Starting phenix.real_space_refine on Fri Sep 19 08:50:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mgm_23829/09_2025/7mgm_23829.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mgm_23829/09_2025/7mgm_23829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mgm_23829/09_2025/7mgm_23829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mgm_23829/09_2025/7mgm_23829.map" model { file = "/net/cci-nas-00/data/ceres_data/7mgm_23829/09_2025/7mgm_23829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mgm_23829/09_2025/7mgm_23829.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 11 5.49 5 Mg 2 5.21 5 S 116 5.16 5 C 15418 2.51 5 N 4045 2.21 5 O 4487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.03s 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: 24079 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 18363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2274, 18363 Classifications: {'peptide': 2274} Link IDs: {'PTRANS': 63, 'TRANS': 2210} Chain breaks: 11 Chain: "C" Number of atoms: 2821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2821 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain breaks: 3 Chain: "B" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2773 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain breaks: 4 Chain: "A" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 122 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 5.40, per 1000 atoms: 0.22 Number of scatterers: 24079 At special positions: 0 Unit cell: (100.87, 141.48, 192.57, 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 116 16.00 P 11 15.00 Mg 2 11.99 O 4487 8.00 N 4045 7.00 C 15418 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: 2.00 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5642 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 30 sheets defined 50.5% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 1510 through 1521 removed outlier: 3.642A pdb=" N ILE A1519 " --> pdb=" O SER A1515 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1532 removed outlier: 3.857A pdb=" N ARG A1529 " --> pdb=" O THR A1525 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A1532 " --> pdb=" O GLU A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1534 through 1540 Processing helix chain 'A' and resid 1541 through 1551 removed outlier: 3.692A pdb=" N LYS A1547 " --> pdb=" O ASP A1543 " (cutoff:3.500A) Processing helix 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: 3.526A pdb=" N TRP A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A1610 " --> pdb=" O GLU A1606 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A1613 " --> pdb=" O ASN A1609 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A1616 " --> pdb=" O ASP A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1640 removed outlier: 3.955A pdb=" N VAL A1639 " --> pdb=" O ASP A1635 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A1640 " --> pdb=" O ILE A1636 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1635 through 1640' Processing helix chain 'A' and resid 1644 through 1665 Processing helix chain 'A' and resid 1669 through 1689 removed outlier: 4.172A pdb=" N ASN A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS A1689 " --> pdb=" O ASP A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1717 removed outlier: 3.793A pdb=" N VAL A1703 " --> pdb=" O GLU A1699 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU A1704 " --> pdb=" O ALA A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1730 removed outlier: 3.627A pdb=" N LYS A1730 " --> pdb=" O LEU A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1742 through 1746 removed outlier: 3.512A pdb=" N ASN A1745 " --> pdb=" O ASP A1742 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1788 removed outlier: 4.150A pdb=" N GLN A1788 " --> pdb=" O ASP A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1813 Processing helix chain 'A' and resid 1827 through 1842 Processing helix chain 'A' and resid 1850 through 1853 removed outlier: 3.703A 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 removed outlier: 3.635A pdb=" N ILE A1929 " --> pdb=" O GLN A1925 " (cutoff:3.500A) Processing helix chain 'A' and resid 1941 through 1960 Processing helix chain 'A' and resid 1969 through 1979 Processing helix chain 'A' and resid 1980 through 1982 No H-bonds generated for 'chain 'A' and resid 1980 through 1982' Processing helix chain 'A' and resid 1983 through 1988 Processing helix chain 'A' and resid 1990 through 2002 removed outlier: 3.550A pdb=" N VAL A1994 " --> pdb=" O GLY A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2006 Processing helix chain 'A' and resid 2008 through 2022 removed outlier: 3.773A pdb=" N LEU A2012 " --> pdb=" O ASP A2008 " (cutoff:3.500A) Processing helix chain 'A' and resid 2031 through 2046 removed outlier: 3.728A pdb=" N CYS A2037 " --> pdb=" O ALA A2033 " (cutoff:3.500A) Processing helix chain 'A' and resid 2050 through 2064 Processing helix chain 'A' and resid 2079 through 2096 Processing helix chain 'A' and resid 2105 through 2109 Processing helix chain 'A' and resid 2110 through 2115 Processing helix chain 'A' and resid 2128 through 2140 Processing helix chain 'A' and resid 2143 through 2146 Processing helix chain 'A' and resid 2159 through 2164 Processing helix chain 'A' and resid 2166 through 2171 Processing helix chain 'A' and resid 2203 through 2208 Processing helix chain 'A' and resid 2221 through 2235 removed outlier: 