Starting phenix.real_space_refine on Thu Sep 18 23:44:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dkx_46972/09_2025/9dkx_46972.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dkx_46972/09_2025/9dkx_46972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dkx_46972/09_2025/9dkx_46972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dkx_46972/09_2025/9dkx_46972.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dkx_46972/09_2025/9dkx_46972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dkx_46972/09_2025/9dkx_46972.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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 95 5.16 5 C 13363 2.51 5 N 3498 2.21 5 O 3840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20808 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 17941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2299, 17941 Classifications: {'peptide': 2299} Incomplete info: {'truncation_to_alanine': 179} Link IDs: {'PTRANS': 65, 'TRANS': 2233} Chain breaks: 15 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 646 Unresolved non-hydrogen angles: 792 Unresolved non-hydrogen dihedrals: 526 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 13, 'TRP:plan': 2, 'GLU:plan': 41, 'PHE:plan': 3, 'TYR:plan': 1, 'ASP:plan': 19, 'ARG:plan': 10, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 382 Chain: "C" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2752 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 16, 'TRANS': 330} Chain breaks: 2 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'ARG%COO:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "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: 4.45, per 1000 atoms: 0.21 Number of scatterers: 20808 At special positions: 0 Unit cell: (111.125, 152.019, 173.355, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 95 16.00 P 9 15.00 Mg 3 11.99 O 3840 8.00 N 3498 7.00 C 13363 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 962.5 milliseconds Enol-peptide restraints added in 1.4 microseconds 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5036 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 24 sheets defined 56.1% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 1443 through 1461 Processing helix chain 'A' and resid 1473 through 1488 Processing helix chain 'A' and resid 1512 through 1523 Processing helix chain 'A' and resid 1523 through 1534 removed outlier: 3.753A pdb=" N PHE A1534 " --> pdb=" O GLN A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1539 removed outlier: 3.770A pdb=" N PHE A1539 " --> pdb=" O ARG A1536 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1551 Processing helix chain 'A' and resid 1562 through 1567 Processing helix chain 'A' and resid 1603 through 1633 removed outlier: 3.597A pdb=" N TRP A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1636 through 1641 removed outlier: 3.814A pdb=" N SER A1641 " --> pdb=" O GLU A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1665 removed outlier: 3.508A pdb=" N ILE A1648 " --> pdb=" O ILE A1644 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1690 removed outlier: 3.732A pdb=" N LYS A1689 " --> pdb=" O ASP A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1717 removed outlier: 4.255A pdb=" N GLU A1704 " --> pdb=" O ALA A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1731 Processing helix chain 'A' and resid 1772 through 1788 removed outlier: 4.059A pdb=" N GLN A1788 " --> pdb=" O ASP A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1813 Processing helix chain 'A' and resid 1829 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 1988 removed outlier: 3.927A pdb=" N SER A1981 " --> pdb=" O LEU A1977 " (cutoff:3.500A) Proline residue: A1982 - end of helix removed outlier: 4.730A pdb=" N SER A1985 " --> pdb=" O SER A1981 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLU A1986 " --> pdb=" O PRO A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1990 through 2003 removed outlier: 3.681A pdb=" N VAL A1994 " --> pdb=" O GLY A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 2004 through 2006 No H-bonds generated for 'chain 'A' and resid 2004 through 2006' Processing helix chain 'A' and resid 2008 through 2022 Processing helix chain 'A' and resid 2031 through 2046 Processing helix chain 'A' and resid 2050 through 2065 Processing helix chain 'A' and resid 2079 through 2096 Processing helix chain 'A' and resid 2110 through 2115 Processing helix chain 'A' and resid 2128 through 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 2165 removed outlier: 3.786A pdb=" N ALA A2165 " --> pdb=" O GLU A2161 " (cutoff:3.500A) Processing helix chain 'A' and resid 2166 through 2171 removed outlier: 3.650A pdb=" N LEU A2170 " --> pdb=" O MET A2166 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP A2171 " --> pdb=" O ASN A2167 " (cutoff:3.500A) No H-bonds generated for '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: 3.820A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP A2271 " --> pdb=" O THR A2267 " (cutoff:3.500A) Processing helix chain 'A' and resid 2279 through 2282 Processing helix chain 'A' and resid 2283 through 2299 removed outlier: 3.844A pdb=" N GLN A2289 " --> pdb=" O GLU A2285 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA A2291 " --> pdb=" O ALA A2287 " (cutoff:3.500A) Processing helix chain 'A' and resid 2300 through 2302 No H-bonds generated for 'chain 'A' and resid 2300 through 2302' Processing helix chain 'A' and resid 2306 through 2326 Processing helix chain 'A' and resid 2331 through 2346 Processing helix chain 'A' and resid 2372 through 2375 removed outlier: 3.961A 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 2385 removed outlier: 3.903A pdb=" N GLU A2384 " --> pdb=" O GLU A2381 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL A2385 " --> pdb=" O ALA A2382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2381 through 2385' Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2423 through 2434 removed outlier: 3.595A pdb=" N ASN A2434 " --> pdb=" O ASN A2430 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2460 removed outlier: 3.937A pdb=" N ILE A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A2460 " --> pdb=" O SER A2456 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2512 removed outlier: 3.524A 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: 3.786A pdb=" N ARG A2586 " --> pdb=" O PRO A2583 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N SER A2587 " --> pdb=" O GLU A2584 " (cutoff:3.500A) Processing helix chain 'A' and resid 2588 through 2607 Processing helix chain 'A' and resid 2618 through 2635 removed