Starting phenix.real_space_refine on Thu Sep 18 16:45:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dkj_46959/09_2025/9dkj_46959.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dkj_46959/09_2025/9dkj_46959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dkj_46959/09_2025/9dkj_46959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dkj_46959/09_2025/9dkj_46959.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dkj_46959/09_2025/9dkj_46959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dkj_46959/09_2025/9dkj_46959.map" } resolution = 2.8 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= 0.042 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 2 5.21 5 S 82 5.16 5 C 11570 2.51 5 N 3012 2.21 5 O 3400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s 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: 18075 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 17961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2291, 17961 Classifications: {'peptide': 2291} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PTRANS': 63, 'TRANS': 2227} Chain breaks: 12 Unresolved non-hydrogen bonds: 567 Unresolved non-hydrogen angles: 702 Unresolved non-hydrogen dihedrals: 465 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 16, 'PHE:plan': 9, 'GLU:plan': 26, 'TYR:plan': 2, 'ARG:plan': 10, 'ASP:plan': 7, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 324 Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 114 Unusual residues: {' MG': 2, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 3.42, per 1000 atoms: 0.19 Number of scatterers: 18075 At special positions: 0 Unit cell: (97.79, 138.684, 168.91, 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 82 16.00 P 9 15.00 Mg 2 11.99 O 3400 8.00 N 3012 7.00 C 11570 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 697.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4360 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 15 sheets defined 63.6% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 1467 through 1470 removed outlier: 3.505A pdb=" N PHE A1470 " --> pdb=" O ILE A1467 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1467 through 1470' Processing helix chain 'A' and resid 1471 through 1495 removed outlier: 3.675A pdb=" N LEU A1495 " --> pdb=" O ARG A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1511 through 1521 removed outlier: 3.590A pdb=" N ILE A1519 " --> pdb=" O SER A1515 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1531 Processing helix chain 'A' and resid 1532 through 1533 No H-bonds generated for 'chain 'A' and resid 1532 through 1533' Processing helix chain 'A' and resid 1534 through 1540 Processing helix chain 'A' and resid 1541 through 1551 Processing helix chain 'A' and resid 1557 through 1560 removed outlier: 3.644A pdb=" N LYS A1560 " --> pdb=" O GLN A1557 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1557 through 1560' Processing helix chain 'A' and resid 1561 through 1566 Processing helix chain 'A' and resid 1603 through 1631 removed outlier: 3.796A pdb=" N ILE A1610 " --> pdb=" O GLU A1606 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS A1616 " --> pdb=" O ASP A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1639 removed outlier: 3.680A pdb=" N VAL A1638 " --> pdb=" O ASP A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1665 Processing helix chain 'A' and resid 1669 through 1689 Processing helix chain 'A' and resid 1691 through 1717 removed outlier: 3.978A pdb=" N VAL A1703 " --> pdb=" O GLU A1699 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU A1704 " --> pdb=" O ALA A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1730 removed outlier: 3.792A pdb=" N LYS A1730 " --> pdb=" O LEU A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1742 through 1745 removed outlier: 3.672A pdb=" N ASN A1745 " --> pdb=" O ASP A1742 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1742 through 1745' Processing helix chain 'A' and resid 1772 through 1788 Processing helix chain 'A' and resid 1801 through 1813 Processing helix chain 'A' and resid 1827 through 1842 Processing helix chain 'A' and resid 1850 through 1853 removed outlier: 3.532A pdb=" N LEU A1853 " --> pdb=" O PHE A1850 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1850 through 1853' Processing helix chain 'A' and resid 1854 through 1861 Processing helix chain 'A' and resid 1861 through 1875 Processing helix chain 'A' and resid 1909 through 1914 Processing helix chain 'A' and resid 1925 through 1938 Processing helix chain 'A' and resid 1941 through 1960 Processing helix chain 'A' and resid 1969 through 1981 removed outlier: 3.781A pdb=" N SER A1981 " --> pdb=" O LEU A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1983 through 1988 Processing helix chain 'A' and resid 1990 through 2002 Processing helix chain 'A' and resid 2003 through 2006 Processing helix chain 'A' and resid 2007 through 2022 removed outlier: 3.605A pdb=" N LEU A2012 " --> pdb=" O ASP A2008 " (cutoff:3.500A) Processing helix chain 'A' and resid 2031 through 2046 Processing helix chain 'A' and resid 2050 through 2064 Processing helix chain 'A' and resid 2079 through 2096 Processing helix chain 'A' and resid 2110 through 2115 Processing helix chain 'A' and resid 2128 through 2140 Processing helix chain 'A' and resid 2159 through 2164 Processing helix chain 'A' and resid 2166 through 2171 Processing helix chain 'A' and resid 2203 through 2208 Processing helix chain 'A' and resid 2221 through 2236 Processing helix chain 'A' and resid 2245 through 2257 Processing helix chain 'A' and resid 2258 through 2269 removed outlier: 4.074A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A2265 " --> pdb=" O SER A2261 " (cutoff:3.500A) Processing helix chain 'A' and resid 2270 through 2272 No H-bonds generated for 'chain 'A' and resid 2270 through 2272' Processing helix chain 'A' and resid 2283 through 2297 Processing helix chain 'A' and resid 2306 through 2327 Processing helix chain 'A' and resid 2331 through 2346 Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2423 through 2434 removed outlier: 3.944A pdb=" N ASN A2434 " --> pdb=" O ASN A2430 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2458 removed outlier: 3.585A pdb=" N ILE A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2513 Processing helix chain 'A' and resid 2547 through 2552 Processing helix chain 'A' and resid 2563 through 2580 removed outlier: 4.294A pdb=" N ILE A2573 " --> pdb=" O GLN A2569 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR A2574 " --> pdb=" O ILE A2570 " (cutoff:3.500A) Processing helix chain 'A' and resid 2582 through 2587 removed outlier: 5.765A pdb=" N SER A2587 " --> pdb=" O GLU A2584 " (cutoff:3.500A) Processing helix chain 'A' and resid 2588 through 2607 Processing helix chain 'A' and resid 2618 through 2635 removed outlier: 3.811A pdb=" N LEU A2622 " --> pdb=" O SER A2618 " (cutoff:3.500A) Processing helix chain 'A' and resid 2640 through 2657 Processing helix chain 'A' and resid 2662 through 2681 Processing helix chain 'A' and resid 2708 through 2727 Processing helix chain 'A' and resid 2735 through 2750 Processing helix chain 'A' and resid 2765 through 2777 Processing helix chain 'A' and resid 2791 through 2809 Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 3.891A pdb=" N LEU A2828 " --> pdb=" O GLU A2824 " (cutoff:3.500A) Processing helix chain 'A' and resid 2846 through 2863 removed outlier: 3.781A pdb=" N ASP A2850 " --> pdb=" O GLY A2846 " (cutoff:3.500A) Processing helix chain 'A' and resid 2869 through 2884 Processing helix chain 'A' and resid 2896 through 2904 Processing helix chain 'A' and resid 2905 through 2911 Processing helix chain 'A' and resid 2921 through 2933 Processing helix chain 'A' and resid 2960 