3.738A pdb=" N GLU A2235 " --> pdb=" O ASN A2231 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2257 removed outlier: 3.547A pdb=" N ASP A2251 " --> pdb=" O ASP A2247 " (cutoff:3.500A) Processing helix chain 'A' and resid 2258 through 2269 removed outlier: 4.397A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) removed outlier: 3.846A 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 2279 through 2282 Processing helix chain 'A' and resid 2283 through 2298 removed outlier: 3.744A pdb=" N TYR A2298 " --> pdb=" O LEU A2294 " (cutoff:3.500A) Processing helix chain 'A' and resid 2299 through 2303 removed outlier: 4.258A pdb=" N GLN A2303 " --> pdb=" O GLN A2300 " (cutoff:3.500A) Processing helix chain 'A' and resid 2306 through 2327 Processing helix chain 'A' and resid 2331 through 2346 removed outlier: 3.655A pdb=" N GLN A2340 " --> pdb=" O ARG A2336 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A2341 " --> pdb=" O ALA A2337 " (cutoff:3.500A) Processing helix chain 'A' and resid 2372 through 2375 removed outlier: 3.659A pdb=" N ILE A2375 " --> pdb=" O CYS A2372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2372 through 2375' Processing helix chain 'A' and resid 2381 through 2387 removed outlier: 3.773A pdb=" N VAL A2385 " --> pdb=" O ALA A2382 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET A2386 " --> pdb=" O HIS A2383 " (cutoff:3.500A) Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2423 through 2434 removed outlier: 3.831A pdb=" N ASN A2434 " --> pdb=" O ASN A2430 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2458 removed outlier: 3.672A 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: 3.991A pdb=" N ILE A2573 " --> pdb=" O GLN A2569 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR A2574 " --> pdb=" O ILE A2570 " (cutoff:3.500A) Processing helix chain 'A' and resid 2581 through 2587 removed outlier: 6.582A pdb=" N GLU A2584 " --> pdb=" O LEU A2581 " (cutoff:3.500A) removed outlier: 5.362A 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: 3.974A 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 2658 through 2660 No H-bonds generated for 'chain 'A' and resid 2658 through 2660' Processing helix chain 'A' and resid 2662 through 2681 Processing helix chain 'A' and resid 2708 through 2727 Processing helix chain 'A' and resid 2735 through 2750 Processing helix chain 'A' and resid 2765 through 2777 Processing helix chain 'A' and resid 2791 through 2809 Processing helix chain 'A' and resid 2820 through 2822 No H-bonds generated for 'chain 'A' and resid 2820 through 2822' Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 3.843A pdb=" N LEU A2828 " --> pdb=" O GLU A2824 " (cutoff:3.500A) Processing helix chain 'A' and resid 2847 through 2863 Processing helix chain 'A' and resid 2869 through 2884 Processing helix chain 'A' and resid 2896 through 2905 removed outlier: 3.713A pdb=" N ALA A2901 " --> pdb=" O ASN A2897 " (cutoff:3.500A) Processing helix chain 'A' and resid 2905 through 2911 removed outlier: 3.847A pdb=" N ARG A2911 " --> pdb=" O ALA A2907 " (cutoff:3.500A) Processing helix chain 'A' and resid 2921 through 2933 Processing helix chain 'A' and resid 2949 through 2953 Processing helix chain 'A' and resid 2960 through 2980 removed outlier: 3.590A pdb=" N ALA A2964 " --> pdb=" O THR A2960 " (cutoff:3.500A) Processing helix chain 'A' and resid 2989 through 3034 removed outlier: 3.925A pdb=" N ALA A3005 " --> pdb=" O LYS A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3290 through 3334 removed outlier: 4.702A pdb=" N PHE A3301 " --> pdb=" O LYS A3297 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLU A3302 " --> pdb=" O SER A3298 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE A3321 " --> pdb=" O SER A3317 " (cutoff:3.500A) removed outlier: 5.097A 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: 4.187A pdb=" N THR A3416 " --> pdb=" O SER A3412 " (cutoff:3.500A) Processing helix chain 'A' and resid 3435 through 3447 Processing helix chain 'A' and resid 3454 through 3458 removed outlier: 3.701A pdb=" N PHE A3458 " --> pdb=" O GLY A3455 " (cutoff:3.500A) Processing helix chain 'A' and resid 3459 through 3461 No H-bonds generated for 'chain 'A' and resid 3459 through 3461' Processing helix chain 'A' and resid 3462 through 3468 Processing helix chain 'A' and resid 3506 through 3511 removed outlier: 3.675A pdb=" N SER A3511 " --> pdb=" O ILE A3507 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3538 Processing helix chain 'A' and resid 3538 through 3572 removed outlier: 3.616A pdb=" N LEU A3567 " --> pdb=" O GLU A3563 " (cutoff:3.500A) Processing helix chain 'A' and resid 3583 through 3605 removed outlier: 4.062A pdb=" N ASN A3588 " --> pdb=" O MET A3584 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A3605 " --> pdb=" O LEU A3601 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3618 Processing helix chain 'A' and resid 3618 through 3639 removed outlier: 3.916A pdb=" N GLY A3622 " --> pdb=" O TYR A3618 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A3638 " --> pdb=" O LYS A3634 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS A3639 " --> pdb=" O PHE A3635 " (cutoff:3.500A) Processing helix chain 'A' and resid 3640 through 3643 removed outlier: 4.151A pdb=" N GLY A3643 " --> pdb=" O TRP A3640 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3640 through 3643' Processing helix chain 'A' and resid 3645 through 3659 removed outlier: 