outlier: 4.099A pdb=" N LEU A2622 " --> pdb=" O SER A2618 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR A2635 " --> pdb=" O THR A2631 " (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 2808 removed outlier: 3.603A pdb=" N PHE A2795 " --> pdb=" O ASN A2791 " (cutoff:3.500A) Processing helix chain 'A' and resid 2820 through 2822 No H-bonds generated for 'chain 'A' and resid 2820 through 2822' Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 3.902A pdb=" N LEU A2828 " --> pdb=" O GLU A2824 " (cutoff:3.500A) Processing helix chain 'A' and resid 2840 through 2844 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 2912 removed outlier: 3.513A pdb=" N ARG A2911 " --> pdb=" O ALA A2907 " (cutoff:3.500A) Processing helix chain 'A' and resid 2921 through 2934 removed outlier: 3.512A pdb=" N ASP A2934 " --> pdb=" O ASN A2930 " (cutoff:3.500A) Processing helix chain 'A' and resid 2949 through 2953 removed outlier: 3.540A pdb=" N LEU A2952 " --> pdb=" O ASN A2949 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A2953 " --> pdb=" O LYS A2950 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2949 through 2953' Processing helix chain 'A' and resid 2960 through 2980 removed outlier: 3.739A 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 3318 removed outlier: 3.535A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) Processing helix chain 'A' and resid 3320 through 3333 Processing helix chain 'A' and resid 3334 through 3337 removed outlier: 3.973A pdb=" N LEU A3337 " --> pdb=" O PHE A3334 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3334 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 Processing helix chain 'A' and resid 3387 through 3399 Processing helix chain 'A' and resid 3413 through 3423 removed outlier: 3.705A pdb=" N VAL A3417 " --> pdb=" O HIS A3413 " (cutoff:3.500A) Processing helix chain 'A' and resid 3424 through 3426 No H-bonds generated for 'chain 'A' and resid 3424 through 3426' Processing helix chain 'A' and resid 3435 through 3447 Processing helix chain 'A' and resid 3454 through 3458 removed outlier: 3.619A 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 Processing helix chain 'A' and resid 3506 through 3511 Processing helix chain 'A' and resid 3521 through 3538 removed outlier: 3.556A pdb=" N ASN A3538 " --> pdb=" O LEU A3534 " (cutoff:3.500A) Processing helix chain 'A' and resid 3538 through 3572 removed outlier: 4.041A pdb=" N GLN A3542 " --> pdb=" O ASN A3538 " (cutoff:3.500A) Processing helix chain 'A' and resid 3583 through 3606 removed outlier: 3.897A pdb=" N GLU A3606 " --> pdb=" O SER A3602 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3618 removed outlier: 3.967A pdb=" N PHE A3611 " --> pdb=" O PHE A3607 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP A3612 " --> pdb=" O PHE A3608 " (cutoff:3.500A) Processing helix chain 'A' and resid 3618 through 3637 removed outlier: 4.008A pdb=" N GLY A3622 " --> pdb=" O TYR A3618 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3659 removed outlier: 3.509A pdb=" N PHE A3649 " --> pdb=" O SER A3645 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A3656 " --> pdb=" O CYS A3652 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) Processing helix chain 'A' and resid 3671 through 3688 removed outlier: 4.658A pdb=" N THR A3688 " --> pdb=" O CYS A3684 " (cutoff:3.500A) 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: 4.538A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.694A 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 3808 Processing helix chain 'A' and resid 3818 through 3833 Processing helix chain 'A' and resid 3847 through 3859 removed outlier: 5.927A pdb=" N HIS A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LYS A3857 " --> pdb=" O THR A3853 " (cutoff:3.500A) Processing helix chain 'A' and resid 3885 through 3891 Processing helix chain 'A' and resid 3902 through 3913 removed outlier: 3.520A pdb=" N THR A3906 " --> pdb=" O GLY A3902 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER A3913 " --> pdb=" O ASP A3909 " (cutoff:3.500A) Processing helix chain 'A' and resid 3922 through 3944 removed outlier: 3.698A pdb=" N ARG A3944 " --> pdb=" O THR A3940 " (cutoff:3.500A) Processing helix chain 'A' and resid 3957 through 3974 removed outlier: 3.721A 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: 3.803A pdb=" N LEU A4004 " --> pdb=" O GLU A4000 " (cutoff:3.500A) Processing helix chain 'A' and resid 4037 through 4052 removed outlier: 3.722A pdb=" N THR A4052 " --> pdb=" O ILE A4048 " (cutoff:3.500A) Processing helix chain 'A' and resid 4066 through 4091 removed outlier: 3.594A pdb=" N ILE A4070 " --> pdb=" O PRO A4066 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU A4091 " --> pdb=" O GLN A4087 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 369 Processing sheet with id=AA1, first strand: chain 'A' and resid 1569 through 1573 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 1818 through 1819 removed outlier: 6.257A pdb=" N VAL A1818 " --> pdb=" O CYS A1846 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY A1845 " --> pdb=" O PHE A1895 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N THR A1897 " --> pdb=" O GLY A1845 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE A1847 " --> pdb=" O THR A1897 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLY A1792 " --> pdb=" O ILE A1896 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LEU A1898 " --> pdb=" O GLY A1792 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE A1794 " --> pdb=" O LEU A1898 " (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: 6.341A pdb=" N ALA A2098 " --> pdb=" O ARG A2149 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N TRP A2151 " --> pdb=" O ALA A2098 " (cutoff:3.500A) removed outlier: 6.313A 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: 6.620A pdb=" N TYR A2102 " --> pdb=" O VAL A2153 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ARG A2191 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A2150 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU A2193 " --> pdb=" O ILE A2150 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL A2152 " --> pdb=" O LEU A2193 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N GLU A2195 " --> pdb=" O VAL A2152 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE A2154 " --> pdb=" O GLU A2195 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2116 through 2119 Processing sheet with id=AA7, first strand: chain 'A' and resid 2175 through 2177 removed outlier: 3.549A pdb=" N LEU A2176 " --> pdb=" O LEU A2184 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A2184 " --> pdb=" O