through 2980 removed outlier: 3.907A 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 3334 removed outlier: 4.905A pdb=" N PHE A3301 " --> pdb=" O LYS A3297 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLU A3302 " --> pdb=" O SER A3298 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ILE A3321 " --> pdb=" O SER A3317 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N GLY A3322 " --> pdb=" O GLN A3318 " (cutoff:3.500A) Processing helix chain 'A' and resid 3335 through 3337 No H-bonds generated for 'chain 'A' and resid 3335 through 3337' Processing helix chain 'A' and resid 3338 through 3356 Processing helix chain 'A' and resid 3365 through 3371 Processing helix chain 'A' and resid 3372 through 3383 Processing helix chain 'A' and resid 3387 through 3399 Processing helix chain 'A' and resid 3412 through 3423 removed outlier: 4.452A pdb=" N THR A3416 " --> pdb=" O SER A3412 " (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 3459 through 3461 No H-bonds generated for 'chain 'A' and resid 3459 through 3461' Processing helix chain 'A' and resid 3462 through 3468 Processing helix chain 'A' and resid 3506 through 3512 removed outlier: 3.657A pdb=" N ARG A3512 " --> pdb=" O PHE A3508 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3538 Processing helix chain 'A' and resid 3538 through 3573 Processing helix chain 'A' and resid 3583 through 3605 Processing helix chain 'A' and resid 3607 through 3639 removed outlier: 3.535A pdb=" N PHE A3611 " --> pdb=" O PHE A3607 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ILE A3620 " --> pdb=" O GLU A3616 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ILE A3621 " --> pdb=" O GLU A3617 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE A3638 " --> pdb=" O LYS A3634 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS A3639 " --> pdb=" O PHE A3635 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3659 removed outlier: 3.503A pdb=" N PHE A3649 " --> pdb=" O SER A3645 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A3656 " --> pdb=" O CYS A3652 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N PHE A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A3658 " --> pdb=" O LYS A3654 " (cutoff:3.500A) Processing helix chain 'A' and resid 3670 through 3687 Processing helix chain 'A' and resid 3691 through 3711 removed outlier: 3.825A pdb=" N ASP A3709 " --> pdb=" O LEU A3705 " (cutoff:3.500A) Processing helix chain 'A' and resid 3712 through 3727 Processing helix chain 'A' and resid 3743 through 3753 removed outlier: 4.113A pdb=" N LEU A3747 " --> pdb=" O ASP A3743 " (cutoff:3.500A) Processing helix chain 'A' and resid 3755 through 3767 removed outlier: 4.336A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LYS A3764 " --> pdb=" O LEU A3760 " (cutoff:3.500A) Processing helix chain 'A' and resid 3773 through 3780 Processing helix chain 'A' and resid 3796 through 3807 removed outlier: 3.567A pdb=" N LEU A3800 " --> pdb=" O GLY A3796 " (cutoff:3.500A) Processing helix chain 'A' and resid 3818 through 3836 removed outlier: 3.795A pdb=" N ILE A3834 " --> pdb=" O SER A3830 " (cutoff:3.500A) Processing helix chain 'A' and resid 3844 through 3846 No H-bonds generated for 'chain 'A' and resid 3844 through 3846' Processing helix chain 'A' and resid 3847 through 3861 removed outlier: 3.724A pdb=" N LEU A3855 " --> pdb=" O VAL A3851 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N HIS A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) Processing helix chain 'A' and resid 3885 through 3891 removed outlier: 3.632A pdb=" N ARG A3891 " --> pdb=" O PRO A3887 " (cutoff:3.500A) Processing helix chain 'A' and resid 3902 through 3913 removed outlier: 3.592A pdb=" N SER A3913 " --> pdb=" O ASP A3909 " (cutoff:3.500A) Processing helix chain 'A' and resid 3923 through 3943 Processing helix chain 'A' and resid 3957 through 3975 Processing helix chain 'A' and resid 3981 through 3992 Processing helix chain 'A' and resid 4000 through 4015 Processing helix chain 'A' and resid 4037 through 4052 Processing helix chain 'A' and resid 4057 through 4062 Processing helix chain 'A' and resid 4066 through 4091 removed outlier: 3.739A pdb=" N ILE A4070 " --> pdb=" O PRO A4066 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP A4072 " --> pdb=" O GLU A4068 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR A4073 " --> pdb=" O SER A4069 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A4091 " --> pdb=" O GLN A4087 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1569 through 1574 removed outlier: 9.497A pdb=" N SER A1578 " --> pdb=" O GLU A1594 " (cutoff:3.500A) removed outlier: 10.917A pdb=" N GLU A1594 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N THR A1580 " --> pdb=" O LEU A1592 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1733 through 1736 removed outlier: 3.523A pdb=" N PHE A1748 " --> pdb=" O TYR A1735 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1817 through 1821 removed outlier: 6.300A pdb=" N VAL A1818 " --> pdb=" O CYS A1846 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP A1848 " --> pdb=" O VAL A1818 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE A1820 " --> pdb=" O ASP A1848 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1878 through 1881 removed outlier: 3.542A pdb=" N LEU A1881 " --> pdb=" O GLU A1884 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2098 through 2104 removed outlier: 6.501A pdb=" N ALA A2098 " --> pdb=" O ARG A2149 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N TRP A2151 " --> pdb=" O ALA A2098 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A2100 " --> pdb=" O TRP A2151 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL A2153 " --> pdb=" O VAL A2100 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TYR A2102 " --> pdb=" O VAL A2153 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ASP A2155 " --> pdb=" O TYR A2102 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A2104 " --> pdb=" O ASP A2155 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ARG A2191 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE A2150 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU A2193 " --> pdb=" O ILE A2150 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL A2152 " --> pdb=" O LEU A2193 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLU A2195 " --> pdb=" O VAL A2152 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N PHE A2154 " --> pdb=" O GLU A2195 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA A2069 " --> pdb=" O GLY A2211 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU A2213 " --> pdb=" O ALA A2069 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE A2071 " --> pdb=" O LEU A2213 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2116 through 2118 Processing sheet with id=AA7, first strand: chain 'A' and resid 2175 through 2177 Processing sheet with id=AA8, first strand: chain 'A' and resid 2438 through 2443 removed outlier: 6.419A pdb=" N ILE A2414 " --> pdb=" O GLY A2533 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N CYS A2535 " --> pdb=" O ILE A2414 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU A2416 " --> pdb=" O CYS A2535 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLY A2413 " --> pdb=" O ALA A2555 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU A2557 " --> pdb=" O GLY A2413 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE A2415 " --> pdb=" O LEU A2557 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2462 through 2465 Processing sheet with id=AB1, first strand: chain 'A' and resid 2696 through 2697 removed outlier: 3.655A pdb=" N LYS A2705 " --> pdb=" O SER A2697 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2780 through 2782 removed outlier: 5.628A pdb=" N LYS A2780 " --> pdb=" O