994 " --> pdb=" O GLY A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 2004 through 2006 No H-bonds generated for 'chain 'A' and resid 2004 through 2006' Processing helix chain 'A' and resid 2007 through 2022 Processing helix chain 'A' and resid 2031 through 2046 Processing helix chain 'A' and resid 2050 through 2067 removed outlier: 4.021A pdb=" N THR A2066 " --> pdb=" O TYR A2062 " (cutoff:3.500A) Processing helix chain 'A' and resid 2079 through 2096 Processing helix chain 'A' and resid 2110 through 2115 Processing helix chain 'A' and resid 2128 through 2140 Processing helix chain 'A' and resid 2144 through 2146 No H-bonds generated for 'chain 'A' and resid 2144 through 2146' Processing helix chain 'A' and resid 2159 through 2164 Processing helix chain 'A' and resid 2166 through 2171 Processing helix chain 'A' and resid 2203 through 2210 Processing helix chain 'A' and resid 2221 through 2236 Processing helix chain 'A' and resid 2246 through 2257 Processing helix chain 'A' and resid 2258 through 2271 removed outlier: 3.725A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP A2271 " --> pdb=" O THR A2267 " (cutoff:3.500A) Processing helix chain 'A' and resid 2279 through 2298 removed outlier: 4.413A pdb=" N GLU A2285 " --> pdb=" O PHE A2281 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N THR A2286 " --> pdb=" O ASN A2282 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN A2289 " --> pdb=" O GLU A2285 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N HIS A2293 " --> pdb=" O GLN A2289 " (cutoff:3.500A) Processing helix chain 'A' and resid 2306 through 2327 Processing helix chain 'A' and resid 2331 through 2346 Processing helix chain 'A' and resid 2372 through 2375 removed outlier: 3.830A pdb=" N ILE A2375 " --> pdb=" O CYS A2372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2372 through 2375' Processing helix chain 'A' and resid 2381 through 2387 removed outlier: 3.676A pdb=" N GLU A2384 " --> pdb=" O GLU A2381 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A2385 " --> pdb=" O ALA A2382 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET A2386 " --> pdb=" O HIS A2383 " (cutoff:3.500A) Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2423 through 2434 Processing helix chain 'A' and resid 2450 through 2460 removed outlier: 3.884A pdb=" N ILE A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A2460 " --> pdb=" O SER A2456 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2512 removed outlier: 3.504A pdb=" N LEU A2504 " --> pdb=" O GLN A2500 " (cutoff:3.500A) Processing helix chain 'A' and resid 2547 through 2552 Processing helix chain 'A' and resid 2563 through 2580 Processing helix chain 'A' and resid 2582 through 2587 removed outlier: 5.433A 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: 3.982A pdb=" N LEU A2622 " --> pdb=" O SER A2618 " (cutoff:3.500A) Processing helix chain 'A' and resid 2640 through 2657 Processing helix chain 'A' and resid 2662 through 2681 Processing helix chain 'A' and resid 2708 through 2727 Processing helix chain 'A' and resid 2735 through 2750 Processing helix chain 'A' and resid 2766 through 2778 Processing helix chain 'A' and resid 2791 through 2809 Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 3.762A 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 2905 Processing helix chain 'A' and resid 2905 through 2910 Processing helix chain 'A' and resid 2921 through 2934 Processing helix chain 'A' and resid 2949 through 2953 removed outlier: 3.554A pdb=" N VAL A2953 " --> pdb=" O LYS A2950 " (cutoff:3.500A) Processing helix chain 'A' and resid 2960 through 2980 removed outlier: 3.809A pdb=" N ALA A2964 " --> pdb=" O THR A2960 " (cutoff:3.500A) Processing helix chain 'A' and resid 2989 through 3034 Processing helix chain 'A' and resid 3290 through 3319 removed outlier: 3.690A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A3319 " --> pdb=" O LYS A3315 " (cutoff:3.500A) Processing helix chain 'A' and resid 3320 through 3334 Processing helix chain 'A' and resid 3335 through 3337 No H-bonds generated for 'chain 'A' and resid 3335 through 3337' Processing helix chain 'A' and resid 3338 through 3356 Processing helix chain 'A' and resid 3365 through 3371 Processing helix chain 'A' and resid 3372 through 3383 removed outlier: 3.513A pdb=" N GLY A3383 " --> pdb=" O TRP A3379 " (cutoff:3.500A) Processing helix chain 'A' and resid 3387 through 3399 Processing helix chain 'A' and resid 3413 through 3423 removed outlier: 3.500A pdb=" N VAL A3417 " --> pdb=" O HIS A3413 " (cutoff:3.500A) Processing helix chain 'A' and resid 3435 through 3447 Processing helix chain 'A' and resid 3454 through 3458 removed outlier: 3.670A 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 3467 removed outlier: 3.525A pdb=" N ILE A3466 " --> pdb=" O ILE A3462 " (cutoff:3.500A) Processing helix chain 'A' and resid 3506 through 3511 Processing helix chain 'A' and resid 3521 through 3538 Processing helix chain 'A' and resid 3538 through 3572 removed outlier: 4.150A pdb=" N GLN A3542 " --> pdb=" O ASN A3538 " (cutoff:3.500A) Processing helix chain 'A' and resid 3583 through 3605 Processing helix chain 'A' and resid 3607 through 3618 removed outlier: 3.674A pdb=" N PHE A3611 " --> pdb=" O PHE A3607 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A3612 " --> pdb=" O PHE A3608 " (cutoff:3.500A) Processing helix chain 'A' and resid 3618 through 3639 removed outlier: 3.662A pdb=" N GLY A3622 " --> pdb=" O TYR A3618 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A3638 " --> pdb=" O LYS A3634 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS A3639 " --> pdb=" O PHE A3635 " (cutoff:3.500A) Processing helix chain 'A' and resid 3640 through 3643 removed outlier: 4.064A pdb=" N GLY A3643 " --> pdb=" O TRP A3640 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3640 through 3643' Processing helix chain 'A' and resid 3645 through 3659 removed outlier: 3.603A pdb=" N VAL A3656 " --> pdb=" O CYS A3652 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) Processing helix chain 'A' and resid 3671 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 Processing helix chain 'A' and resid 3755 through 3767 removed outlier: 4.539A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.628A 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: 4.098A pdb=" N ILE A3834 " --> pdb=" O SER A3830 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3846 removed outlier: 4.151A pdb=" N MET A3846 " --> pdb=" O ASN A3843 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3843 through 3846' Processing helix chain 'A' and resid 3847 through 3854 Processing helix chain 'A' and resid 3854 through 3859 Processing helix chain 'A' and resid 3885 through 3892 Processing helix chain 'A' and resid 3903 through 3912 Processing helix chain 'A' and resid 3923 through 3944 removed outlier: 3.829A pdb=" N ARG A3944 " --> pdb=" O THR A3940 " (cutoff:3.500A) Processing helix chain 'A' and resid 3957 through 3974 removed outlier: 3.813A 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: 3.673A pdb=" N LEU A4004 " --> pdb=" O GLU A4000 " (cutoff:3.500A) Processing helix chain 'A' and resid 4037 through 4052 removed outlier: 3.602A pdb=" N THR A4052 " --> pdb=" O ILE A4048 " (cutoff:3.500A) Processing helix chain 'A' and resid 4066 through 4090 removed outlier: 3.520A pdb=" N ILE A4070 " --> pdb=" O PRO A4066 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'B' and resid 362 through 369 Processing sheet with id=AA1, first strand: chain 'A' and resid 1569 through 1575 removed outlier: 6.230A pdb=" N PHE A1575 " --> pdb=" O ILE A1579 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ILE A1579 " --> pdb=" O PHE A1575 " (cutoff:3.500A) removed outlier: 10.064A pdb=" N SER A1578 " --> pdb=" O GLU A1594 " (cutoff:3.500A) removed outlier: 10.932A pdb=" N GLU A1594 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N THR A1580 " --> pdb=" O LEU A1592 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1733 through 1736 Processing sheet with id=AA3, first strand: chain 'A' and resid 1817 through 1821 removed outlier: 6.206A pdb=" N GLY A1845 " --> pdb=" O PHE A1895 