LEU A2176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 2357 through 2360 Processing sheet with id=AA9, first strand: chain 'A' and resid 2441 through 2444 removed outlier: 6.206A pdb=" N VAL A2441 " --> pdb=" O PHE A2485 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASP A2487 " --> pdb=" O VAL A2441 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE A2443 " --> pdb=" O ASP A2487 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU A2482 " --> pdb=" O HIS A2530 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL A2532 " --> pdb=" O LEU A2482 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU A2484 " --> pdb=" O VAL A2532 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ALA A2534 " --> pdb=" O LEU A2484 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N CYS A2486 " --> pdb=" O ALA A2534 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE A2414 " --> pdb=" O GLY A2533 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N CYS A2535 " --> pdb=" O ILE A2414 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU A2416 " --> pdb=" O CYS A2535 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLY A2413 " --> pdb=" O ALA A2555 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU A2557 " --> pdb=" O GLY A2413 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE A2415 " --> pdb=" O LEU A2557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 2462 through 2464 removed outlier: 3.727A pdb=" N LYS A2522 " --> pdb=" O LYS A2517 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2696 through 2697 removed outlier: 3.805A 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: 6.375A pdb=" N LYS A2780 " --> pdb=" O CYS A2814 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE A2816 " --> pdb=" O LYS A2780 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A2782 " --> pdb=" O ILE A2816 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ASP A2818 " --> pdb=" O VAL A2782 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N MET A2757 " --> pdb=" O ASN A2915 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N MET A2917 " --> pdb=" O MET A2757 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ILE A2759 " --> pdb=" O MET A2917 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3427 through 3430 removed outlier: 6.035A pdb=" N VAL A3450 " --> pdb=" O PHE A3495 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N HIS A3497 " --> pdb=" O VAL A3450 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE A3452 " --> pdb=" O HIS A3497 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL A3404 " --> pdb=" O ARG A3514 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL A3516 " --> pdb=" O VAL A3404 " (cutoff:3.500A) removed outlier: 6.330A 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 removed outlier: 3.530A pdb=" N HIS A3484 " --> pdb=" O ILE A3481 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3811 through 3815 removed outlier: 5.931A pdb=" N LYS A3812 " --> pdb=" O LEU A3840 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLN A3842 " --> pdb=" O LYS A3812 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE A3814 " --> pdb=" O GLN A3842 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE A3839 " --> pdb=" O PHE A3874 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N THR A3876 " --> pdb=" O ILE A3839 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A3841 " --> pdb=" O THR A3876 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N HIS A3878 " --> pdb=" O LEU A3841 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A3790 " --> pdb=" O CYS A3877 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N TYR A3785 " --> pdb=" O ASP A3893 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL A3895 " --> pdb=" O TYR A3785 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THR A3787 " --> pdb=" O VAL A3895 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 4020 through 4021 removed outlier: 3.572A pdb=" N LEU A4021 " --> pdb=" O ILE A4029 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 161 through 163 removed outlier: 3.571A pdb=" N ALA C 181 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA C 192 " --> pdb=" O ALA C 181 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 201 through 208 removed outlier: 6.825A pdb=" N ALA C 225 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N MET C 204 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL C 223 " --> pdb=" O MET C 204 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL C 206 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL C 221 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG C 247 " --> pdb=" O VAL C 233 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 236 through 237 removed outlier: 3.543A pdb=" N LYS C 242 " --> pdb=" O VAL C 237 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 256 through 263 removed outlier: 3.790A pdb=" N ALA C 258 " --> pdb=" O CYS C 273 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 281 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS C 291 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASP C 283 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 6.733A 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: 6.889A pdb=" N GLY C 313 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE C 303 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE C 311 " --> pdb=" O ILE C 303 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL C 305 " --> pdb=" O TYR C 309 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU C 321 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN C 328 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 340 through 345 removed outlier: 6.647A pdb=" N ALA C 376 " --> pdb=" O GLU C 341 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL C 343 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL C 374 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N PHE C 345 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N TYR C 372 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 377 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU C 411 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLU C 386 " --> pdb=" O CYS C 409 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N CYS C 409 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 420 through 426 removed outlier: 4.657A pdb=" N SER C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS C 451 " --> pdb=" O CYS C 441 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 461 through 465 1137 hydrogen bonds defined for protein. 