CYS A2814 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE A2816 " --> pdb=" O LYS A2780 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL A2782 " --> pdb=" O ILE A2816 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ASP A2818 " --> pdb=" O VAL A2782 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR A2813 " --> pdb=" O HIS A2886 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL A2888 " --> pdb=" O THR A2813 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU A2815 " --> pdb=" O VAL A2888 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR A2890 " --> pdb=" O LEU A2815 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE A2817 " --> pdb=" O THR A2890 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N HIS A2755 " --> pdb=" O ILE A2913 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ASN A2915 " --> pdb=" O HIS A2755 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N MET A2757 " --> pdb=" O ASN A2915 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N MET A2917 " --> pdb=" O MET A2757 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ILE A2759 " --> pdb=" O MET A2917 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3427 through 3430 removed outlier: 6.153A pdb=" N VAL A3427 " --> pdb=" O ILE A3451 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N GLN A3453 " --> pdb=" O VAL A3427 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU A3429 " --> pdb=" O GLN A3453 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL A3450 " --> pdb=" O PHE A3495 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N HIS A3497 " --> pdb=" O VAL A3450 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE A3452 " --> pdb=" O HIS A3497 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A3404 " --> pdb=" O ARG A3514 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL A3516 " --> pdb=" O VAL A3404 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE A3406 " --> pdb=" O VAL A3516 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3471 through 3473 removed outlier: 4.685A pdb=" N VAL A3477 " --> pdb=" O VAL A3488 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3811 through 3815 removed outlier: 6.164A pdb=" N LYS A3812 " --> pdb=" O LEU A3840 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLN A3842 " --> pdb=" O LYS A3812 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE A3814 " --> pdb=" O GLN A3842 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLY A3837 " --> pdb=" O LYS A3872 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N PHE A3874 " --> pdb=" O GLY A3837 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE A3839 " --> pdb=" O PHE A3874 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N THR A3876 " --> pdb=" O ILE A3839 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU A3841 " --> pdb=" O THR A3876 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N HIS A3878 " --> pdb=" O LEU A3841 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER A3790 " --> pdb=" O CYS A3877 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 4020 through 4021 1081 hydrogen bonds defined for protein. 3192 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: 5.16 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5751 1.34 - 1.46: 2761 1.46 - 1.57: 9776 1.57 - 1.69: 15 1.69 - 1.81: 129 Bond restraints: 18432 Sorted by residual: bond pdb=" CG1 ILE A2968 " pdb=" CD1 ILE A2968 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.29e+00 bond pdb=" C THR A2518 " pdb=" N PRO A2519 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.82e+00 bond pdb=" C VAL A3946 " pdb=" N PRO A3947 " ideal model delta sigma weight residual 1.334 1.369 -0.036 2.34e-02 1.83e+03 2.31e+00 bond pdb=" CA VAL A2278 " pdb=" CB VAL A2278 " ideal model delta sigma weight residual 1.542 1.559 -0.017 1.26e-02 6.30e+03 1.85e+00 bond pdb=" CB ASN A2501 " pdb=" CG ASN A2501 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.73e+00 ... (remaining 18427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 24615 2.19 - 4.39: 311 4.39 - 6.58: 52 6.58 - 8.78: 5 8.78 - 10.97: 2 Bond angle restraints: 24985 Sorted by residual: angle pdb=" N GLU A2572 " pdb=" CA GLU A2572 " pdb=" CB GLU A2572 " ideal model delta sigma weight residual 110.22 117.33 -7.11 1.54e+00 4.22e-01 2.13e+01 angle pdb=" C LEU A3945 " pdb=" N VAL A3946 " pdb=" CA VAL A3946 " ideal model delta sigma weight residual 120.33 123.94 -3.61 8.00e-01 1.56e+00 2.03e+01 angle pdb=" N LEU A2491 " pdb=" CA LEU A2491 " pdb=" C LEU A2491 " ideal model delta sigma weight residual 109.81 118.93 -9.12 2.21e+00 2.05e-01 1.70e+01 angle pdb=" CB MET A3345 " pdb=" CG MET A3345 " pdb=" SD MET A3345 " ideal model delta sigma weight residual 112.70 101.73 10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CA TRP A2084 " pdb=" CB TRP A2084 " pdb=" CG TRP A2084 " ideal model delta sigma weight residual 113.60 120.02 -6.42 1.90e+00 2.77e-01 1.14e+01 ... (remaining 24980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.66: 10503 25.66 - 51.33: 500 51.33 - 76.99: 38 76.99 - 102.66: 6 102.66 - 128.32: 1 Dihedral angle restraints: 11048 sinusoidal: 4338 harmonic: 6710 Sorted by residual: dihedral pdb=" C2' ADP A4104 " pdb=" C1' ADP A4104 " pdb=" N9 ADP A4104 " pdb=" C4 ADP A4104 " ideal model delta sinusoidal sigma weight residual 91.55 -140.13 -128.32 1 2.00e+01 2.50e-03 3.89e+01 dihedral pdb=" CA MET A1963 " pdb=" C MET A1963 " pdb=" N ASN A1964 " pdb=" CA ASN A1964 " ideal model delta harmonic sigma weight residual 180.00 -150.31 -29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" C5' ADP A4103 " pdb=" O5' ADP A4103 " pdb=" PA ADP A4103 " pdb=" O2A ADP A4103 " ideal model delta sinusoidal sigma weight residual -60.00 -139.83 79.83 1 2.00e+01 2.50e-03 1.98e+01 ... (remaining 11045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2125 0.043 - 0.086: 549 0.086 - 0.129: 178 0.129 - 0.172: 22 0.172 - 0.216: 4 Chirality restraints: 2878 Sorted by residual: chirality pdb=" CA MET A3345 " pdb=" N MET A3345 " pdb=" C MET A3345 " pdb=" CB MET A3345 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE A3321 " pdb=" CA ILE A3321 " pdb=" CG1 ILE A3321 " pdb=" CG2 ILE A3321 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA LEU A2491 " pdb=" N LEU A2491 " pdb=" C LEU A2491 " pdb=" CB LEU A2491 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2875 not shown) Planarity restraints: 3143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A2618 " -0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO A2619 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A2619 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A2619 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A2956 " 0.038 5.00e-02 4.00e+02 5.70e-02 5.21e+00 pdb=" N PRO A2957 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A2957 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A2957 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A4024 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO A4025 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A4025 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A4025 " 0.027 5.00e-02 4.00e+02 ... (remaining 3140 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 158 2.62 - 3.19: 14978 3.19 - 3.76: 29261 3.76 - 4.33: 40129 4.33 - 4.90: 66710 Nonbonded interactions: 151236 Sorted by model distance: nonbonded pdb=" OG1 THR A1803 " pdb="MG MG A4105 " model vdw 2.048 2.170 nonbonded pdb=" O3B ADP A4103 " pdb="MG MG A4105 " model vdw 2.061 2.170 nonbonded pdb=" ND2 ASN A2832 " pdb=" OG SER A2905 " model vdw 2.234 3.120 nonbonded pdb=" O GLY A3902 " pdb=" OG1 THR A3906 " model vdw 2.279 3.040 nonbonded pdb=" OH TYR A3642 " pdb=" OD2 ASP A3691 " model vdw 2.283 3.040 ... (remaining 151231 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.220 