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N THR A1897 " --> pdb=" O GLY A1845 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N PHE A1847 " --> pdb=" O THR A1897 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A1917 " --> pdb=" O GLY A1791 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1878 through 1881 Processing sheet with id=AA5, first strand: chain 'A' and resid 2098 through 2103 removed outlier: 6.215A pdb=" N ALA A2098 " --> pdb=" O ARG A2149 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N TRP A2151 " --> pdb=" O ALA A2098 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL A2100 " --> pdb=" O TRP A2151 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL A2153 " --> pdb=" O VAL A2100 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TYR A2102 " --> pdb=" O VAL A2153 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ARG A2191 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE A2150 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU A2193 " --> pdb=" O ILE A2150 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A2152 " --> pdb=" O LEU A2193 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N GLU A2195 " --> pdb=" O VAL A2152 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE A2154 " --> pdb=" O GLU A2195 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A2070 " --> pdb=" O PHE A2194 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N THR A2196 " --> pdb=" O LEU A2070 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU A2072 " --> pdb=" O THR A2196 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE A2071 " --> pdb=" O LEU A2213 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N PHE A2215 " --> pdb=" O ILE A2071 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL A2073 " --> pdb=" O PHE A2215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 2116 through 2117 removed outlier: 3.507A pdb=" N SER A2117 " --> pdb=" O ARG A2126 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A2126 " --> pdb=" O SER A2117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 2175 through 2177 Processing sheet with id=AA8, first strand: chain 'A' and resid 2357 through 2361 Processing sheet with id=AA9, first strand: chain 'A' and resid 2438 through 2444 removed outlier: 6.210A pdb=" N ASP A2439 " --> pdb=" O VAL A2483 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE A2485 " --> pdb=" O ASP A2439 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL A2441 " --> pdb=" O PHE A2485 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ASP A2487 " --> pdb=" O VAL A2441 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE A2443 " --> pdb=" O ASP A2487 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A2414 " --> pdb=" O GLY A2533 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N CYS A2535 " --> pdb=" O ILE A2414 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU A2416 " --> pdb=" O CYS A2535 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLY A2413 " --> pdb=" O ALA A2555 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU A2557 " --> pdb=" O GLY A2413 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE A2415 " --> pdb=" O LEU A2557 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2462 through 2465 Processing sheet with id=AB2, first strand: chain 'A' and resid 2696 through 2697 removed outlier: 3.547A pdb=" N LYS A2705 " --> pdb=" O SER A2697 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2780 through 2782 removed outlier: 6.365A pdb=" N THR A2813 " --> pdb=" O HIS A2886 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL A2888 " --> pdb=" O THR A2813 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU A2815 " --> pdb=" O VAL A2888 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR A2890 " --> pdb=" O LEU A2815 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE A2817 " --> pdb=" O THR A2890 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N MET A2757 " --> pdb=" O ASN A2915 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N MET A2917 " --> pdb=" O MET A2757 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE A2759 " --> pdb=" O MET A2917 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3426 through 3430 removed outlier: 6.350A pdb=" N VAL A3450 " --> pdb=" O PHE A3495 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N HIS A3497 " --> pdb=" O VAL A3450 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE A3452 " --> pdb=" O HIS A3497 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE A3406 " --> pdb=" O VAL A3516 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3471 through 3473 Processing sheet with id=AB6, first strand: chain 'A' and resid 3811 through 3815 removed outlier: 6.208A pdb=" N LYS A3812 " --> pdb=" O LEU A3840 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N GLN A3842 " --> pdb=" O LYS A3812 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A3814 " --> pdb=" O GLN A3842 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE A3839 " --> pdb=" O PHE A3874 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR A3876 " --> pdb=" O ILE A3839 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A3841 " --> pdb=" O THR A3876 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N HIS A3878 " --> pdb=" O LEU A3841 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A3790 " --> pdb=" O CYS A3877 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 4020 through 4022 Processing sheet with id=AB8, first strand: chain 'C' and resid 150 through 153 removed outlier: 4.097A pdb=" N LYS C 488 " --> pdb=" O GLY C 484 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 158 through 163 removed outlier: 4.432A pdb=" N LYS C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 201 through 208 removed outlier: 3.540A pdb=" N SER C 203 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU C 220 " --> pdb=" O TRP C 236 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LYS C 235 " --> pdb=" O GLN C 245 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N GLN C 245 " --> pdb=" O LYS C 235 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL C 237 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N PHE C 243 " --> pdb=" O VAL C 237 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 256 through 263 removed outlier: 3.550A pdb=" N ALA C 258 " --> pdb=" O CYS C 273 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASP C 283 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N SER C 289 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 300 through 306 removed outlier: 6.876A pdb=" N GLY C 313 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE C 303 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE C 311 " --> pdb=" O ILE C 303 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL C 305 " --> pdb=" O TYR C 309 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TYR C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N HIS C 323 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLY C 329 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 340 through 345 removed outlier: 4.290A pdb=" N THR C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE C 382 " --> pdb=" O THR C 412 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N THR C 412 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE C 384 " --> pdb=" O VAL C 410 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 420 through 426 removed outlier: 3.691A pdb=" N ASP C 422 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 434 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASP C 443 " --> pdb=" O CYS C 449 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N CYS C 449 " --> pdb=" O ASP C 443 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 150 through 153 removed outlier: 3.553A pdb=" N CYS B 150 " --> pdb=" O VAL B 491 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 484 " --> pdb=" O LYS B 488 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS B 463 " --> pdb=" O GLY B 483 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 160 through 163 removed outlier: 4.090A pdb=" N SER B 160 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 