3.917A pdb=" N PHE A3649 " --> pdb=" O SER A3645 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A3656 " --> pdb=" O CYS A3652 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE A3658 " --> pdb=" O LYS A3654 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A3659 " --> pdb=" O ARG A3655 " (cutoff:3.500A) Processing helix chain 'A' and resid 3670 through 3687 Processing helix chain 'A' and resid 3691 through 3711 removed outlier: 4.076A pdb=" N ASP A3709 " --> pdb=" O LEU A3705 " (cutoff:3.500A) Processing helix chain 'A' and resid 3712 through 3728 removed outlier: 3.616A pdb=" N LYS A3716 " --> pdb=" O SER A3712 " (cutoff:3.500A) Processing helix chain 'A' and resid 3742 through 3753 removed outlier: 4.080A pdb=" N TYR A3746 " --> pdb=" O ASP A3742 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A3747 " --> pdb=" O ASP A3743 " (cutoff:3.500A) Processing helix chain 'A' and resid 3755 through 3767 removed outlier: 4.224A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.493A 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: 3.657A pdb=" N LEU A3800 " --> pdb=" O GLY A3796 " (cutoff:3.500A) Processing helix chain 'A' and resid 3818 through 3836 removed outlier: 3.894A pdb=" N ILE A3834 " --> pdb=" O SER A3830 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3846 Processing helix chain 'A' and resid 3847 through 3861 removed outlier: 3.615A pdb=" N LEU A3855 " --> pdb=" O VAL A3851 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N HIS A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) Processing helix chain 'A' and resid 3885 through 3891 removed outlier: 3.567A pdb=" N ARG A3891 " --> pdb=" O PRO A3887 " (cutoff:3.500A) Processing helix chain 'A' and resid 3903 through 3912 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 removed outlier: 3.714A pdb=" N LEU A4004 " --> pdb=" O GLU A4000 " (cutoff:3.500A) Processing helix chain 'A' and resid 4037 through 4052 removed outlier: 3.609A pdb=" N THR A4052 " --> pdb=" O ILE A4048 " (cutoff:3.500A) Processing helix chain 'A' and resid 4057 through 4062 Processing helix chain 'A' and resid 4066 through 4090 removed outlier: 3.564A pdb=" N ILE A4070 " --> pdb=" O PRO A4066 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A4072 " --> pdb=" O GLU A4068 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR A4073 " --> pdb=" O SER A4069 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A4081 " --> pdb=" O GLN A4077 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'C' and resid 401 through 405 removed outlier: 4.019A pdb=" N SER C 405 " --> pdb=" O PRO C 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 Processing sheet with id=AA1, first strand: chain 'A' and resid 1569 through 1574 removed outlier: 6.687A pdb=" N ARG A1583 " --> pdb=" O GLU A1570 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE A1572 " --> pdb=" O GLY A1581 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLY A1581 " --> pdb=" O ILE A1572 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N PHE A1574 " --> pdb=" O ILE A1579 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ILE A1579 " --> pdb=" O PHE A1574 " (cutoff:3.500A) removed outlier: 10.039A pdb=" N SER A1578 " --> pdb=" O GLU A1594 " (cutoff:3.500A) removed outlier: 10.756A pdb=" N GLU A1594 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N THR A1580 " --> pdb=" O LEU A1592 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1733 through 1734 Processing sheet with id=AA3, first strand: chain 'A' and resid 1817 through 1821 removed outlier: 6.446A pdb=" N VAL A1818 " --> pdb=" O CYS A1846 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP A1848 " --> pdb=" O VAL A1818 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N PHE A1820 " --> pdb=" O ASP A1848 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A1897 " --> pdb=" O PHE A1847 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLY A1792 " --> pdb=" O ILE A1896 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU A1898 " --> pdb=" O GLY A1792 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE A1794 " --> pdb=" O LEU A1898 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1878 through 1881 removed outlier: 3.812A pdb=" N LEU A1881 " --> pdb=" O GLU A1884 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A1884 " --> pdb=" O LEU A1881 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2098 through 2104 removed outlier: 7.866A pdb=" N ARG A2191 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ILE A2150 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU A2193 " --> pdb=" O ILE A2150 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL A2152 " --> pdb=" O LEU A2193 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLU A2195 " --> pdb=" O VAL A2152 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE A2154 " --> pdb=" O GLU A2195 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA A2069 " --> pdb=" O GLY A2211 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LEU A2213 " --> pdb=" O ALA A2069 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE A2071 " --> pdb=" O LEU A2213 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N PHE A2215 " --> pdb=" O ILE A2071 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A2073 " --> pdb=" O PHE A2215 " (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 2357 through 2360 Processing sheet with id=AA9, first strand: chain 'A' and resid 2438 through 2444 removed outlier: 