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.630 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 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 0.071 18432 Z= 0.155 Angle : 0.628 10.974 24985 Z= 0.330 Chirality : 0.044 0.216 2878 Planarity : 0.005 0.067 3143 Dihedral : 14.022 128.320 6688 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: 0.38 (0.16), residues: 2265 helix: 0.78 (0.13), residues: 1379 sheet: 0.42 (0.34), residues: 227 loop : -0.76 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2183 TYR 0.016 0.001 TYR A2630 PHE 0.019 0.002 PHE A2827 TRP 0.026 0.001 TRP A2084 HIS 0.005 0.001 HIS A3413 Details of bonding type rmsd covalent geometry : bond 0.00338 (18432) covalent geometry : angle 0.62841 (24985) hydrogen bonds : bond 0.09017 ( 1081) hydrogen bonds : angle 5.14802 ( 3192) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 1518 MET cc_start: 0.4737 (ptt) cc_final: 0.3401 (tpt) REVERT: A 1579 ILE cc_start: 0.7529 (mm) cc_final: 0.7224 (mm) REVERT: A 1855 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7444 (mt-10) REVERT: A 1907 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7712 (mp0) REVERT: A 2264 ASN cc_start: 0.4493 (m110) cc_final: 0.4056 (m110) REVERT: A 2402 LYS cc_start: 0.7611 (tptt) cc_final: 0.7315 (mttm) REVERT: A 2829 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7796 (tp30) REVERT: A 2883 LYS cc_start: 0.8128 (mttt) cc_final: 0.7835 (mtpp) REVERT: A 2987 ARG cc_start: 0.7609 (mtt180) cc_final: 0.7103 (mtt90) REVERT: A 2997 ARG cc_start: 0.8302 (mtt180) cc_final: 0.8032 (mtt180) REVERT: A 3013 ASN cc_start: 0.6225 (m-40) cc_final: 0.5577 (t0) REVERT: A 3331 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7656 (mt-10) REVERT: A 3355 LYS cc_start: 0.7754 (ttmt) cc_final: 0.7288 (tppt) REVERT: A 3373 LEU cc_start: 0.7208 (mm) cc_final: 0.6989 (mm) REVERT: A 3528 ARG cc_start: 0.6525 (mtp180) cc_final: 0.5506 (mtm-85) REVERT: A 3715 TYR cc_start: 0.7747 (t80) cc_final: 0.7309 (t80) REVERT: A 3856 HIS cc_start: 0.7714 (t-90) cc_final: 0.7462 (t-90) REVERT: A 4028 ARG cc_start: 0.7685 (ttm170) cc_final: 0.7173 (mtp85) REVERT: A 4038 GLU cc_start: 0.7914 (pm20) cc_final: 0.7390 (pp20) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.6174 time to fit residues: 167.7886 Evaluate side-chains 176 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 216 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.0570 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1688 ASN A1979 ASN A3318 GLN A3680 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.170608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.136061 restraints weight = 21756.422| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.95 r_work: 0.3449 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18432 Z= 0.111 Angle : 0.485 7.491 24985 Z= 0.249 Chirality : 0.039 0.145 2878 Planarity : 0.004 0.062 3143 Dihedral : 6.797 129.640 2505 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.56 % Allowed : 7.37 % Favored : 91.07 % 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: 1.39 (0.17), residues: 2265 helix: 1.73 (0.14), residues: 1384 sheet: 0.35 (0.34), residues: 229 loop : -0.55 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3894 TYR 0.014 0.001 TYR A2630 PHE 0.016 0.001 PHE A1574 TRP 0.021 0.001 TRP A2084 HIS 0.004 0.001 HIS A3484 Details of bonding type rmsd covalent geometry : bond 0.00249 (18432) covalent geometry : angle 0.48467 (24985) hydrogen bonds : bond 0.03242 ( 1081) hydrogen bonds : angle 4.14522 ( 3192) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 1579 ILE cc_start: 0.7758 (mm) cc_final: 0.7381 (mm) REVERT: A 1742 ASP cc_start: 0.7648 (t0) cc_final: 0.6378 (m-30) REVERT: A 1827 ASP cc_start: 0.8549 (p0) cc_final: 0.8283 (p0) REVERT: A 1855 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7531 (mt-10) REVERT: A 1907 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7853 (mp0) REVERT: A 1987 PHE cc_start: 0.8411 (m-10) cc_final: 0.8211 (m-10) REVERT: A 2264 ASN cc_start: 0.4672 (m110) cc_final: 0.4201 (m110) REVERT: A 2402 LYS cc_start: 0.7674 (tptt) cc_final: 0.7388 (mttm) REVERT: A 2569 GLN cc_start: 0.7907 (mt0) cc_final: 0.7300 (tt0) REVERT: A 2829 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7568 (tp30) REVERT: A 2883 LYS cc_start: 0.8258 (mttt) cc_final: 0.8001 (mtpp) REVERT: A 2987 ARG cc_start: 0.7611 (mtt180) cc_final: 0.7127 (mtt90) REVERT: A 2997 ARG cc_start: 0.8354 (mtt180) cc_final: 0.8052 (mtt180) REVERT: A 3013 ASN cc_start: 0.6334 (m-40) cc_final: 0.5682 (t0) REVERT: A 3355 LYS cc_start: 0.7833 (ttmt) cc_final: 0.7332 (tppt) REVERT: A 3377 MET cc_start: 0.7796 (mmm) cc_final: 0.7478 (mmt) REVERT: A 3715 TYR cc_start: 0.7719 (t80) cc_final: 0.7198 (t80) REVERT: A 3856 HIS cc_start: 0.7710 (t-90) cc_final: 0.7454 (t-90) REVERT: A 4028 ARG cc_start: 0.7893 (ttm170) cc_final: 0.7276 (mtp85) REVERT: A 4038 GLU cc_start: 0.7954 (pm20) cc_final: 0.7502 (pp20) outliers start: 30 outliers final: 8 residues processed: 213 average time/residue: 0.5588 time to fit residues: 133.3414 Evaluate side-chains 178 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 170 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 2009 THR Chi-restraints excluded: chain A residue 2526 ILE Chi-restraints excluded: chain A residue 2818 ASP Chi-restraints excluded: chain A residue 2899 SER Chi-restraints excluded: chain A residue 3680 GLN Chi-restraints excluded: chain A residue 3773 ASN Chi-restraints excluded: chain A residue 4071 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 122 optimal weight: 0.8980 chunk 188 optimal weight: 0.9980 chunk 199 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1688 ASN A1979 ASN A2434 ASN ** A3387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3413 HIS ** A3680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.168216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.134120 restraints weight = 21786.876| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.07 r_work: 0.3435 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18432 Z= 0.122 Angle : 0.481 6.942 24985 Z= 0.245 Chirality : 0.039 0.144 2878 Planarity : 0.003 0.048 3143 Dihedral : 6.737 129.491 2505 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.92 % Allowed : 9.81 % Favored : 88.27 % 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: 1.69 (0.18), residues: 2265 helix: 1.99 (0.14), residues: 1385 sheet: 0.39 (0.32), residues: 250 loop : -0.50 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3340 TYR 0.015 0.001 TYR A2630 PHE 0.015 0.001 PHE A2877 TRP 0.021 0.001 TRP A2084 HIS 0.004 0.001 HIS A1965 Details of bonding type rmsd covalent geometry : bond 0.00280 (18432) covalent geometry : angle 0.48107 (24985) hydrogen bonds : bond 0.03290 ( 1081) hydrogen bonds : angle 4.00662 ( 3192) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 181 time to evaluate : 0.682 Fit side-chains REVERT: A 1579 ILE cc_start: 0.7756 (mm) cc_final: 0.7411 (mm) REVERT: A 1827 ASP cc_start: 0.8543 (p0) cc_final: 0.8278 (p0) REVERT: A 1855 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7520 (mt-10) REVERT: A 1907 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7955 (mp0) REVERT: A 2011 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7654 (mt-10) REVERT: A 2049 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7701 (mmt) REVERT: A 2147 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7790 (t0) REVERT: A 2402 LYS cc_start: 0.7717 (tptt) cc_final: 0.7401 (mttm) REVERT: A 2569 GLN cc_start: 0.7939 (mt0) cc_final: 0.7335 (tt0) REVERT: A 2572 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.8015 (mp0) REVERT: A 2829 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7544 (tp30) REVERT: A 