192 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 201 through 208 removed outlier: 4.654A pdb=" N LEU B 220 " --> pdb=" O TRP B 236 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP B 236 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG B 247 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS B 235 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLN B 245 " --> pdb=" O LYS B 235 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 237 " --> pdb=" O PHE B 243 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N PHE B 243 " --> pdb=" O VAL B 237 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 256 through 263 removed outlier: 6.807A pdb=" N CYS B 273 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL B 259 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA B 271 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ILE B 261 " --> pdb=" O HIS B 269 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N HIS B 269 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 270 " --> pdb=" O TRP B 282 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 300 through 306 removed outlier: 3.992A pdb=" N TYR B 309 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B 321 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER B 331 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N HIS B 323 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY B 329 " --> pdb=" O HIS B 323 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 340 through 346 removed outlier: 4.834A pdb=" N TYR B 372 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS B 373 " --> pdb=" O TRP B 385 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER B 377 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 413 " --> pdb=" O ILE B 382 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 420 through 426 removed outlier: 3.651A pdb=" N ASP B 422 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR B 429 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 440 " --> pdb=" O SER B 432 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA B 434 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N SER B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N HIS B 451 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP B 443 " --> pdb=" O CYS B 449 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N CYS B 449 " --> pdb=" O ASP B 443 " (cutoff:3.500A) 1258 hydrogen bonds defined for protein. 3696 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.31 Time building geometry restraints manager: 6.54 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: 7369 1.34 - 1.46: 4477 1.46 - 1.58: 11466 1.58 - 1.70: 12 1.70 - 1.82: 154 Bond restraints: 23478 Sorted by residual: bond pdb=" CG1 ILE A1865 " pdb=" CD1 ILE A1865 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.37e+00 bond pdb=" CB ARG A1624 " pdb=" CG ARG A1624 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.06e+00 bond pdb=" CG LEU C 464 " pdb=" CD1 LEU C 464 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.85e+00 bond pdb=" CB GLN A3610 " pdb=" CG GLN A3610 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.69e+00 bond pdb=" C4 ADP A4102 " pdb=" C5 ADP A4102 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.55e+00 ... (remaining 23473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 31491 2.12 - 4.24: 354 4.24 - 6.36: 67 6.36 - 8.48: 10 8.48 - 10.59: 1 Bond angle restraints: 31923 Sorted by residual: angle pdb=" C ASP C 316 " pdb=" N THR C 317 " pdb=" CA THR C 317 " ideal model delta sigma weight residual 121.54 129.09 -7.55 1.91e+00 2.74e-01 1.56e+01 angle pdb=" CA ARG A1624 " pdb=" CB ARG A1624 " pdb=" CG ARG A1624 " ideal model delta sigma weight residual 114.10 121.25 -7.15 2.00e+00 2.50e-01 1.28e+01 angle pdb=" CB MET A2831 " pdb=" CG MET A2831 " pdb=" SD MET A2831 " ideal model delta sigma weight residual 112.70 123.29 -10.59 3.00e+00 1.11e-01 1.25e+01 angle pdb=" CB GLU A3820 " pdb=" CG GLU A3820 " pdb=" CD GLU A3820 " ideal model delta sigma weight residual 112.60 117.93 -5.33 1.70e+00 3.46e-01 9.84e+00 angle pdb=" CB ARG A2911 " pdb=" CG ARG A2911 " pdb=" CD ARG A2911 " ideal model delta sigma weight residual 111.30 118.40 -7.10 2.30e+00 1.89e-01 9.54e+00 ... (remaining 31918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.85: 13219 24.85 - 49.69: 649 49.69 - 74.54: 49 74.54 - 99.38: 8 99.38 - 124.23: 2 Dihedral angle restraints: 13927 sinusoidal: 5130 harmonic: 8797 Sorted by residual: dihedral pdb=" O2A ADP A4103 " pdb=" O3A ADP A4103 " pdb=" PA ADP A4103 " pdb=" PB ADP A4103 " ideal model delta sinusoidal sigma weight residual -60.00 64.23 -124.23 1 2.00e+01 2.50e-03 3.75e+01 dihedral pdb=" C2' ADP A4101 " pdb=" C1' ADP A4101 " pdb=" N9 ADP A4101 " pdb=" C4 ADP A4101 " ideal model delta sinusoidal sigma weight residual 91.55 -151.92 -116.54 1 2.00e+01 2.50e-03 3.47e+01 dihedral pdb=" CA CYS A2220 " pdb=" C CYS A2220 " pdb=" N SER A2221 " pdb=" CA SER A2221 " ideal model delta harmonic sigma weight residual 180.00 158.57 21.43 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 13924 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2603 0.042 - 0.083: 808 0.083 - 0.125: 253 0.125 - 0.166: 41 0.166 - 0.208: 5 Chirality restraints: 3710 Sorted by residual: chirality pdb=" CB ILE C 311 " pdb=" CA ILE C 311 " pdb=" CG1 ILE C 311 " pdb=" CG2 ILE C 311 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE A2822 " pdb=" CA ILE A2822 " pdb=" CG1 ILE A2822 " pdb=" CG2 ILE A2822 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.95e-01 chirality pdb=" CA TRP C 324 " pdb=" N TRP C 324 " pdb=" C TRP C 324 " pdb=" CB TRP C 324 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.52e-01 ... (remaining 3707 not shown) Planarity restraints: 4025 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A4024 " 0.038 5.00e-02 4.00e+02 5.80e-02 5.39e+00 pdb=" N PRO A4025 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A4025 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A4025 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A2618 " -0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO A2619 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A2619 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A2619 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A2491 " 0.035 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO A2492 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A2492 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A2492 " 0.029 5.00e-02 4.00e+02 ... (remaining 4022 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 168 2.55 - 3.14: 17090 3.14 - 3.73: 36174 3.73 - 4.31: 48518 4.31 - 4.90: 83714 Nonbonded interactions: 185664 Sorted by model distance: nonbonded pdb=" O2B ATP A4104 " pdb="MG MG A4107 " model vdw 1.967 2.170 nonbonded pdb=" O3B ADP A4103 " pdb="MG MG A4106 " model vdw 2.001 2.170 nonbonded pdb=" O2G ATP A4104 " pdb="MG MG A4107 " model vdw 2.021 2.170 nonbonded pdb=" O1B ADP A4102 " pdb="MG MG A4105 " model vdw 2.040 2.170 nonbonded pdb=" OE2 GLU A2195 " pdb="MG MG A4107 " model vdw 2.065 2.170 ... (remaining 185659 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 139 through 211 or (resid 217 and (name N or name CA or na \ me C or name O or name CB )) or resid 218 through 238 or (resid 239 through 240 \ and (name N or name CA or name C or name O or name CB )) or resid 241 through 24 \ 3 or (resid 244 and (name N or name CA or name C or name O or name CB )) or resi \ d 245 through 494)) selection = (chain 'C' and ((resid 139 through 143 and (name N or name CA or name C or name \ O or name CB )) or resid 144 or (resid 145 through 157 and (name N or name CA or \ name C or name O or name CB )) or resid 158 or (resid 159 through 160 and (name \ N or name CA or name C or name O or name CB )) or resid 161 or (resid 162 and ( \ name N or name CA or name C or name O or name CB )) or resid 163 through 173 or \ (resid 174 through 175 and (name N or name CA or name C or name O or name CB )) \ or resid 176 through 177 or (resid 178 and (name N or name CA or name C or name \ O or name CB )) or resid 179 through 182 or (resid 183 and (name N or