3348 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: 8.28 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6645 1.34 - 1.46: 5030 1.46 - 1.58: 9417 1.58 - 1.70: 11 1.70 - 1.82: 146 Bond restraints: 21249 Sorted by residual: bond pdb=" C4 ADP A4102 " pdb=" C5 ADP A4102 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.66e+00 bond pdb=" CG1 ILE A1936 " pdb=" CD1 ILE A1936 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.63e+00 bond pdb=" CB GLU A3820 " pdb=" CG GLU A3820 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.52e+00 bond pdb=" CB GLU A4040 " pdb=" CG GLU A4040 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.48e+00 bond pdb=" CB GLN A4035 " pdb=" CG GLN A4035 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.38e+00 ... (remaining 21244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 28449 2.25 - 4.51: 325 4.51 - 6.76: 57 6.76 - 9.01: 4 9.01 - 11.27: 4 Bond angle restraints: 28839 Sorted by residual: angle pdb=" C LEU A3945 " pdb=" N VAL A3946 " pdb=" CA VAL A3946 " ideal model delta sigma weight residual 120.33 124.05 -3.72 8.00e-01 1.56e+00 2.16e+01 angle pdb=" CB MET A2831 " pdb=" CG MET A2831 " pdb=" SD MET A2831 " ideal model delta sigma weight residual 112.70 123.97 -11.27 3.00e+00 1.11e-01 1.41e+01 angle pdb=" C ASP C 316 " pdb=" N THR C 317 " pdb=" CA THR C 317 " ideal model delta sigma weight residual 122.08 127.35 -5.27 1.47e+00 4.63e-01 1.28e+01 angle pdb=" CB MET A2980 " pdb=" CG MET A2980 " pdb=" SD MET A2980 " ideal model delta sigma weight residual 112.70 122.05 -9.35 3.00e+00 1.11e-01 9.71e+00 angle pdb=" N VAL A2984 " pdb=" CA VAL A2984 " pdb=" C VAL A2984 " ideal model delta sigma weight residual 111.91 109.36 2.55 8.90e-01 1.26e+00 8.21e+00 ... (remaining 28834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.77: 12094 27.77 - 55.55: 510 55.55 - 83.32: 36 83.32 - 111.09: 4 111.09 - 138.86: 2 Dihedral angle restraints: 12646 sinusoidal: 4901 harmonic: 7745 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 78.86 -138.86 1 2.00e+01 2.50e-03 4.21e+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 -147.21 -121.24 1 2.00e+01 2.50e-03 3.64e+01 dihedral pdb=" CA TYR A3333 " pdb=" C TYR A3333 " pdb=" N PHE A3334 " pdb=" CA PHE A3334 " ideal model delta harmonic sigma weight residual -180.00 -160.74 -19.26 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 12643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2542 0.047 - 0.095: 600 0.095 - 0.142: 175 0.142 - 0.190: 8 0.190 - 0.237: 1 Chirality restraints: 3326 Sorted by residual: chirality pdb=" CB ILE A2531 " pdb=" CA ILE A2531 " pdb=" CG1 ILE A2531 " pdb=" CG2 ILE A2531 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB ILE A2689 " pdb=" CA ILE A2689 " pdb=" CG1 ILE A2689 " pdb=" CG2 ILE A2689 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CA THR C 317 " pdb=" N THR C 317 " pdb=" C THR C 317 " pdb=" CB THR C 317 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.04e-01 ... (remaining 3323 not shown) Planarity restraints: 3611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A2618 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO A2619 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A2619 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A2619 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A4024 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO A4025 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A4025 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A4025 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A3459 " -0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A3460 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A3460 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A3460 " -0.025 5.00e-02 4.00e+02 ... (remaining 3608 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 164 2.58 - 3.16: 16014 3.16 - 3.74: 33107 3.74 - 4.32: 43562 4.32 - 4.90: 74183 Nonbonded interactions: 167030 Sorted by model distance: nonbonded pdb=" O2B ATP A4104 " pdb="MG MG A4106 " model vdw 1.999 2.170 nonbonded pdb=" O2G ATP A4104 " pdb="MG MG A4106 " model vdw 1.999 2.170 nonbonded pdb=" O3B ADP A4103 " pdb="MG MG A4107 " model vdw 2.017 2.170 nonbonded pdb=" O1B ADP A4102 " pdb="MG MG A4105 " model vdw 2.028 2.170 nonbonded pdb=" OG SER C 226 " pdb=" OD1 ASP C 228 " model vdw 2.228 3.040 ... (remaining 167025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.760 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 24.710 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 0.050 21249 Z= 0.148 Angle : 0.622 11.267 28839 Z= 0.316 Chirality : 0.044 0.237 3326 Planarity : 0.004 0.056 3611 Dihedral : 14.602 138.863 7610 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.15), residues: 2608 helix: 0.76 (0.13), residues: 1372 sheet: -0.01 (0.30), residues: 339 loop : -1.24 (0.18), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3543 TYR 0.024 0.001 TYR A1828 PHE 0.025 0.002 PHE A1623 TRP 0.018 0.001 TRP A2084 HIS 0.005 0.001 HIS A2553 Details of bonding type rmsd covalent geometry : bond 0.00332 (21249) covalent geometry : angle 0.62181 (28839) hydrogen bonds : bond 0.13740 ( 1137) hydrogen bonds : angle 6.00190 ( 3348) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1745 ASN cc_start: 0.7693 (m110) cc_final: 0.7442 (p0) REVERT: A 1867 GLN cc_start: 0.8011 (tp40) cc_final: 0.7610 (tp40) REVERT: A 2049 MET cc_start: 0.5739 (mmt) cc_final: 0.5437 (mmt) REVERT: A 2198 ASN cc_start: 0.7893 (t0) cc_final: 0.7456 (p0) REVERT: A 2428 MET cc_start: 0.8177 (tpt) cc_final: 0.7857 (tpt) REVERT: A 2520 GLU cc_start: 0.7637 (pm20) cc_final: 0.7346 (pm20) REVERT: A 2616 LEU cc_start: 0.8903 (tt) cc_final: 0.8610 (mt) REVERT: A 3480 GLU cc_start: 0.8316 (tt0) cc_final: 0.7411 (mp0) REVERT: C 370 MET cc_start: 0.6736 (mmt) cc_final: 0.6358 (mmt) REVERT: C 465 ASP cc_start: 0.7836 (t70) cc_final: 0.7529 (t70) REVERT: C 493 MET cc_start: 0.7068 (ttt) cc_final: 0.6846 (mtm) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.1486 time to fit residues: 60.1921 Evaluate side-chains 197 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.0670 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1811 GLN A2521 ASN A3784 ASN C 263 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.151561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.133103 restraints weight = 33560.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.132224 restraints weight = 45937.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132862 restraints weight = 44578.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132969 restraints weight = 32936.