2883 LYS cc_start: 0.8281 (mttt) cc_final: 0.8012 (mtpp) REVERT: A 2900 SER cc_start: 0.7608 (t) cc_final: 0.7309 (p) REVERT: A 2997 ARG cc_start: 0.8338 (mtt180) cc_final: 0.8048 (mtt180) REVERT: A 3013 ASN cc_start: 0.6237 (m-40) cc_final: 0.5600 (t0) REVERT: A 3355 LYS cc_start: 0.7913 (ttmt) cc_final: 0.7325 (tppt) REVERT: A 3377 MET cc_start: 0.7843 (mmm) cc_final: 0.7480 (mmt) REVERT: A 3715 TYR cc_start: 0.7714 (t80) cc_final: 0.7153 (t80) REVERT: A 3856 HIS cc_start: 0.7664 (t-90) cc_final: 0.7403 (t-90) REVERT: A 4001 GLU cc_start: 0.6748 (tp30) cc_final: 0.6527 (tp30) REVERT: A 4028 ARG cc_start: 0.7866 (ttm170) cc_final: 0.7196 (mtp85) REVERT: A 4038 GLU cc_start: 0.7963 (pm20) cc_final: 0.7528 (pp20) outliers start: 37 outliers final: 13 residues processed: 203 average time/residue: 0.5157 time to fit residues: 117.5582 Evaluate side-chains 191 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1942 SER Chi-restraints excluded: chain A residue 2009 THR Chi-restraints excluded: chain A residue 2011 GLU Chi-restraints excluded: chain A residue 2049 MET Chi-restraints excluded: chain A residue 2147 ASN Chi-restraints excluded: chain A residue 2265 ILE Chi-restraints excluded: chain A residue 2526 ILE Chi-restraints excluded: chain A residue 2572 GLU Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2818 ASP Chi-restraints excluded: chain A residue 2899 SER Chi-restraints excluded: chain A residue 3359 LYS Chi-restraints excluded: chain A residue 3399 ASN Chi-restraints excluded: chain A residue 3529 ILE Chi-restraints excluded: chain A residue 3773 ASN Chi-restraints excluded: chain A residue 4071 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 4 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 184 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1688 ASN A1979 ASN A2030 ASN A2967 ASN ** A3387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3413 HIS A3637 GLN ** A3680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3780 ASN A3856 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.165302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.130470 restraints weight = 21699.060| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.97 r_work: 0.3389 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18432 Z= 0.169 Angle : 0.525 7.487 24985 Z= 0.266 Chirality : 0.041 0.151 2878 Planarity : 0.004 0.049 3143 Dihedral : 6.903 131.010 2505 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.82 % Allowed : 10.96 % Favored : 87.23 % 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: 1.68 (0.18), residues: 2265 helix: 1.98 (0.14), residues: 1382 sheet: 0.34 (0.32), residues: 242 loop : -0.44 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3340 TYR 0.018 0.002 TYR A2464 PHE 0.016 0.002 PHE A2877 TRP 0.020 0.001 TRP A2084 HIS 0.004 0.001 HIS A1878 Details of bonding type rmsd covalent geometry : bond 0.00402 (18432) covalent geometry : angle 0.52461 (24985) hydrogen bonds : bond 0.03634 ( 1081) hydrogen bonds : angle 4.05958 ( 3192) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.671 Fit side-chains REVERT: A 1855 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7579 (mt-10) REVERT: A 1907 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7996 (mp0) REVERT: A 1987 PHE cc_start: 0.8454 (m-10) cc_final: 0.8194 (m-10) REVERT: A 1992 LYS cc_start: 0.7574 (tptt) cc_final: 0.6957 (mtmt) REVERT: A 2011 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: A 2049 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.6827 (mpt) REVERT: A 2147 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7811 (t0) REVERT: A 2402 LYS cc_start: 0.7717 (tptt) cc_final: 0.7378 (mttm) REVERT: A 2447 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8230 (ptpp) REVERT: A 2569 GLN cc_start: 0.8008 (mt0) cc_final: 0.7213 (pt0) REVERT: A 2572 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8012 (mp0) REVERT: A 2658 ASP cc_start: 0.7515 (m-30) cc_final: 0.7159 (m-30) REVERT: A 2829 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7586 (tp30) REVERT: A 2883 LYS cc_start: 0.8281 (mttt) cc_final: 0.8051 (mtpp) REVERT: A 2900 SER cc_start: 0.7765 (t) cc_final: 0.7486 (p) REVERT: A 2997 ARG cc_start: 0.8388 (mtt180) cc_final: 0.8119 (mtt180) REVERT: A 3355 LYS cc_start: 0.8031 (ttmt) cc_final: 0.7366 (tppt) REVERT: A 3373 LEU cc_start: 0.7233 (mm) cc_final: 0.7028 (mm) REVERT: A 3715 TYR cc_start: 0.7779 (t80) cc_final: 0.7173 (t80) REVERT: A 3856 HIS cc_start: 0.7648 (t70) cc_final: 0.7367 (t-90) REVERT: A 4001 GLU cc_start: 0.6750 (tp30) cc_final: 0.6527 (tp30) REVERT: A 4028 ARG cc_start: 0.7946 (ttm170) cc_final: 0.7285 (mtp85) REVERT: A 4038 GLU cc_start: 0.7990 (pm20) cc_final: 0.7553 (pp20) outliers start: 35 outliers final: 16 residues processed: 204 average time/residue: 0.5685 time to fit residues: 130.7404 Evaluate side-chains 193 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1942 SER Chi-restraints excluded: chain A residue 2009 THR Chi-restraints excluded: chain A residue 2011 GLU Chi-restraints excluded: chain A residue 2049 MET Chi-restraints excluded: chain A residue 2147 ASN Chi-restraints excluded: chain A residue 2265 ILE Chi-restraints excluded: chain A residue 2447 LYS Chi-restraints excluded: chain A residue 2450 THR Chi-restraints excluded: chain A residue 2526 ILE Chi-restraints excluded: chain A residue 2572 GLU Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2806 CYS Chi-restraints excluded: chain A residue 2818 ASP Chi-restraints excluded: chain A residue 3359 LYS Chi-restraints excluded: chain A residue 3399 ASN Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3677 LEU Chi-restraints excluded: chain A residue 3773 ASN Chi-restraints excluded: chain A residue 4071 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 46 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 228 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 182 optimal weight: 50.0000 chunk 84 optimal weight: 1.9990 chunk 151 optimal weight: 20.0000 chunk 60 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1688 ASN A1979 ASN ** A3387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3413 HIS ** A3680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3780 ASN A3856 HIS A3878 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.165934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.131997 restraints weight = 21677.384| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.02 r_work: 0.3410 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18432 Z= 0.118 Angle : 0.482 8.057 24985 Z= 0.244 Chirality : 0.039 0.145 2878 Planarity : 0.003 0.046 3143 Dihedral : 6.784 130.814 2505 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.61 % Allowed : 11.73 % Favored : 86.66 % 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: 1.86 (0.18), residues: 2265 helix: 2.15 (0.14), residues: 1382 sheet: 0.28 (0.32), residues: 242 loop : -0.37 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3340 TYR 0.021 0.001 TYR A2464 PHE 0.015 0.001 PHE A2281 TRP 0.021 0.001 TRP A2084 HIS 0.004 0.001 HIS A1965 Details of bonding type rmsd covalent geometry : bond 0.00271 (18432) covalent geometry : angle 0.48159 (24985) hydrogen bonds : bond 0.03303 ( 1081) hydrogen bonds : angle 3.94514 ( 3192) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.711 Fit side-chains REVERT: A 1827 ASP cc_start: 0.8555 (p0) cc_final: 0.8333 (p0) REVERT: A 1855 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7576 (mt-10) REVERT: A 1907 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8031 (mp0) REVERT: A 1987 PHE cc_start: 0.8433 (m-10) cc_final: 0.8152 (m-10) REVERT: A 1992 LYS cc_start: 0.7603 (tptt) cc_final: 0.6981 (mtmt) REVERT: A 2402 LYS cc_start: 0.7779 (tptt) cc_final: 0.7424 (mttm) REVERT: A 