name CA or \ name C or name O or name CB )) or resid 184 through 188 or (resid 189 and (name \ N or name CA or name C or name O or name CB )) or resid 190 through 198 or (res \ id 199 through 200 and (name N or name CA or name C or name O or name CB )) or r \ esid 201 through 202 or (resid 203 and (name N or name CA or name C or name O or \ name CB )) or resid 204 through 211 or resid 217 through 228 or (resid 229 and \ (name N or name CA or name C or name O or name CB )) or resid 230 or (resid 231 \ and (name N or name CA or name C or name O or name CB )) or resid 232 through 25 \ 2 or (resid 253 through 254 and (name N or name CA or name C or name O or name C \ B )) or resid 255 or (resid 256 through 258 and (name N or name CA or name C or \ name O or name CB )) or resid 259 or (resid 260 and (name N or name CA or name C \ or name O or name CB )) or resid 261 through 265 or (resid 266 through 267 and \ (name N or name CA or name C or name O or name CB )) or resid 268 through 269 or \ (resid 270 through 271 and (name N or name CA or name C or name O or name CB )) \ or resid 272 through 273 or (resid 274 through 281 and (name N or name CA or na \ me C or name O or name CB )) or resid 282 or (resid 283 and (name N or name CA o \ r name C or name O or name CB )) or resid 284 through 288 or (resid 289 through \ 294 and (name N or name CA or name C or name O or name CB )) or resid 295 or (re \ sid 296 through 299 and (name N or name CA or name C or name O or name CB )) or \ resid 300 or (resid 301 through 302 and (name N or name CA or name C or name O o \ r name CB )) or resid 303 through 304 or (resid 305 through 306 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 307 through 311 and (name N o \ r name CA or name C or name O or name CB )) or resid 312 through 313 or (resid 3 \ 14 through 326 and (name N or name CA or name C or name O or name CB )) or (resi \ d 327 through 332 and (name N or name CA or name C or name O or name CB )) or re \ sid 333 or (resid 334 and (name N or name CA or name C or name O or name CB )) o \ r resid 335 or (resid 336 through 343 and (name N or name CA or name C or name O \ or name CB )) or resid 344 through 345 or (resid 346 through 349 and (name N or \ name CA or name C or name O or name CB )) or (resid 356 through 367 and (name N \ or name CA or name C or name O or name CB )) or resid 368 through 369 or (resid \ 370 through 372 and (name N or name CA or name C or name O or name CB )) or res \ id 373 or (resid 374 through 382 and (name N or name CA or name C or name O or n \ ame CB )) or resid 383 or (resid 384 and (name N or name CA or name C or name O \ or name CB )) or resid 385 or (resid 386 through 387 and (name N or name CA or n \ ame C or name O or name CB )) or resid 388 or (resid 389 and (name N or name CA \ or name C or name O or name CB )) or (resid 405 through 414 and (name N or name \ CA or name C or name O or name CB )) or resid 415 or (resid 416 through 420 and \ (name N or name CA or name C or name O or name CB )) or resid 421 or (resid 422 \ and (name N or name CA or name C or name O or name CB )) or resid 423 through 42 \ 4 or (resid 425 through 426 and (name N or name CA or name C or name O or name C \ B )) or resid 427 or (resid 428 through 429 and (name N or name CA or name C or \ name O or name CB )) or resid 430 or (resid 431 and (name N or name CA or name C \ or name O or name CB )) or resid 432 through 434 or (resid 435 through 443 and \ (name N or name CA or name C or name O or name CB )) or resid 444 or (resid 445 \ through 446 and (name N or name CA or name C or name O or name CB )) or resid 44 \ 7 or (resid 448 through 458 and (name N or name CA or name C or name O or name C \ B )) or resid 459 or (resid 460 through 467 and (name N or name CA or name C or \ name O or name CB )) or resid 468 or (resid 469 through 476 and (name N or name \ CA or name C or name O or name CB )) or resid 477 through 479 or (resid 480 and \ (name N or name CA or name C or name O or name CB )) or resid 481 through 484 or \ (resid 485 through 490 and (name N or name CA or name C or name O or name CB )) \ or resid 491 through 492 or (resid 493 through 494 and (name N or name CA or na \ me C or name O or name CB )))) } 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 individual isotropic 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: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.990 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 57.850 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 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 0.060 23478 Z= 0.150 Angle : 0.598 10.594 31923 Z= 0.311 Chirality : 0.045 0.208 3710 Planarity : 0.004 0.058 4025 Dihedral : 14.160 124.229 8205 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.04 % Allowed : 0.51 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 2972 helix: 1.01 (0.13), residues: 1378 sheet: 0.38 (0.24), residues: 461 loop : -1.13 (0.17), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A3850 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE A2972 TYR 0.033 0.002 TYR C 372 ARG 0.008 0.000 ARG A3556 Details of bonding type rmsd hydrogen bonds : bond 0.14599 ( 1258) hydrogen bonds : angle 6.21214 ( 3696) covalent geometry : bond 0.00348 (23478) covalent geometry : angle 0.59808 (31923) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 300 time to evaluate : 2.578 Fit side-chains REVERT: A 1620 PHE cc_start: 0.7531 (t80) cc_final: 0.6969 (t80) REVERT: A 2044 ARG cc_start: 0.6740 (tmt170) cc_final: 0.6351 (ttm110) REVERT: A 2217 THR cc_start: 0.8384 (m) cc_final: 0.8179 (m) REVERT: A 2678 ASP cc_start: 0.8643 (t70) cc_final: 0.8436 (t70) REVERT: A 2785 LYS cc_start: 0.8097 (ptpt) cc_final: 0.6842 (mmtm) REVERT: A 2875 ASP cc_start: 0.6755 (p0) cc_final: 0.6332 (m-30) REVERT: A 2949 ASN cc_start: 0.7781 (t0) cc_final: 0.7579 (t0) REVERT: A 3345 MET cc_start: 0.8568 (mmp) cc_final: 0.8104 (mmp) REVERT: A 3446 PHE cc_start: 0.7323 (t80) cc_final: 0.7017 (t80) REVERT: A 3812 LYS cc_start: 0.6845 (mtpt) cc_final: 0.6101 (ttpt) REVERT: A 3987 ASP cc_start: 0.7908 (t0) cc_final: 0.7671 (t0) REVERT: C 299 TRP cc_start: 0.6889 (p-90) cc_final: 0.6110 (p-90) REVERT: C 364 ARG cc_start: 0.7635 (ttm-80) cc_final: 0.7230 (tpt-90) REVERT: B 208 PHE cc_start: 0.6308 (t80) cc_final: 0.5916 (t80) REVERT: B 262 TRP cc_start: 0.6607 (p90) cc_final: 0.5665 (p90) REVERT: B 383 LYS cc_start: 0.2744 (tptt) cc_final: 0.1492 (tttp) outliers start: 1 outliers final: 1 residues processed: 301 average time/residue: 0.3550 time to fit residues: 171.3790 Evaluate side-chains 239 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1757 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 0.8980 chunk 227 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 235 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 175 optimal weight: 0.0170 chunk 272 optimal weight: 7.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1873 GLN A1967 HIS A2351 GLN ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3821 ASN ** A3845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.181334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.146870 restraints weight = 30409.943| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.40 r_work: 0.3506 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23478 Z= 0.115 Angle : 0.492 6.560 31923 Z= 0.255 Chirality : 0.041 0.156 3710 Planarity : 0.004 0.049 4025 Dihedral : 6.063 120.900 3250 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.47 % Allowed : 6.43 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.15), residues: 2972 helix: 1.68 (0.14), residues: 1393 sheet: 0.41 (0.23), residues: 474 loop : -1.01 (0.17), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2084 HIS 0.006 0.001 HIS A2293 PHE 0.022 0.001 PHE A3016 TYR 0.020 0.001 TYR A2571 ARG 0.004 0.000 ARG A3894 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 1258) hydrogen bonds : angle 4.64229 ( 3696) covalent geometry : bond 0.00256 (23478) covalent geometry : angle 0.49205 (31923) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 256 time to evaluate : 2.346 Fit side-chains REVERT: A 1620 PHE cc_start: 0.7546 (t80) cc_final: 0.7012 (t80) REVERT: A 2044 ARG cc_start: 0.6857 (tmt170) cc_final: 0.6480 (ttm110) REVERT: A 2678 ASP cc_start: 0.8630 (t70) cc_final: 0.8418 (t70) REVERT: A 2875 ASP cc_start: 0.6700 (p0) cc_final: 0.6341 (m-30) REVERT: A 2949 ASN cc_start: 0.7697 (t0) cc_final: 0.7438 (t0) REVERT: A 3345 MET cc_start: 0.8600 (mmp) cc_final: 0.8113 (mmt) REVERT: A 3446 PHE cc_start: 0.7316 (t80) cc_final: 0.6993 (t80) REVERT: C 364 ARG cc_start: 0.7576 (ttm-80) cc_final: 0.7197 (tpt-90) REVERT: C 424 SER cc_start: 0.8872 (t) cc_final: 0.8650 (p) REVERT: B 208 PHE cc_start: 0.6311 (t80) cc_final: 0.6031 (t80) REVERT: B 262 TRP cc_start: 0.6697 (p90) cc_final: 0.5790 (p90) REVERT: B 383 LYS cc_start: 0.1769 (tptt) cc_final: 0.0929 (tttm) outliers start: 11 outliers final: 9 residues processed: 260 average time/residue: 0.3562 time to fit residues: 146.6292 Evaluate side-chains 245 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 236 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2489 ILE Chi-restraints excluded: chain A residue 2500 GLN Chi-restraints excluded: chain A residue 2787 HIS Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3932 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain B residue 238 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 205 optimal weight: 5.9990 chunk 268 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 2 optimal weight: 0.0670 chunk 28 optimal weight: 5.9990 chunk 240 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 overall best weight: 2.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1870 ASN ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2351 GLN A2832 ASN ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.174453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.139777 restraints weight = 30519.925| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.65 r_work: 0.3395 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 23478 Z= 0.230 Angle : 0.579 9.153 31923 Z= 0.299 Chirality : 0.045 0.167 3710 Planarity : 0.004 0.045 4025 Dihedral : 6.374 122.720 3247 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.71 % Allowed : 9.82 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.15), residues: 2972 helix: 1.58 (0.14), residues: 1393 sheet: 0.21 (0.23), residues: 482 loop : -0.95 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 299 HIS 0.006 0.001 HIS A2735 PHE 0.022 0.002 PHE A3016 TYR 0.028 0.002 TYR A2571 ARG 0.004 0.001 ARG A1768 Details of bonding type rmsd hydrogen bonds : bond 0.04248 ( 1258) hydrogen bonds : angle 4.56029 ( 3696) covalent geometry : bond 0.00556 (23478) covalent geometry : angle 0.57858 (31923) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 252 time to evaluate : 2.541 Fit side-chains REVERT: A 1620 PHE cc_start: 0.7560 (t80) cc_final: 0.6979 (t80) REVERT: A 1690 SER cc_start: 0.7531 (m) cc_final: 0.7175 (m) REVERT: A 1804 GLU cc_start: 0.7678 (mp0) cc_final: 0.7461 (mp0) REVERT: A 2044 ARG cc_start: 0.6780 (tmt170) cc_final: 0.6315 (ttm110) REVERT: A 2875 ASP cc_start: 0.6771 (p0) cc_final: 0.6429 (m-30) REVERT: A 2949 ASN cc_start: 0.7757 (t0) cc_final: 0.7458 (t0) REVERT: A 3446 PHE cc_start: 0.7451 (t80) cc_final: 0.7202 (t80) REVERT: A 3536 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.5774 (mp0) REVERT: A 3812 LYS cc_start: 0.6878 (mtpt) cc_final: 0.6091 (ttpt) REVERT: A 4001 GLU cc_start: 0.7973 (mp0) cc_final: 0.7634 (mp0) REVERT: C 205 ASP cc_start: 0.8355 (t0) cc_final: 0.8107 (t0) REVERT: C 299 TRP cc_start: 0.7205 (p-90) cc_final: 0.6241 (p-90) REVERT: C 309 TYR cc_start: 0.7329 (m-80) cc_final: 0.7032 (m-80) REVERT: C 364 ARG cc_start: 0.7604 (ttm-80) cc_final: 0.7209 (tpt-90) REVERT: C 424 SER cc_start: 0.8970 (t) cc_final: 0.8602 (p) REVERT: B 383 LYS cc_start: 0.1846 (tptt) cc_final: 0.1078 (tttm) outliers start: 40 outliers final: 30 residues processed: 276 average time/residue: 0.3524 time to fit residues: 153.8070 Evaluate side-chains 264 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1750 SER Chi-restraints excluded: chain A residue 2193 LEU Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2360 VAL Chi-restraints excluded: chain A residue 2489 ILE Chi-restraints excluded: chain A residue 2500 GLN Chi-restraints excluded: chain A residue 2689 ILE Chi-restraints excluded: chain A residue 2787 HIS Chi-restraints excluded: chain A residue 2792 LEU Chi-restraints excluded: chain A residue 2803 ILE Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2900 SER Chi-restraints excluded: chain A residue 3362 VAL Chi-restraints excluded: chain A residue 3367 ILE Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3536 GLU Chi-restraints excluded: chain A residue 3757 ILE Chi-restraints excluded: chain A residue 3900 ILE Chi-restraints excluded: chain A residue 3943 THR Chi-restraints excluded: chain A residue 4029 ILE Chi-restraints excluded: chain A residue 4033 LEU Chi-restraints excluded: chain A residue 4052 THR Chi-restraints excluded: chain A residue 4060 SER Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 479 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 183 optimal weight: 0.1980 chunk 230 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 291 optimal weight: 40.0000 chunk 259 optimal weight: 0.9990 chunk 229 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 266 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1811 GLN ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2351 GLN A2927 GLN ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3842 GLN ** A3845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN B 186 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.178440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.143316 restraints weight = 30835.365| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.52 r_work: 0.3460 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23478 Z= 0.109 Angle : 0.488 9.703 31923 Z= 0.248 Chirality : 0.041 0.153 3710 Planarity : 0.003 0.044 4025 Dihedral : 6.079 120.635 3247 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.24 % Allowed : 11.23 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.15), residues: 2972 helix: 1.93 (0.14), residues: 1396 sheet: 0.42 (0.24), residues: 474 loop : -0.94 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2084 HIS 0.004 0.001 HIS A2293 PHE 0.025 0.001 PHE A3016 TYR 0.019 0.001 TYR A2571 ARG 0.004 0.000 ARG A1768 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 1258) hydrogen bonds : angle 4.26138 ( 3696) covalent geometry : bond 0.00248 (23478) covalent geometry : angle 0.48818 (31923) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 257 time to evaluate : 3.383 Fit side-chains revert: symmetry clash REVERT: A 1620 PHE cc_start: 0.7510 (t80) cc_final: 0.6871 (t80) REVERT: A 1690 SER cc_start: 0.7452 (m) cc_final: 0.7096 (m) REVERT: A 1804 GLU cc_start: 0.7558 (mp0) cc_final: 0.7341 (mp0) REVERT: A 2044 ARG cc_start: 0.6861 (tmt170) cc_final: 0.6395 (ttm110) REVERT: A 2875 ASP cc_start: 0.6880 (p0) cc_final: 0.6465 (m-30) REVERT: A 2949 ASN cc_start: 0.7762 (t0) cc_final: 0.7466 (t0) REVERT: A 2950 LYS cc_start: 0.8007 (mttt) cc_final: 0.7702 (tppt) REVERT: A 3446 PHE cc_start: 0.7442 (t80) cc_final: 0.7209 (t80) REVERT: A 3536 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.5565 (mp0) REVERT: A 3812 LYS cc_start: 0.6822 (mtpt) cc_final: 0.6033 (ttpt) REVERT: C 309 TYR cc_start: 0.7263 (m-80) cc_final: 0.6986 (m-80) REVERT: C 364 ARG cc_start: 0.7602 (ttm-80) cc_final: 0.7224 (tpt-90) REVERT: C 424 SER cc_start: 0.8847 (t) cc_final: 0.8572 (p) REVERT: B 262 TRP cc_start: 0.6704 (p90) cc_final: 0.5851 (p90) REVERT: B 383 LYS cc_start: 0.1731 (tptt) cc_final: 0.1021 (tttm) outliers start: 29 outliers final: 20 residues processed: 273 average time/residue: 0.3762 time to fit residues: 164.8025 Evaluate side-chains 259 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 238 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1750 SER Chi-restraints excluded: chain A residue 2217 THR Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2489 ILE Chi-restraints excluded: chain A