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.133080 restraints weight = 29756.044| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21249 Z= 0.103 Angle : 0.492 7.234 28839 Z= 0.250 Chirality : 0.040 0.167 3326 Planarity : 0.003 0.043 3611 Dihedral : 6.225 136.097 2878 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.68 % Allowed : 6.49 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.16), residues: 2608 helix: 1.74 (0.14), residues: 1377 sheet: -0.12 (0.29), residues: 341 loop : -0.99 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3894 TYR 0.024 0.001 TYR A3824 PHE 0.017 0.001 PHE A3016 TRP 0.020 0.001 TRP A2301 HIS 0.004 0.001 HIS A2293 Details of bonding type rmsd covalent geometry : bond 0.00223 (21249) covalent geometry : angle 0.49158 (28839) hydrogen bonds : bond 0.03521 ( 1137) hydrogen bonds : angle 4.39646 ( 3348) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 226 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: C 386 GLU cc_start: 0.5074 (pt0) cc_final: 0.4792 (pt0) REVERT: C 408 ARG cc_start: 0.5835 (mtt90) cc_final: 0.5544 (mtm-85) outliers start: 15 outliers final: 9 residues processed: 232 average time/residue: 0.1452 time to fit residues: 54.2295 Evaluate side-chains 203 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 194 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2865 LEU Chi-restraints excluded: chain A residue 2919 ASP Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3525 ILE Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3848 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 166 optimal weight: 9.9990 chunk 242 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 136 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2521 ASN A3685 GLN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.150264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.128122 restraints weight = 33502.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.127714 restraints weight = 43020.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.128778 restraints weight = 37608.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.128722 restraints weight = 28334.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.128883 restraints weight = 27175.644| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 21249 Z= 0.173 Angle : 0.534 6.116 28839 Z= 0.274 Chirality : 0.042 0.157 3326 Planarity : 0.003 0.042 3611 Dihedral : 6.415 136.415 2878 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.31 % Allowed : 9.73 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.17), residues: 2608 helix: 1.84 (0.14), residues: 1386 sheet: -0.35 (0.29), residues: 343 loop : -0.90 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2044 TYR 0.025 0.002 TYR A3824 PHE 0.024 0.002 PHE A3629 TRP 0.018 0.001 TRP A2301 HIS 0.004 0.001 HIS C 416 Details of bonding type rmsd covalent geometry : bond 0.00414 (21249) covalent geometry : angle 0.53405 (28839) hydrogen bonds : bond 0.03644 ( 1137) hydrogen bonds : angle 4.21885 ( 3348) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 224 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1987 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7402 (t80) REVERT: A 2443 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.6971 (tt) REVERT: C 386 GLU cc_start: 0.5153 (pt0) cc_final: 0.4922 (pt0) REVERT: C 408 ARG cc_start: 0.5972 (mtt90) cc_final: 0.5674 (mtm-85) outliers start: 29 outliers final: 17 residues processed: 238 average time/residue: 0.1456 time to fit residues: 55.5080 Evaluate side-chains 218 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1987 PHE Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2443 ILE Chi-restraints excluded: chain A residue 2465 VAL Chi-restraints excluded: chain A residue 2521 ASN Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2865 LEU Chi-restraints excluded: chain A residue 2919 ASP Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 3525 ILE Chi-restraints excluded: chain A residue 3719 VAL Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3848 LEU Chi-restraints excluded: chain A residue 3855 LEU Chi-restraints excluded: chain A residue 3900 ILE Chi-restraints excluded: chain A residue 3943 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 174 optimal weight: 0.0060 chunk 106 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1707 HIS A1866 GLN ** A2293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2521 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.152702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.131893 restraints weight = 33344.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.131353 restraints weight = 41277.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.132172 restraints weight = 36513.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.131922 restraints weight = 31188.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.131961 restraints weight = 29184.182| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21249 Z= 0.101 Angle : 0.476 6.569 28839 Z= 0.243 Chirality : 0.040 0.144 3326 Planarity : 0.003 0.041 3611 Dihedral : 6.226 135.204 2878 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.22 % Allowed : 11.22 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.17), residues: 2608 helix: 2.18 (0.14), residues: 1376 sheet: -0.23 (0.30), residues: 322 loop : -0.82 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 364 TYR 0.024 0.001 TYR A3824 PHE 0.019 0.001 PHE C 470 TRP 0.031 0.001 TRP A2301 HIS 0.002 0.001 HIS A3856 Details of bonding type rmsd covalent geometry : bond 0.00226 (21249) covalent geometry : angle 0.47588 (28839) hydrogen bonds : bond 0.03173 ( 1137) hydrogen bonds : angle 4.01282 ( 3348) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1987 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.7335 (t80) REVERT: C 386 GLU cc_start: 0.5044 (pt0) cc_final: 0.4752 (pt0) REVERT: C 408 ARG cc_start: 0.5902 (mtt90) cc_final: 0.5632 (mtm-85) outliers start: 27 outliers final: 17 residues processed: 222 average time/residue: 0.1416 time to fit residues: 50.8135 Evaluate side-chains 210 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1987 PHE Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2531 ILE Chi-restraints excluded: chain A residue 2546 MET Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2865 LEU Chi-restraints excluded: chain A residue 2919 ASP Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3362 VAL Chi-restraints excluded: chain A residue 3525 ILE Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3839 ILE Chi-restraints excluded: chain A residue 3848 LEU Chi-restraints excluded: chain A residue 3855 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 114 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 225 optimal weight: 0.9980 chunk 229 optimal weight: 0.0370 chunk 109 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 chunk 130 optimal weight: 10.0000 chunk 257 optimal weight: 0.5980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.153472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.133120 restraints weight = 33182.