2447 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8256 (ptpp) REVERT: A 2569 GLN cc_start: 0.7987 (mt0) cc_final: 0.7237 (pt0) REVERT: A 2572 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7928 (tm-30) REVERT: A 2829 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7578 (tp30) REVERT: A 2883 LYS cc_start: 0.8318 (mttt) cc_final: 0.8083 (mtpp) REVERT: A 2900 SER cc_start: 0.7679 (t) cc_final: 0.7471 (p) REVERT: A 2997 ARG cc_start: 0.8424 (mtt180) cc_final: 0.8161 (mtt180) REVERT: A 3355 LYS cc_start: 0.8053 (ttmt) cc_final: 0.7391 (tppt) REVERT: A 3715 TYR cc_start: 0.7751 (t80) cc_final: 0.7143 (t80) REVERT: A 3856 HIS cc_start: 0.7771 (t-90) cc_final: 0.7506 (t-90) REVERT: A 4028 ARG cc_start: 0.7960 (ttm170) cc_final: 0.7276 (mtm180) REVERT: A 4038 GLU cc_start: 0.7980 (pm20) cc_final: 0.7574 (pp20) outliers start: 31 outliers final: 13 residues processed: 208 average time/residue: 0.5661 time to fit residues: 132.7365 Evaluate side-chains 188 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1942 SER Chi-restraints excluded: chain A residue 2009 THR Chi-restraints excluded: chain A residue 2265 ILE Chi-restraints excluded: chain A residue 2447 LYS Chi-restraints excluded: chain A residue 2572 GLU Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2806 CYS Chi-restraints excluded: chain A residue 2818 ASP Chi-restraints excluded: chain A residue 2899 SER Chi-restraints excluded: chain A residue 3399 ASN Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3773 ASN Chi-restraints excluded: chain A residue 4071 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 9 optimal weight: 5.9990 chunk 187 optimal weight: 0.8980 chunk 179 optimal weight: 30.0000 chunk 206 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 151 optimal weight: 20.0000 chunk 47 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1688 ASN ** A3387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3413 HIS ** A3680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3780 ASN A3856 HIS A4077 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.165119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.130991 restraints weight = 21618.075| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.15 r_work: 0.3394 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18432 Z= 0.148 Angle : 0.509 7.685 24985 Z= 0.258 Chirality : 0.040 0.149 2878 Planarity : 0.003 0.047 3143 Dihedral : 6.861 130.803 2505 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.92 % Allowed : 12.36 % Favored : 85.72 % 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: 1.83 (0.18), residues: 2265 helix: 2.11 (0.14), residues: 1376 sheet: 0.33 (0.34), residues: 227 loop : -0.35 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3340 TYR 0.022 0.001 TYR A2464 PHE 0.015 0.001 PHE A2972 TRP 0.020 0.001 TRP A2084 HIS 0.004 0.001 HIS A1965 Details of bonding type rmsd covalent geometry : bond 0.00348 (18432) covalent geometry : angle 0.50884 (24985) hydrogen bonds : bond 0.03520 ( 1081) hydrogen bonds : angle 3.98649 ( 3192) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 0.775 Fit side-chains REVERT: A 1687 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7884 (tt) REVERT: A 1855 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7558 (mt-10) REVERT: A 1907 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8066 (mp0) REVERT: A 1987 PHE cc_start: 0.8466 (m-10) cc_final: 0.8217 (m-10) REVERT: A 1992 LYS cc_start: 0.7581 (tptt) cc_final: 0.6943 (mtmt) REVERT: A 2402 LYS cc_start: 0.7757 (tptt) cc_final: 0.7334 (mttm) REVERT: A 2447 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8270 (ptpp) REVERT: A 2569 GLN cc_start: 0.7875 (mt0) cc_final: 0.7222 (pt0) REVERT: A 2572 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: A 2715 PHE cc_start: 0.7682 (t80) cc_final: 0.7128 (t80) REVERT: A 2829 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7557 (tp30) REVERT: A 2883 LYS cc_start: 0.8281 (mttt) cc_final: 0.8051 (mtpp) REVERT: A 2900 SER cc_start: 0.7767 (t) cc_final: 0.7542 (p) REVERT: A 2997 ARG cc_start: 0.8401 (mtt180) cc_final: 0.8146 (mtt180) REVERT: A 3355 LYS cc_start: 0.8114 (ttmt) cc_final: 0.7413 (tppt) REVERT: A 3359 LYS cc_start: 0.6945 (ptpt) cc_final: 0.6372 (mtmt) REVERT: A 3434 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6632 (mm-30) REVERT: A 3715 TYR cc_start: 0.7754 (t80) cc_final: 0.7125 (t80) REVERT: A 3748 TRP cc_start: 0.7486 (t-100) cc_final: 0.7193 (t-100) REVERT: A 3856 HIS cc_start: 0.7676 (t70) cc_final: 0.7408 (t-90) REVERT: A 4028 ARG cc_start: 0.7959 (ttm170) cc_final: 0.7247 (mtm180) REVERT: A 4038 GLU cc_start: 0.7970 (pm20) cc_final: 0.7548 (pp20) outliers start: 37 outliers final: 17 residues processed: 208 average time/residue: 0.5757 time to fit residues: 134.9266 Evaluate side-chains 195 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1942 SER Chi-restraints excluded: chain A residue 2009 THR Chi-restraints excluded: chain A residue 2265 ILE Chi-restraints excluded: chain A residue 2447 LYS Chi-restraints excluded: chain A residue 2526 ILE Chi-restraints excluded: chain A residue 2572 GLU Chi-restraints excluded: chain A residue 2626 VAL Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2806 CYS Chi-restraints excluded: chain A residue 2818 ASP Chi-restraints excluded: chain A residue 2899 SER Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3399 ASN Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3705 LEU Chi-restraints excluded: chain A residue 3773 ASN Chi-restraints excluded: chain A residue 4071 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 64 optimal weight: 0.9990 chunk 184 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 164 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1688 ASN ** A3387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3413 HIS ** A3680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3780 ASN A3914 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.164067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.129742 restraints weight = 21718.489| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.90 r_work: 0.3369 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18432 Z= 0.159 Angle : 0.523 8.782 24985 Z= 0.266 Chirality : 0.041 0.151 2878 Planarity : 0.003 0.048 3143 Dihedral : 6.914 131.195 2505 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.02 % Allowed : 12.67 % Favored : 85.31 % 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: 1.80 (0.18), residues: 2265 helix: 2.09 (0.14), residues: 1376 sheet: 0.30 (0.34), residues: 227 loop : -0.36 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3340 TYR 0.020 0.001 TYR A2464 PHE 0.024 0.002 PHE A2281 TRP 0.020 0.001 TRP A2084 HIS 0.004 0.001 HIS A1965 Details of bonding type rmsd covalent geometry : bond 0.00378 (18432) covalent geometry : angle 0.52296 (24985) hydrogen bonds : bond 0.03636 ( 1081) hydrogen bonds : angle 4.01711 ( 3192) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 0.691 Fit side-chains REVERT: A 1687 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7910 (tt) REVERT: A 1855 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7620 (mt-10) REVERT: A 1907 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8140 (mp0) REVERT: A 1986 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7489 (pm20) REVERT: A 1987 PHE cc_start: 0.8512 (m-10) cc_final: 0.8246 (m-10) REVERT: A 1992 LYS cc_start: 0.7659 (tptt) cc_final: 0.7022 (mtmt) REVERT: A 2402 LYS cc_start: 0.7854 (tptt) cc_final: 0.7460 (mttm) REVERT: A 2447 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8336 (ptpp) REVERT: A 2572 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: A 2715 PHE cc_start: 0.7721 (t80) cc_final: 0.7154 (t80) REVERT: A 2829 