residue 2678 ASP Chi-restraints excluded: chain A residue 2689 ILE Chi-restraints excluded: chain A residue 2787 HIS Chi-restraints excluded: chain A residue 2792 LEU Chi-restraints excluded: chain A residue 2803 ILE Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2863 LEU Chi-restraints excluded: chain A residue 2900 SER Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3536 GLU Chi-restraints excluded: chain A residue 3943 THR Chi-restraints excluded: chain A residue 4033 LEU Chi-restraints excluded: chain A residue 4060 SER Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 442 TRP Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 261 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 111 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 203 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 171 optimal weight: 7.9990 chunk 255 optimal weight: 4.9990 chunk 270 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2351 GLN ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.174643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.139642 restraints weight = 30668.145| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.55 r_work: 0.3408 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23478 Z= 0.192 Angle : 0.539 9.069 31923 Z= 0.276 Chirality : 0.043 0.192 3710 Planarity : 0.003 0.048 4025 Dihedral : 6.247 122.749 3247 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.67 % Allowed : 11.62 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.15), residues: 2972 helix: 1.83 (0.14), residues: 1396 sheet: 0.18 (0.24), residues: 471 loop : -0.93 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2084 HIS 0.005 0.001 HIS A2735 PHE 0.024 0.002 PHE A3016 TYR 0.025 0.002 TYR A2571 ARG 0.003 0.000 ARG A1768 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 1258) hydrogen bonds : angle 4.33091 ( 3696) covalent geometry : bond 0.00465 (23478) covalent geometry : angle 0.53944 (31923) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 246 time to evaluate : 2.397 Fit side-chains REVERT: A 1620 PHE cc_start: 0.7559 (t80) cc_final: 0.7071 (t80) REVERT: A 2044 ARG cc_start: 0.6889 (tmt170) cc_final: 0.6422 (ttm110) REVERT: A 2156 SER cc_start: 0.9110 (t) cc_final: 0.8885 (t) REVERT: A 2875 ASP cc_start: 0.6879 (p0) cc_final: 0.6485 (m-30) REVERT: A 2911 ARG cc_start: 0.7754 (tpm170) cc_final: 0.7520 (tpm170) REVERT: A 2949 ASN cc_start: 0.7764 (t0) cc_final: 0.7465 (t0) REVERT: A 2950 LYS cc_start: 0.8042 (mttt) cc_final: 0.7755 (tppt) REVERT: A 3446 PHE cc_start: 0.7467 (t80) cc_final: 0.7261 (t80) REVERT: A 3536 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.5720 (mp0) REVERT: C 309 TYR cc_start: 0.7289 (m-80) cc_final: 0.7004 (m-80) REVERT: C 364 ARG cc_start: 0.7536 (ttm-80) cc_final: 0.7170 (tpt-90) REVERT: C 424 SER cc_start: 0.8910 (t) cc_final: 0.8570 (p) REVERT: B 383 LYS cc_start: 0.1950 (tptt) cc_final: 0.1231 (tttm) outliers start: 39 outliers final: 32 residues processed: 267 average time/residue: 0.3662 time to fit residues: 153.7995 Evaluate side-chains 267 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1750 SER Chi-restraints excluded: chain A residue 2163 VAL Chi-restraints excluded: chain A residue 2193 LEU Chi-restraints excluded: chain A residue 2217 THR Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2360 VAL Chi-restraints excluded: chain A residue 2489 ILE Chi-restraints excluded: chain A residue 2678 ASP Chi-restraints excluded: chain A residue 2689 ILE Chi-restraints excluded: chain A residue 2787 HIS Chi-restraints excluded: chain A residue 2792 LEU Chi-restraints excluded: chain A residue 2803 ILE Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2863 LEU Chi-restraints excluded: chain A residue 2900 SER Chi-restraints excluded: chain A residue 3362 VAL Chi-restraints excluded: chain A residue 3367 ILE Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3536 GLU Chi-restraints excluded: chain A residue 3757 ILE Chi-restraints excluded: chain A residue 3943 THR Chi-restraints excluded: chain A residue 4029 ILE Chi-restraints excluded: chain A residue 4033 LEU Chi-restraints excluded: chain A residue 4052 THR Chi-restraints excluded: chain A residue 4060 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 442 TRP Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 479 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 56 optimal weight: 0.4980 chunk 155 optimal weight: 10.0000 chunk 270 optimal weight: 0.5980 chunk 233 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 296 optimal weight: 50.0000 chunk 48 optimal weight: 1.9990 chunk 237 optimal weight: 7.9990 chunk 145 optimal weight: 0.5980 chunk 238 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2351 GLN ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3845 GLN ** A3948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN B 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.176859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.142119 restraints weight = 30377.530| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.30 r_work: 0.3464 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23478 Z= 0.120 Angle : 0.493 8.556 31923 Z= 0.251 Chirality : 0.041 0.158 3710 Planarity : 0.003 0.049 4025 Dihedral : 6.097 121.416 3247 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.59 % Allowed : 12.73 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.15), residues: 2972 helix: 2.03 (0.14), residues: 1397 sheet: 0.33 (0.24), residues: 466 loop : -0.90 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2084 HIS 0.004 0.001 HIS A2735 PHE 0.026 0.001 PHE A3016 TYR 0.020 0.001 TYR A2571 ARG 0.003 0.000 ARG A1768 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 1258) hydrogen bonds : angle 4.19093 ( 3696) covalent geometry : bond 0.00277 (23478) covalent geometry : angle 0.49253 (31923) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 246 time to evaluate : 2.465 Fit side-chains REVERT: A 1538 TYR cc_start: 0.5444 (t80) cc_final: 0.5144 (t80) REVERT: A 1620 PHE cc_start: 0.7542 (t80) cc_final: 0.7029 (t80) REVERT: A 1804 GLU cc_start: 0.7747 (mp0) cc_final: 0.7511 (mp0) REVERT: A 2044 ARG cc_start: 0.6898 (tmt170) cc_final: 0.6413 (ttm110) REVERT: A 2156 SER cc_start: 0.9155 (t) cc_final: 0.8943 (t) REVERT: A 2464 TYR cc_start: 0.5560 (m-80) cc_final: 0.5312 (m-80) REVERT: A 2875 ASP cc_start: 0.6946 (p0) cc_final: 0.6527 (m-30) REVERT: A 2911 ARG cc_start: 0.7843 (tpm170) cc_final: 0.7617 (tpm170) REVERT: A 2949 ASN cc_start: 0.7721 (t0) cc_final: 0.7359 (t0) REVERT: A 2950 LYS cc_start: 0.8071 (mttt) cc_final: 0.7715 (tppt) REVERT: A 3536 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.5717 (mp0) REVERT: C 299 TRP cc_start: 0.7374 (p-90) cc_final: 0.7125 (p-90) REVERT: C 309 TYR cc_start: 0.7391 (m-80) cc_final: 0.7109 (m-80) REVERT: C 364 ARG cc_start: 0.7612 (ttm-80) cc_final: 0.7264 (tpt-90) REVERT: C 424 SER cc_start: 0.8973 (t) cc_final: 0.8666 (p) REVERT: B 383 LYS cc_start: 0.1878 (tptt) cc_final: 0.1187 (tttm) outliers start: 37 outliers final: 33 residues processed: 267 average time/residue: 0.4014 time to fit residues: 169.5832 Evaluate side-chains 269 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1683 LEU Chi-restraints excluded: chain A residue 1750 SER Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 2009 THR Chi-restraints excluded: chain A residue 2193 LEU Chi-restraints excluded: chain A residue 2217 THR Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2489 ILE Chi-restraints excluded: chain A residue 2678 ASP Chi-restraints excluded: chain A residue 2689 ILE Chi-restraints excluded: chain A residue 2787 HIS Chi-restraints excluded: chain A residue 2792 LEU Chi-restraints excluded: chain A residue 2803 ILE Chi-restraints excluded: chain A residue 2813 THR Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2863 LEU Chi-restraints excluded: chain A residue 2900 SER Chi-restraints excluded: chain A residue 3362 VAL Chi-restraints excluded: chain A residue 3367 ILE Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3536 GLU Chi-restraints excluded: chain A residue 3900 ILE Chi-restraints excluded: chain A