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.132786 restraints weight = 39803.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.133801 restraints weight = 37385.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.133586 restraints weight = 28301.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.133774 restraints weight = 27885.858| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21249 Z= 0.097 Angle : 0.470 7.807 28839 Z= 0.238 Chirality : 0.039 0.150 3326 Planarity : 0.003 0.040 3611 Dihedral : 6.119 134.436 2878 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.58 % Allowed : 11.63 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.17), residues: 2608 helix: 2.35 (0.14), residues: 1378 sheet: -0.20 (0.30), residues: 322 loop : -0.75 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 364 TYR 0.023 0.001 TYR A3824 PHE 0.027 0.001 PHE A3016 TRP 0.028 0.001 TRP A2301 HIS 0.003 0.001 HIS A3856 Details of bonding type rmsd covalent geometry : bond 0.00216 (21249) covalent geometry : angle 0.47034 (28839) hydrogen bonds : bond 0.02995 ( 1137) hydrogen bonds : angle 3.85959 ( 3348) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 213 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1678 MET cc_start: 0.7535 (mmp) cc_final: 0.7278 (mmt) REVERT: A 1987 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.7237 (t80) REVERT: C 386 GLU cc_start: 0.5031 (pt0) cc_final: 0.4748 (pt0) REVERT: C 408 ARG cc_start: 0.5873 (mtt90) cc_final: 0.5602 (mtm-85) outliers start: 35 outliers final: 22 residues processed: 233 average time/residue: 0.1411 time to fit residues: 54.0921 Evaluate side-chains 214 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1987 PHE Chi-restraints excluded: chain A residue 2339 ILE Chi-restraints excluded: chain A residue 2531 ILE Chi-restraints excluded: chain A residue 2546 MET Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2865 LEU Chi-restraints excluded: chain A residue 2919 ASP Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3362 VAL Chi-restraints excluded: chain A residue 3491 ASP Chi-restraints excluded: chain A residue 3525 ILE Chi-restraints excluded: chain A residue 3536 GLU Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3839 ILE Chi-restraints excluded: chain A residue 3848 LEU Chi-restraints excluded: chain A residue 3855 LEU Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 276 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 191 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 186 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 217 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 170 optimal weight: 0.0170 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3596 ASN A3975 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.153433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.132181 restraints weight = 33309.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.131629 restraints weight = 39892.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.132529 restraints weight = 36813.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.132606 restraints weight = 28650.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.132602 restraints weight = 28588.882| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21249 Z= 0.103 Angle : 0.478 7.322 28839 Z= 0.241 Chirality : 0.039 0.149 3326 Planarity : 0.003 0.039 3611 Dihedral : 6.080 133.955 2878 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.62 % Allowed : 12.53 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.17), residues: 2608 helix: 2.41 (0.14), residues: 1376 sheet: -0.17 (0.30), residues: 322 loop : -0.73 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 145 TYR 0.022 0.001 TYR A3824 PHE 0.022 0.001 PHE C 470 TRP 0.027 0.001 TRP A2301 HIS 0.003 0.001 HIS A2274 Details of bonding type rmsd covalent geometry : bond 0.00232 (21249) covalent geometry : angle 0.47787 (28839) hydrogen bonds : bond 0.02984 ( 1137) hydrogen bonds : angle 3.81618 ( 3348) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1987 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.7232 (t80) REVERT: A 2011 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6908 (tm-30) outliers start: 36 outliers final: 24 residues processed: 228 average time/residue: 0.1486 time to fit residues: 54.7260 Evaluate side-chains 217 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1987 PHE Chi-restraints excluded: chain A residue 1994 VAL Chi-restraints excluded: chain A residue 2465 VAL Chi-restraints excluded: chain A residue 2531 ILE Chi-restraints excluded: chain A residue 2546 MET Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2919 ASP Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3362 VAL Chi-restraints excluded: chain A residue 3491 ASP Chi-restraints excluded: chain A residue 3525 ILE Chi-restraints excluded: chain A residue 3536 GLU Chi-restraints excluded: chain A residue 3596 ASN Chi-restraints excluded: chain A residue 3719 VAL Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3753 THR Chi-restraints excluded: chain A residue 3839 ILE Chi-restraints excluded: chain A residue 3848 LEU Chi-restraints excluded: chain A residue 3855 LEU Chi-restraints excluded: chain A residue 3923 VAL Chi-restraints excluded: chain C residue 276 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 201 optimal weight: 7.9990 chunk 219 optimal weight: 2.9990 chunk 181 optimal weight: 20.0000 chunk 221 optimal weight: 3.9990 chunk 258 optimal weight: 0.9990 chunk 186 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 234 optimal weight: 8.9990 chunk 225 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3453 GLN A3975 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.151768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.130561 restraints weight = 33432.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.130391 restraints weight = 38567.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.131294 restraints weight = 36172.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.131466 restraints weight = 28241.