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7668 (tp30) REVERT: A 2883 LYS cc_start: 0.8389 (mttt) cc_final: 0.8172 (mtpp) REVERT: A 2900 SER cc_start: 0.7911 (t) cc_final: 0.7702 (p) REVERT: A 2997 ARG cc_start: 0.8447 (mtt180) cc_final: 0.8181 (mtt180) REVERT: A 3355 LYS cc_start: 0.8206 (ttmt) cc_final: 0.7528 (tppt) REVERT: A 3359 LYS cc_start: 0.7048 (ptpt) cc_final: 0.6482 (mtmt) REVERT: A 3434 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6674 (mm-30) REVERT: A 3705 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7503 (mt) REVERT: A 3715 TYR cc_start: 0.7811 (t80) cc_final: 0.7174 (t80) REVERT: A 3748 TRP cc_start: 0.7546 (t-100) cc_final: 0.7284 (t-100) REVERT: A 3856 HIS cc_start: 0.7760 (t70) cc_final: 0.7414 (t-90) REVERT: A 4028 ARG cc_start: 0.8016 (ttm170) cc_final: 0.7344 (mtm180) REVERT: A 4038 GLU cc_start: 0.7989 (pm20) cc_final: 0.7572 (pp20) outliers start: 39 outliers final: 15 residues processed: 204 average time/residue: 0.5461 time to fit residues: 126.1100 Evaluate side-chains 188 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 1942 SER Chi-restraints excluded: chain A residue 1986 GLU Chi-restraints excluded: chain A residue 2009 THR Chi-restraints excluded: chain A residue 2265 ILE Chi-restraints excluded: chain A residue 2447 LYS Chi-restraints excluded: chain A residue 2450 THR Chi-restraints excluded: chain A residue 2526 ILE Chi-restraints excluded: chain A residue 2572 GLU Chi-restraints excluded: chain A residue 2626 VAL Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2753 GLN Chi-restraints excluded: chain A residue 2806 CYS Chi-restraints excluded: chain A residue 2818 ASP Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3705 LEU Chi-restraints excluded: chain A residue 3773 ASN Chi-restraints excluded: chain A residue 4071 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 209 optimal weight: 0.9980 chunk 87 optimal weight: 0.0370 chunk 31 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 203 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1864 ASN ** A3387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3413 HIS ** A3680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3780 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.166073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.132297 restraints weight = 21563.053| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.99 r_work: 0.3418 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18432 Z= 0.105 Angle : 0.475 7.857 24985 Z= 0.241 Chirality : 0.039 0.153 2878 Planarity : 0.003 0.045 3143 Dihedral : 6.651 130.315 2505 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.51 % Allowed : 13.60 % Favored : 84.89 % 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: 2.03 (0.18), residues: 2265 helix: 2.26 (0.14), residues: 1380 sheet: 0.36 (0.34), residues: 227 loop : -0.24 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2044 TYR 0.017 0.001 TYR A2464 PHE 0.014 0.001 PHE A2281 TRP 0.022 0.001 TRP A2084 HIS 0.005 0.001 HIS A1965 Details of bonding type rmsd covalent geometry : bond 0.00235 (18432) covalent geometry : angle 0.47453 (24985) hydrogen bonds : bond 0.03168 ( 1081) hydrogen bonds : angle 3.89126 ( 3192) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.689 Fit side-chains REVERT: A 1687 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7902 (tt) REVERT: A 1827 ASP cc_start: 0.8534 (p0) cc_final: 0.8315 (p0) REVERT: A 1855 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7560 (mt-10) REVERT: A 1907 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8102 (mp0) REVERT: A 1987 PHE cc_start: 0.8433 (m-10) cc_final: 0.8173 (m-10) REVERT: A 1992 LYS cc_start: 0.7617 (tptt) cc_final: 0.6962 (mtmt) REVERT: A 2212 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8406 (tt) REVERT: A 2402 LYS cc_start: 0.7796 (tptt) cc_final: 0.7346 (mttm) REVERT: A 2447 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8284 (ptpp) REVERT: A 2572 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: A 2655 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8407 (mt) REVERT: A 2715 PHE cc_start: 0.7610 (t80) cc_final: 0.7100 (t80) REVERT: A 2829 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7587 (tp30) REVERT: A 2883 LYS cc_start: 0.8281 (mttt) cc_final: 0.8079 (mtpp) REVERT: A 2959 GLN cc_start: 0.6972 (mp10) cc_final: 0.6713 (mp10) REVERT: A 2997 ARG cc_start: 0.8393 (mtt180) cc_final: 0.8153 (mtt180) REVERT: A 3355 LYS cc_start: 0.8202 (ttmt) cc_final: 0.7493 (tppt) REVERT: A 3359 LYS cc_start: 0.6984 (ptpt) cc_final: 0.6376 (mtmt) REVERT: A 3705 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7437 (mt) REVERT: A 3715 TYR cc_start: 0.7737 (t80) cc_final: 0.7117 (t80) REVERT: A 3748 TRP cc_start: 0.7540 (t-100) cc_final: 0.7165 (t-100) REVERT: A 3856 HIS cc_start: 0.7682 (t70) cc_final: 0.7376 (t-90) REVERT: A 4028 ARG cc_start: 0.7938 (ttm170) cc_final: 0.7258 (mtm180) REVERT: A 4038 GLU cc_start: 0.7955 (pm20) cc_final: 0.7567 (pp20) outliers start: 29 outliers final: 13 residues processed: 203 average time/residue: 0.5423 time to fit residues: 124.9864 Evaluate side-chains 190 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 2009 THR Chi-restraints excluded: chain A residue 2212 LEU Chi-restraints excluded: chain A residue 2447 LYS Chi-restraints excluded: chain A residue 2572 GLU Chi-restraints excluded: chain A residue 2626 VAL Chi-restraints excluded: chain A residue 2655 ILE Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2753 GLN Chi-restraints excluded: chain A residue 2806 CYS Chi-restraints excluded: chain A residue 2818 ASP Chi-restraints excluded: chain A residue 2899 SER Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3399 ASN Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3705 LEU Chi-restraints excluded: chain A residue 4071 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 134 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 200 optimal weight: 0.0370 chunk 28 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 211 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3413 HIS ** A3680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3780 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.166041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.131951 restraints weight = 21513.507| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.96 r_work: 0.3409 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18432 Z= 0.111 Angle : 0.484 7.684 24985 Z= 0.245 Chirality : 0.039 0.153 2878 Planarity : 0.003 0.046 3143 Dihedral : 6.623 129.900 2505 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.40 % Allowed : 14.07 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.08 (0.18), residues: 2265 helix: 2.31 (0.14), residues: 1380 sheet: 0.44 (0.33), residues: 237 loop : -0.28 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2044 TYR 0.022 0.001 TYR A2464 PHE 0.021 0.001 PHE A2281 TRP 0.021 0.001 TRP A2084 HIS 0.005 0.001 HIS A1965 Details of bonding type rmsd covalent geometry : bond 0.00253 (18432) covalent geometry : angle 0.48398 (24985) hydrogen bonds : bond 0.03206 ( 1081) hydrogen bonds : angle 3.87851 ( 3192) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.651 Fit side-chains REVERT: A 1687 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7910 (tt) REVERT: A 1745 ASN cc_start: 0.7891 (m110) cc_final: 0.7625 (m110) REVERT: A 1827 ASP cc_start: 0.8544 (p0) cc_final: 0.8331 (p0) REVERT: A 1855 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7595 (mt-10) REVERT: A 1907 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8085 (mp0) REVERT: A 1987 PHE cc_start: 0.8439 (m-10) cc_final: 0.8157 (m-10) REVERT: A 1992 LYS cc_start: 0.7618 (tptt) cc_final: 0.6964 (mtmt) REVERT: A 2049 MET cc_start: 0.8099 (mmm) cc_final: 