residue 3943 THR Chi-restraints excluded: chain A residue 4029 ILE Chi-restraints excluded: chain A residue 4033 LEU Chi-restraints excluded: chain A residue 4052 THR Chi-restraints excluded: chain A residue 4060 SER Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 442 TRP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 479 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 27 optimal weight: 2.9990 chunk 146 optimal weight: 0.0470 chunk 220 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 196 optimal weight: 3.9990 chunk 226 optimal weight: 8.9990 chunk 182 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 246 optimal weight: 0.0980 chunk 115 optimal weight: 0.5980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2351 GLN A2787 HIS ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.179506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.144654 restraints weight = 30584.168| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.42 r_work: 0.3487 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23478 Z= 0.093 Angle : 0.471 8.041 31923 Z= 0.238 Chirality : 0.041 0.156 3710 Planarity : 0.003 0.049 4025 Dihedral : 5.857 121.941 3247 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.50 % Allowed : 12.94 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.16), residues: 2972 helix: 2.24 (0.14), residues: 1401 sheet: 0.41 (0.24), residues: 470 loop : -0.85 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2084 HIS 0.003 0.000 HIS A2293 PHE 0.029 0.001 PHE A3016 TYR 0.018 0.001 TYR A2571 ARG 0.003 0.000 ARG A1768 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 1258) hydrogen bonds : angle 4.03425 ( 3696) covalent geometry : bond 0.00204 (23478) covalent geometry : angle 0.47146 (31923) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 3.995 Fit side-chains REVERT: A 1620 PHE cc_start: 0.7507 (t80) cc_final: 0.7030 (t80) REVERT: A 1690 SER cc_start: 0.7568 (m) cc_final: 0.7176 (m) REVERT: A 1804 GLU cc_start: 0.7770 (mp0) cc_final: 0.7525 (mp0) REVERT: A 2044 ARG cc_start: 0.6907 (tmt170) cc_final: 0.6310 (ttm110) REVERT: A 2464 TYR cc_start: 0.5470 (m-80) cc_final: 0.5231 (m-80) REVERT: A 2875 ASP cc_start: 0.6948 (p0) cc_final: 0.6496 (m-30) REVERT: A 2911 ARG cc_start: 0.7749 (tpm170) cc_final: 0.7533 (tpm170) REVERT: A 2938 MET cc_start: 0.8310 (ttm) cc_final: 0.8063 (mtp) REVERT: A 2949 ASN cc_start: 0.7577 (t0) cc_final: 0.7188 (t0) REVERT: A 2950 LYS cc_start: 0.8048 (mttt) cc_final: 0.7686 (tppt) REVERT: A 3536 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.5359 (mp0) REVERT: C 364 ARG cc_start: 0.7624 (ttm-80) cc_final: 0.7270 (tpt-90) REVERT: C 424 SER cc_start: 0.8929 (t) cc_final: 0.8650 (p) REVERT: B 383 LYS cc_start: 0.1844 (tptt) cc_final: 0.1171 (tttm) outliers start: 35 outliers final: 26 residues processed: 281 average time/residue: 0.5105 time to fit residues: 232.1341 Evaluate side-chains 272 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 245 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1750 SER Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 2009 THR Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2193 LEU Chi-restraints excluded: chain A residue 2217 THR Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2678 ASP Chi-restraints excluded: chain A residue 2689 ILE Chi-restraints excluded: chain A residue 2792 LEU Chi-restraints excluded: chain A residue 2803 ILE Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2863 LEU Chi-restraints excluded: chain A residue 2900 SER Chi-restraints excluded: chain A residue 3362 VAL Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3536 GLU Chi-restraints excluded: chain A residue 4033 LEU Chi-restraints excluded: chain A residue 4060 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 442 TRP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 479 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 195 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 142 optimal weight: 0.0980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2351 GLN ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3842 GLN ** A3948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.178111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.143589 restraints weight = 30478.408| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.56 r_work: 0.3457 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23478 Z= 0.118 Angle : 0.491 10.239 31923 Z= 0.248 Chirality : 0.042 0.154 3710 Planarity : 0.003 0.050 4025 Dihedral : 5.915 122.907 3247 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.54 % Allowed : 13.37 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.16), residues: 2972 helix: 2.25 (0.14), residues: 1398 sheet: 0.31 (0.24), residues: 476 loop : -0.84 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2084 HIS 0.006 0.001 HIS B 197 PHE 0.030 0.001 PHE A2404 TYR 0.021 0.001 TYR A2571 ARG 0.005 0.000 ARG A1536 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 1258) hydrogen bonds : angle 4.04988 ( 3696) covalent geometry : bond 0.00275 (23478) covalent geometry : angle 0.49066 (31923) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 245 time to evaluate : 2.381 Fit side-chains REVERT: A 1620 PHE cc_start: 0.7494 (t80) cc_final: 0.6952 (t80) REVERT: A 1690 SER cc_start: 0.7538 (m) cc_final: 0.7128 (m) REVERT: A 1804 GLU cc_start: 0.7573 (mp0) cc_final: 0.7345 (mp0) REVERT: A 2044 ARG cc_start: 0.6969 (tmt170) cc_final: 0.6431 (ttm110) REVERT: A 2875 ASP cc_start: 0.6858 (p0) cc_final: 0.6437 (m-30) REVERT: A 2911 ARG cc_start: 0.7661 (tpm170) cc_final: 0.7454 (tpm170) REVERT: A 2949 ASN cc_start: 0.7655 (t0) cc_final: 0.7285 (t0) REVERT: A 2950 LYS cc_start: 0.8022 (mttt) cc_final: 0.7773 (tppt) REVERT: A 3394 MET cc_start: 0.8391 (tpt) cc_final: 0.7950 (tpt) REVERT: A 3536 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.5412 (mp0) REVERT: C 364 ARG cc_start: 0.7589 (ttm-80) cc_final: 0.7260 (tpt-90) REVERT: C 366 LYS cc_start: 0.7358 (ttpt) cc_final: 0.7018 (ptmm) REVERT: C 424 SER cc_start: 0.8887 (t) cc_final: 0.8572 (p) REVERT: B 383 LYS cc_start: 0.1774 (tptt) cc_final: 0.1094 (tttm) outliers start: 36 outliers final: 30 residues processed: 265 average time/residue: 0.3620 time to fit residues: 151.4190 Evaluate side-chains 273 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 242 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1683 LEU Chi-restraints excluded: chain A residue 1750 SER Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 2009 THR Chi-restraints excluded: chain A residue 2193 LEU Chi-restraints excluded: chain A residue 2217 THR Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2500 GLN Chi-restraints excluded: chain A residue 2678 ASP Chi-restraints excluded: chain A residue 2683 ASN Chi-restraints excluded: chain A residue 2689 ILE Chi-restraints excluded: chain A residue 2787 HIS Chi-restraints excluded: chain A residue 2792 LEU Chi-restraints excluded: chain A residue 2803 ILE Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2863 LEU Chi-restraints excluded: chain A residue 2900 SER Chi-restraints excluded: chain A residue 3362 VAL Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3536 GLU Chi-restraints excluded: chain A residue 3875 MET Chi-restraints excluded: chain A residue 4033 LEU Chi-restraints excluded: chain A residue 4060 SER Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 442 TRP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 479 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 37 optimal weight: 0.7980 chunk 218 optimal weight: 0.6980 chunk 184 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 219 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 103 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 289 optimal weight: 40.0000 chunk 265 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2351 GLN ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.179304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.144922 restraints weight = 30538.266| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.56 r_work: 0.3477 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23478 Z= 