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.131513 restraints weight = 27651.322| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21249 Z= 0.125 Angle : 0.497 8.880 28839 Z= 0.251 Chirality : 0.040 0.152 3326 Planarity : 0.003 0.040 3611 Dihedral : 6.143 133.802 2878 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.58 % Allowed : 13.25 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.17), residues: 2608 helix: 2.37 (0.14), residues: 1377 sheet: -0.24 (0.29), residues: 324 loop : -0.71 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2044 TYR 0.023 0.001 TYR A3824 PHE 0.020 0.001 PHE A3016 TRP 0.027 0.001 TRP A2301 HIS 0.003 0.001 HIS A3484 Details of bonding type rmsd covalent geometry : bond 0.00291 (21249) covalent geometry : angle 0.49660 (28839) hydrogen bonds : bond 0.03119 ( 1137) hydrogen bonds : angle 3.83178 ( 3348) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1834 LEU cc_start: 0.6491 (OUTLIER) cc_final: 0.6050 (mp) REVERT: A 3377 MET cc_start: 0.7596 (mmp) cc_final: 0.7049 (mmm) REVERT: C 370 MET cc_start: 0.6965 (mmt) cc_final: 0.6360 (mmt) REVERT: C 408 ARG cc_start: 0.5907 (mtt180) cc_final: 0.5616 (mtm-85) outliers start: 35 outliers final: 26 residues processed: 216 average time/residue: 0.1389 time to fit residues: 48.6828 Evaluate side-chains 219 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1834 LEU Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1994 VAL Chi-restraints excluded: chain A residue 2339 ILE Chi-restraints excluded: chain A residue 2465 VAL Chi-restraints excluded: chain A residue 2531 ILE Chi-restraints excluded: chain A residue 2546 MET Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2919 ASP Chi-restraints excluded: chain A residue 2948 VAL Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 3362 VAL Chi-restraints excluded: chain A residue 3525 ILE Chi-restraints excluded: chain A residue 3536 GLU Chi-restraints excluded: chain A residue 3596 ASN Chi-restraints excluded: chain A residue 3719 VAL Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3753 THR Chi-restraints excluded: chain A residue 3839 ILE Chi-restraints excluded: chain A residue 3848 LEU Chi-restraints excluded: chain A residue 3855 LEU Chi-restraints excluded: chain A residue 3923 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 276 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 41 optimal weight: 0.0970 chunk 155 optimal weight: 5.9990 chunk 104 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 4 optimal weight: 30.0000 chunk 259 optimal weight: 0.0060 chunk 69 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3596 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.151856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.131963 restraints weight = 33259.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.131056 restraints weight = 42614.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.132329 restraints weight = 38604.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.132099 restraints weight = 29708.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.132319 restraints weight = 30266.573| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21249 Z= 0.117 Angle : 0.495 7.726 28839 Z= 0.250 Chirality : 0.040 0.168 3326 Planarity : 0.003 0.043 3611 Dihedral : 6.117 133.599 2878 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.40 % Allowed : 13.70 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.17), residues: 2608 helix: 2.41 (0.14), residues: 1377 sheet: -0.18 (0.30), residues: 314 loop : -0.68 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2044 TYR 0.023 0.001 TYR A3824 PHE 0.023 0.001 PHE C 470 TRP 0.028 0.001 TRP A2301 HIS 0.003 0.001 HIS A3484 Details of bonding type rmsd covalent geometry : bond 0.00271 (21249) covalent geometry : angle 0.49491 (28839) hydrogen bonds : bond 0.03066 ( 1137) hydrogen bonds : angle 3.80416 ( 3348) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1834 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.6074 (mp) REVERT: A 3377 MET cc_start: 0.7531 (mmp) cc_final: 0.6975 (mmm) REVERT: C 370 MET cc_start: 0.6942 (mmt) cc_final: 0.6350 (mmt) REVERT: C 408 ARG cc_start: 0.5869 (mtt180) cc_final: 0.5609 (mtm-85) outliers start: 31 outliers final: 26 residues processed: 213 average time/residue: 0.1452 time to fit residues: 49.7006 Evaluate side-chains 217 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1834 LEU Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1994 VAL Chi-restraints excluded: chain A residue 2339 ILE Chi-restraints excluded: chain A residue 2465 VAL Chi-restraints excluded: chain A residue 2531 ILE Chi-restraints excluded: chain A residue 2546 MET Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2919 ASP Chi-restraints excluded: chain A residue 2948 VAL Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 3362 VAL Chi-restraints excluded: chain A residue 3465 LEU Chi-restraints excluded: chain A residue 3525 ILE Chi-restraints excluded: chain A residue 3536 GLU Chi-restraints excluded: chain A residue 3596 ASN Chi-restraints excluded: chain A residue 3719 VAL Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3753 THR Chi-restraints excluded: chain A residue 3839 ILE Chi-restraints excluded: chain A residue 3855 LEU Chi-restraints excluded: chain A residue 3923 VAL Chi-restraints excluded: chain C residue 273 CYS Chi-restraints excluded: chain C residue 276 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 110 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 254 optimal weight: 0.2980 chunk 136 optimal weight: 8.9990 chunk 187 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 154 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 144 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3596 ASN A3975 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.153159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.132370 restraints weight = 33211.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.132225 restraints weight = 38351.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.133561 restraints weight = 34980.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.133149 restraints weight = 26434.