0.7694 (mpm) REVERT: A 2212 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8452 (tt) REVERT: A 2402 LYS cc_start: 0.7768 (tptt) cc_final: 0.7362 (mttm) REVERT: A 2447 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8282 (ptpp) REVERT: A 2572 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7925 (mp0) REVERT: A 2655 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8401 (mt) REVERT: A 2715 PHE cc_start: 0.7639 (t80) cc_final: 0.7123 (t80) REVERT: A 2829 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7572 (tp30) REVERT: A 2959 GLN cc_start: 0.6932 (mp10) cc_final: 0.6670 (mp10) REVERT: A 2997 ARG cc_start: 0.8415 (mtt180) cc_final: 0.8161 (mtt180) REVERT: A 3355 LYS cc_start: 0.8217 (ttmt) cc_final: 0.7487 (tppt) REVERT: A 3359 LYS cc_start: 0.6987 (ptpt) cc_final: 0.6413 (mtmt) REVERT: A 3434 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6620 (mm-30) REVERT: A 3705 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7437 (mt) REVERT: A 3715 TYR cc_start: 0.7730 (t80) cc_final: 0.7131 (t80) REVERT: A 3748 TRP cc_start: 0.7472 (t-100) cc_final: 0.7137 (t-100) REVERT: A 3856 HIS cc_start: 0.7692 (t70) cc_final: 0.7391 (t-90) REVERT: A 4028 ARG cc_start: 0.7928 (ttm170) cc_final: 0.7234 (mtm180) REVERT: A 4038 GLU cc_start: 0.7955 (pm20) cc_final: 0.7539 (pp20) outliers start: 27 outliers final: 12 residues processed: 192 average time/residue: 0.5512 time to fit residues: 119.5476 Evaluate side-chains 192 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 2009 THR Chi-restraints excluded: chain A residue 2212 LEU Chi-restraints excluded: chain A residue 2265 ILE Chi-restraints excluded: chain A residue 2447 LYS Chi-restraints excluded: chain A residue 2572 GLU Chi-restraints excluded: chain A residue 2626 VAL Chi-restraints excluded: chain A residue 2655 ILE Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2753 GLN Chi-restraints excluded: chain A residue 2818 ASP Chi-restraints excluded: chain A residue 2899 SER Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3705 LEU Chi-restraints excluded: chain A residue 4071 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 1 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 219 optimal weight: 0.0980 chunk 69 optimal weight: 0.7980 chunk 210 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 chunk 222 optimal weight: 0.3980 chunk 117 optimal weight: 7.9990 chunk 59 optimal weight: 0.4980 chunk 194 optimal weight: 0.0020 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2832 ASN ** A3387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3413 HIS A3624 HIS A3780 ASN A3856 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.168655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.134822 restraints weight = 21570.018| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.13 r_work: 0.3459 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18432 Z= 0.090 Angle : 0.465 9.466 24985 Z= 0.234 Chirality : 0.038 0.189 2878 Planarity : 0.003 0.044 3143 Dihedral : 6.409 128.441 2505 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.09 % Allowed : 14.59 % 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: 2.23 (0.18), residues: 2265 helix: 2.44 (0.14), residues: 1381 sheet: 0.44 (0.33), residues: 238 loop : -0.22 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2044 TYR 0.019 0.001 TYR A2464 PHE 0.015 0.001 PHE A2281 TRP 0.022 0.001 TRP A2084 HIS 0.005 0.000 HIS A1965 Details of bonding type rmsd covalent geometry : bond 0.00193 (18432) covalent geometry : angle 0.46485 (24985) hydrogen bonds : bond 0.02932 ( 1081) hydrogen bonds : angle 3.79406 ( 3192) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.722 Fit side-chains REVERT: A 1687 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7909 (tt) REVERT: A 1827 ASP cc_start: 0.8513 (p0) cc_final: 0.8257 (p0) REVERT: A 1855 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7562 (mt-10) REVERT: A 1907 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8002 (mp0) REVERT: A 1987 PHE cc_start: 0.8345 (m-10) cc_final: 0.8066 (m-10) REVERT: A 2279 ARG cc_start: 0.6743 (mtp-110) cc_final: 0.6488 (ptt180) REVERT: A 2387 ARG cc_start: 0.7479 (mtp85) cc_final: 0.6910 (mtt180) REVERT: A 2402 LYS cc_start: 0.7741 (tptt) cc_final: 0.7300 (mttm) REVERT: A 2447 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8198 (ptpp) REVERT: A 2569 GLN cc_start: 0.7874 (mt0) cc_final: 0.7095 (pt0) REVERT: A 2572 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7646 (tm-30) REVERT: A 2655 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8357 (mt) REVERT: A 2715 PHE cc_start: 0.7542 (t80) cc_final: 0.7047 (t80) REVERT: A 2829 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7491 (tp30) REVERT: A 2959 GLN cc_start: 0.6955 (mp10) cc_final: 0.6676 (mp10) REVERT: A 2997 ARG cc_start: 0.8331 (mtt180) cc_final: 0.8081 (mtt180) REVERT: A 3345 MET cc_start: 0.6779 (mmp) cc_final: 0.6527 (mmt) REVERT: A 3355 LYS cc_start: 0.8163 (ttmt) cc_final: 0.7383 (tppt) REVERT: A 3359 LYS cc_start: 0.6928 (ptpt) cc_final: 0.6318 (mtmt) REVERT: A 3528 ARG cc_start: 0.6190 (mtp180) cc_final: 0.5237 (mtm-85) REVERT: A 3705 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7325 (mt) REVERT: A 3715 TYR cc_start: 0.7632 (t80) cc_final: 0.7044 (t80) REVERT: A 3748 TRP cc_start: 0.7398 (t-100) cc_final: 0.7069 (t-100) REVERT: A 3856 HIS cc_start: 0.7643 (t-90) cc_final: 0.7389 (t-90) REVERT: A 4038 GLU cc_start: 0.7932 (pm20) cc_final: 0.7533 (pp20) outliers start: 21 outliers final: 11 residues processed: 199 average time/residue: 0.5468 time to fit residues: 122.7357 Evaluate side-chains 188 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1687 LEU Chi-restraints excluded: chain A residue 2009 THR Chi-restraints excluded: chain A residue 2447 LYS Chi-restraints excluded: chain A residue 2572 GLU Chi-restraints excluded: chain A residue 2655 ILE Chi-restraints excluded: chain A residue 2661 VAL Chi-restraints excluded: chain A residue 2753 GLN Chi-restraints excluded: chain A residue 2818 ASP Chi-restraints excluded: chain A residue 2899 SER Chi-restraints excluded: chain A residue 3346 LEU Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3705 LEU Chi-restraints excluded: chain A residue 4071 LEU Chi-restraints excluded: chain A residue 4076 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 5 optimal weight: 0.8980 chunk 221 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 152 optimal weight: 30.0000 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2832 ASN A3318 GLN ** A3387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3413 HIS A3780 ASN A3856 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.165995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.132536 restraints weight = 21596.375| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.13 r_work: 0.3423 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18432 Z= 0.122 Angle : 0.500 9.693 24985 Z= 0.251 Chirality : 0.040 0.185 2878 Planarity : 0.003 0.045 3143 Dihedral : 6.535 129.014 2505 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.14 % Allowed : 14.95 % Favored : 83.90 % 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: 2.20 (0.18), residues: 2265 helix: 2.40 (0.14), residues: 1380 sheet: 0.48 (0.33), residues: 239 loop : -0.21 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2044 TYR 0.020 0.001 TYR A2464 PHE 0.026 0.001 PHE A3436 TRP 0.021 0.001 TRP A2084 HIS 0.005 0.001 HIS A1965 Details of bonding type rmsd covalent geometry : bond 0.00284 (18432) covalent geometry : angle 0.49958 (24985) hydrogen bonds : bond 0.03223 ( 1081) hydrogen bonds : angle 3.85397 ( 3192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6204.11 seconds wall clock time: 106 minutes 20.68 seconds (6380.68 seconds total)