0.099 Angle : 0.479 9.737 31923 Z= 0.241 Chirality : 0.041 0.166 3710 Planarity : 0.003 0.051 4025 Dihedral : 5.829 123.333 3247 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.46 % Allowed : 13.42 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.16), residues: 2972 helix: 2.32 (0.14), residues: 1399 sheet: 0.40 (0.24), residues: 470 loop : -0.80 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2084 HIS 0.005 0.001 HIS B 197 PHE 0.028 0.001 PHE A2404 TYR 0.019 0.001 TYR A2571 ARG 0.005 0.000 ARG A1536 Details of bonding type rmsd hydrogen bonds : bond 0.03087 ( 1258) hydrogen bonds : angle 3.99227 ( 3696) covalent geometry : bond 0.00222 (23478) covalent geometry : angle 0.47916 (31923) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 254 time to evaluate : 2.369 Fit side-chains REVERT: A 1620 PHE cc_start: 0.7435 (t80) cc_final: 0.6829 (t80) REVERT: A 1690 SER cc_start: 0.7504 (m) cc_final: 0.7103 (m) REVERT: A 1804 GLU cc_start: 0.7573 (mp0) cc_final: 0.7358 (mp0) REVERT: A 2044 ARG cc_start: 0.6999 (tmt170) cc_final: 0.6472 (ttm110) REVERT: A 2875 ASP cc_start: 0.6818 (p0) cc_final: 0.6392 (m-30) REVERT: A 2949 ASN cc_start: 0.7628 (t0) cc_final: 0.7261 (t0) REVERT: A 2950 LYS cc_start: 0.8019 (mttt) cc_final: 0.7733 (tppt) REVERT: A 3536 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.5259 (mp0) REVERT: C 364 ARG cc_start: 0.7542 (ttm-80) cc_final: 0.7225 (tpt-90) REVERT: C 366 LYS cc_start: 0.7287 (ttpt) cc_final: 0.6949 (ptmm) REVERT: C 424 SER cc_start: 0.8827 (t) cc_final: 0.8542 (p) REVERT: B 383 LYS cc_start: 0.1699 (tptt) cc_final: 0.1029 (tttm) outliers start: 34 outliers final: 30 residues processed: 270 average time/residue: 0.3643 time to fit residues: 157.2209 Evaluate side-chains 274 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 243 time to evaluate : 2.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1683 LEU Chi-restraints excluded: chain A residue 1750 SER Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 2009 THR Chi-restraints excluded: chain A residue 2193 LEU Chi-restraints excluded: chain A residue 2217 THR Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2678 ASP Chi-restraints excluded: chain A residue 2683 ASN Chi-restraints excluded: chain A residue 2689 ILE Chi-restraints excluded: chain A residue 2787 HIS Chi-restraints excluded: chain A residue 2792 LEU Chi-restraints excluded: chain A residue 2803 ILE Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2900 SER Chi-restraints excluded: chain A residue 3362 VAL Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3536 GLU Chi-restraints excluded: chain A residue 3875 MET Chi-restraints excluded: chain A residue 4029 ILE Chi-restraints excluded: chain A residue 4033 LEU Chi-restraints excluded: chain A residue 4060 SER Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 442 TRP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 479 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 26 optimal weight: 1.9990 chunk 291 optimal weight: 0.0670 chunk 107 optimal weight: 0.9990 chunk 273 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 266 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2351 GLN ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.178924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.144517 restraints weight = 30662.479| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.57 r_work: 0.3471 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23478 Z= 0.106 Angle : 0.488 10.676 31923 Z= 0.245 Chirality : 0.041 0.181 3710 Planarity : 0.003 0.050 4025 Dihedral : 5.834 124.131 3247 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.46 % Allowed : 13.59 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.16), residues: 2972 helix: 2.31 (0.14), residues: 1401 sheet: 0.38 (0.24), residues: 470 loop : -0.79 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2084 HIS 0.006 0.001 HIS B 197 PHE 0.028 0.001 PHE A3016 TYR 0.026 0.001 TYR C 372 ARG 0.006 0.000 ARG A1536 Details of bonding type rmsd hydrogen bonds : bond 0.03128 ( 1258) hydrogen bonds : angle 3.98191 ( 3696) covalent geometry : bond 0.00243 (23478) covalent geometry : angle 0.48807 (31923) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 2.723 Fit side-chains REVERT: A 1620 PHE cc_start: 0.7444 (t80) cc_final: 0.6932 (t80) REVERT: A 1690 SER cc_start: 0.7503 (m) cc_final: 0.7099 (m) REVERT: A 1804 GLU cc_start: 0.7578 (mp0) cc_final: 0.7364 (mp0) REVERT: A 2044 ARG cc_start: 0.7005 (tmt170) cc_final: 0.6479 (ttm110) REVERT: A 2875 ASP cc_start: 0.6825 (p0) cc_final: 0.6405 (m-30) REVERT: A 2949 ASN cc_start: 0.7640 (t0) cc_final: 0.7270 (t0) REVERT: A 2950 LYS cc_start: 0.8024 (mttt) cc_final: 0.7740 (tppt) REVERT: A 3394 MET cc_start: 0.8354 (tpt) cc_final: 0.7996 (tpt) REVERT: A 3536 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.5339 (mp0) REVERT: C 364 ARG cc_start: 0.7538 (ttm-80) cc_final: 0.7228 (tpt-90) REVERT: C 366 LYS cc_start: 0.7274 (ttpt) cc_final: 0.6945 (ptmm) REVERT: C 424 SER cc_start: 0.8829 (t) cc_final: 0.8547 (p) REVERT: B 383 LYS cc_start: 0.1691 (tptt) cc_final: 0.1020 (tttm) outliers start: 34 outliers final: 33 residues processed: 264 average time/residue: 0.3537 time to fit residues: 149.0744 Evaluate side-chains 280 residues out of total 2749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 246 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1683 LEU Chi-restraints excluded: chain A residue 1750 SER Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 2009 THR Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain A residue 2193 LEU Chi-restraints excluded: chain A residue 2217 THR Chi-restraints excluded: chain A residue 2247 ASP Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2500 GLN Chi-restraints excluded: chain A residue 2678 ASP Chi-restraints excluded: chain A residue 2683 ASN Chi-restraints excluded: chain A residue 2689 ILE Chi-restraints excluded: chain A residue 2787 HIS Chi-restraints excluded: chain A residue 2792 LEU Chi-restraints excluded: chain A residue 2803 ILE Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2900 SER Chi-restraints excluded: chain A residue 3362 VAL Chi-restraints excluded: chain A residue 3373 LEU Chi-restraints excluded: chain A residue 3536 GLU Chi-restraints excluded: chain A residue 3875 MET Chi-restraints excluded: chain A residue 4029 ILE Chi-restraints excluded: chain A residue 4033 LEU Chi-restraints excluded: chain A residue 4052 THR Chi-restraints excluded: chain A residue 4060 SER Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 442 TRP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 479 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 19 optimal weight: 2.9990 chunk 280 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 265 optimal weight: 0.7980 chunk 289 optimal weight: 40.0000 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 198 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 254 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2351 GLN ** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.176380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.142148 restraints weight = 30464.456| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.43 r_work: 0.3446 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23478 Z= 0.146 Angle : 0.512 10.726 31923 Z= 0.260 Chirality : 0.042 0.175 3710 Planarity : 0.003 0.046 4025 Dihedral : 6.032 123.969 3247 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.50 % Allowed : 13.54 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.16), residues: 2972 helix: 2.20 (0.14), residues: 1400 sheet: 0.20 (0.24), residues: 476 loop : -0.80 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2084 HIS 0.006 0.001 HIS B 197 PHE 0.027 0.001 PHE A3016 TYR 0.025 0.001 TYR C 372 ARG 0.004 0.000 ARG B 247 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 1258) hydrogen bonds : angle 4.06934 ( 3696) covalent geometry : bond 0.00350 (23478) covalent geometry : angle 0.51194 (31923) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12901.34 seconds wall clock time: 224 minutes 18.29 seconds (13458.29 seconds total)