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.133429 restraints weight = 26708.348| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21249 Z= 0.098 Angle : 0.483 7.724 28839 Z= 0.242 Chirality : 0.039 0.159 3326 Planarity : 0.003 0.048 3611 Dihedral : 6.034 133.339 2878 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.35 % Allowed : 14.02 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.17), residues: 2608 helix: 2.49 (0.14), residues: 1377 sheet: -0.14 (0.30), residues: 324 loop : -0.65 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2044 TYR 0.023 0.001 TYR A3824 PHE 0.022 0.001 PHE A3016 TRP 0.028 0.001 TRP A2301 HIS 0.003 0.001 HIS A2274 Details of bonding type rmsd covalent geometry : bond 0.00219 (21249) covalent geometry : angle 0.48268 (28839) hydrogen bonds : bond 0.02942 ( 1137) hydrogen bonds : angle 3.75227 ( 3348) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3377 MET cc_start: 0.7551 (mmp) cc_final: 0.6995 (mmm) REVERT: A 3722 MET cc_start: 0.6761 (mmm) cc_final: 0.6018 (mtp) REVERT: C 370 MET cc_start: 0.6874 (mmt) cc_final: 0.6301 (mmt) REVERT: C 408 ARG cc_start: 0.5893 (mtt180) cc_final: 0.5620 (mtm-85) outliers start: 30 outliers final: 25 residues processed: 215 average time/residue: 0.1412 time to fit residues: 49.2169 Evaluate side-chains 214 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1994 VAL Chi-restraints excluded: chain A residue 2339 ILE Chi-restraints excluded: chain A residue 2465 VAL Chi-restraints excluded: chain A residue 2531 ILE Chi-restraints excluded: chain A residue 2546 MET Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2919 ASP Chi-restraints excluded: chain A residue 2948 VAL Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 3330 TYR Chi-restraints excluded: chain A residue 3362 VAL Chi-restraints excluded: chain A residue 3525 ILE Chi-restraints excluded: chain A residue 3536 GLU Chi-restraints excluded: chain A residue 3596 ASN Chi-restraints excluded: chain A residue 3719 VAL Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3753 THR Chi-restraints excluded: chain A residue 3839 ILE Chi-restraints excluded: chain A residue 3855 LEU Chi-restraints excluded: chain A residue 3923 VAL Chi-restraints excluded: chain C residue 276 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 240 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 101 optimal weight: 0.0030 chunk 182 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 223 optimal weight: 2.9990 chunk 237 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1866 GLN ** A2293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3596 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.150555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.132058 restraints weight = 33406.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.131499 restraints weight = 44268.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.132479 restraints weight = 40013.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.132007 restraints weight = 31157.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.132338 restraints weight = 30436.528| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21249 Z= 0.154 Angle : 0.534 8.219 28839 Z= 0.270 Chirality : 0.041 0.206 3326 Planarity : 0.003 0.050 3611 Dihedral : 6.206 133.112 2878 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.40 % Allowed : 14.29 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.17), residues: 2608 helix: 2.33 (0.14), residues: 1376 sheet: -0.26 (0.30), residues: 324 loop : -0.66 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 364 TYR 0.024 0.001 TYR A1643 PHE 0.016 0.001 PHE A3518 TRP 0.028 0.001 TRP A2301 HIS 0.003 0.001 HIS C 416 Details of bonding type rmsd covalent geometry : bond 0.00365 (21249) covalent geometry : angle 0.53445 (28839) hydrogen bonds : bond 0.03266 ( 1137) hydrogen bonds : angle 3.87470 ( 3348) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2356 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.6290 (t80) REVERT: A 2371 PHE cc_start: 0.8027 (m-80) cc_final: 0.7363 (m-80) REVERT: A 2839 ASP cc_start: 0.7357 (t70) cc_final: 0.6801 (t0) REVERT: A 3377 MET cc_start: 0.7556 (mmp) cc_final: 0.7007 (mmm) REVERT: C 370 MET cc_start: 0.7060 (mmt) cc_final: 0.6409 (mmt) outliers start: 31 outliers final: 24 residues processed: 214 average time/residue: 0.1470 time to fit residues: 51.1145 Evaluate side-chains 218 residues out of total 2417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1921 MET Chi-restraints excluded: chain A residue 1953 LEU Chi-restraints excluded: chain A residue 1994 VAL Chi-restraints excluded: chain A residue 2339 ILE Chi-restraints excluded: chain A residue 2356 TYR Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2465 VAL Chi-restraints excluded: chain A residue 2531 ILE Chi-restraints excluded: chain A residue 2546 MET Chi-restraints excluded: chain A residue 2823 LEU Chi-restraints excluded: chain A residue 2919 ASP Chi-restraints excluded: chain A residue 2948 VAL Chi-restraints excluded: chain A residue 2952 LEU Chi-restraints excluded: chain A residue 3362 VAL Chi-restraints excluded: chain A residue 3465 LEU Chi-restraints excluded: chain A residue 3525 ILE Chi-restraints excluded: chain A residue 3536 GLU Chi-restraints excluded: chain A residue 3719 VAL Chi-restraints excluded: chain A residue 3720 LEU Chi-restraints excluded: chain A residue 3725 VAL Chi-restraints excluded: chain A residue 3839 ILE Chi-restraints excluded: chain A residue 3855 LEU Chi-restraints excluded: chain A residue 3923 VAL Chi-restraints excluded: chain C residue 276 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 249 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 254 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 54 optimal weight: 0.0570 chunk 44 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2536 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.152199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.131397 restraints weight = 33325.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.130967 restraints weight = 39751.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.131715 restraints weight = 38063.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.131782 restraints weight = 30078.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.131957 restraints weight = 28429.786| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21249 Z= 0.108 Angle : 0.513 11.066 28839 Z= 0.256 Chirality : 0.040 0.219 3326 Planarity : 0.003 0.053 3611 Dihedral : 6.079 132.803 2878 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.13 % Allowed : 14.92 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.17), residues: 2608 helix: 2.40 (0.14), residues: 1378 sheet: -0.18 (0.30), residues: 323 loop : -0.63 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 364 TYR 0.023 0.001 TYR A3824 PHE 0.022 0.001 PHE A3016 TRP 0.027 0.001 TRP A2301 HIS 0.003 0.001 HIS A2274 Details of bonding type rmsd covalent geometry : bond 0.00247 (21249) covalent geometry : angle 0.51333 (28839) hydrogen bonds : bond 0.03019 ( 1137) hydrogen bonds : angle 3.80534 ( 3348) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2922.18 seconds wall clock time: 51 minutes 54.57 seconds (3114.57 seconds total)