6.431A pdb=" N LEU A2482 " --> pdb=" O HIS A2530 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL A2532 " --> pdb=" O LEU A2482 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU A2484 " --> pdb=" O VAL A2532 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ALA A2534 " --> pdb=" O LEU A2484 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N CYS A2486 " --> pdb=" O ALA A2534 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A2414 " --> pdb=" O ILE A2531 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLY A2413 " --> pdb=" O ALA A2555 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU A2557 " --> pdb=" O GLY A2413 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A2415 " --> pdb=" O LEU A2557 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2462 through 2465 Processing sheet with id=AB2, first strand: chain 'A' and resid 2696 through 2697 Processing sheet with id=AB3, first strand: chain 'A' and resid 2780 through 2782 removed outlier: 6.196A pdb=" N LYS A2780 " --> pdb=" O CYS A2814 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE A2816 " --> pdb=" O LYS A2780 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A2782 " --> pdb=" O ILE A2816 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ASP A2818 " --> pdb=" O VAL A2782 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR A2813 " --> pdb=" O HIS A2886 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL A2888 " --> pdb=" O THR A2813 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A2815 " --> pdb=" O VAL A2888 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N THR A2890 " --> pdb=" O LEU A2815 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE A2817 " --> pdb=" O THR A2890 " (cutoff:3.500A) removed outlier: 10.479A pdb=" N HIS A2755 " --> pdb=" O ILE A2914 " (cutoff:3.500A) removed outlier: 10.713A pdb=" N TRP A2916 " --> pdb=" O HIS A2755 " (cutoff:3.500A) removed outlier: 10.741A pdb=" N MET A2757 " --> pdb=" O TRP A2916 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N GLY A2918 " --> pdb=" O MET A2757 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE A2759 " --> pdb=" O GLY A2918 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3426 through 3430 removed outlier: 6.419A pdb=" N VAL A3427 " --> pdb=" O ILE A3451 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N GLN A3453 " --> pdb=" O VAL A3427 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU A3429 " --> pdb=" O GLN A3453 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL A3450 " --> pdb=" O PHE A3495 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N HIS A3497 " --> pdb=" O VAL A3450 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE A3452 " --> pdb=" O HIS A3497 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3471 through 3473 removed outlier: 3.621A pdb=" N ILE A3481 " --> pdb=" O HIS A3484 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS A3484 " --> pdb=" O ILE A3481 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3811 through 3815 removed outlier: 6.401A pdb=" N GLY A3837 " --> pdb=" O LYS A3872 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N PHE A3874 " --> pdb=" O GLY A3837 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE A3839 " --> pdb=" O PHE A3874 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR A3876 " --> pdb=" O ILE A3839 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A3841 " --> pdb=" O THR A3876 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N HIS A3878 " --> pdb=" O LEU A3841 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A3790 " --> pdb=" O CYS A3877 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TYR A3785 " --> pdb=" O ASP A3893 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N VAL A3895 " --> pdb=" O TYR A3785 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N THR A3787 " --> pdb=" O VAL A3895 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 4020 through 4021 Processing sheet with id=AB8, first strand: chain 'C' and resid 150 through 153 removed outlier: 4.351A pdb=" N LYS C 488 " --> pdb=" O GLY C 484 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 158 through 163 removed outlier: 4.007A pdb=" N SER C 160 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR C 174 " --> pdb=" O LYS C 178 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 192 " --> pdb=" O ALA C 181 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 201 through 208 removed outlier: 4.825A pdb=" N LEU C 220 " --> pdb=" O TRP C 236 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE C 231 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER C 248 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL C 233 " --> pdb=" O ILE C 246 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 256 through 263 removed outlier: 6.622A pdb=" N CYS C 273 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL C 259 " --> pdb=" O ALA C 271 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA C 271 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE C 261 " --> pdb=" O HIS C 269 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N HIS C 269 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL C 279 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR C 292 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE C 281 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 300 through 306 removed outlier: 6.006A pdb=" N HIS C 323 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLY C 329 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 340 through 345 removed outlier: 6.615A pdb=" N ALA C 376 " --> pdb=" O GLU C 341 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL C 343 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL C 374 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N PHE C 345 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N TYR C 372 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER C 377 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 411 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU C 386 " --> pdb=" O CYS C 409 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N CYS C 409 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 420 through 426 removed outlier: 3.516A pdb=" N ASP C 422 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL C 439 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL C 452 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N CYS C 441 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN C 448 " --> pdb=" O ASP C 443 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 150 through 153 removed outlier: 4.333A pdb=" N LYS B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 158 through 163 removed outlier: 6.917A pdb=" N ALA B 173 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL B 161 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N PHE B 171 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU B 163 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE B 169 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS B 178 " --> pdb=" O THR B 174 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 201 through 208 removed outlier: 4.516A pdb=" N LEU B 220 " --> pdb=" O TRP B 236 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LYS B 235 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLN B 245 " --> pdb=" O LYS B 235 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL B 237 " --> pdb=" O PHE B 243 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N PHE B 243 " --> pdb=" O VAL B 237 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 256 through 263 removed outlier: 6.710A pdb=" N CYS B 273 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL B 259 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA B 271 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE B 261 " --> pdb=" O HIS B 269 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N HIS B 269 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 279 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR B 292 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE B 281 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 300 through 306 removed outlier: 6.563A pdb=" N GLY B 313 " --> pdb=" O ARG B 301 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE B 303 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 311 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL B 305 " --> pdb=" O TYR B 309 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N TYR B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 319 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL B 332 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU B 321 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 340 through 345 removed outlier: 6.621A pdb=" N ALA B 376 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL B 343 " --> pdb=" O VAL B 374 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL B 374 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N PHE B 345 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N TYR B 372 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS B 373 " --> pdb=" O TRP B 385 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 420 through 426 removed outlier: 3.536A pdb=" N ASP B 422 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG B 426 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 434 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL B 439 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL B 452 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N CYS B 441 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN B 448 " --> pdb=" O ASP B 443 " (cutoff:3.500A) 1205 hydrogen bonds defined for protein. 3492 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.82 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3936 1.31 - 1.44: 6611 1.44 - 1.56: 13857 1.56 - 1.69: 18 1.69 - 1.81: 177 Bond restraints: 24599 Sorted by residual: bond pdb=" C4 ADP A4104 " pdb=" C5 ADP A4104 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C5 ADP A4104 " pdb=" C6 ADP A4104 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C PRO A2937 " pdb=" O PRO A2937 " ideal model delta sigma weight residual 1.235 1.183 0.053 1.30e-02 5.92e+03 1.63e+01 bond pdb=" N VAL A2935 " pdb=" CA VAL A2935 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.07e-02 8.73e+03 7.76e+00 bond pdb=" N PRO A2937 " pdb=" CA PRO A2937 " ideal model delta sigma weight residual 1.469 1.439 0.030 1.28e-02 6.10e+03 5.57e+00 ... (remaining 24594 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 33046 2.38 - 4.77: 227 4.77 - 7.15: 17 7.15 - 9.53: 9 9.53 - 11.92: 4 Bond angle restraints: 33303 Sorted by residual: angle pdb=" PB ATP A4103 " pdb=" O3B ATP A4103 " pdb=" PG ATP A4103 " ideal model delta sigma weight residual 139.87 127.95 11.92 1.00e+00 1.00e+00 1.42e+02 angle pdb=" PB ATP A4102 " pdb=" O3B ATP A4102 " pdb=" PG ATP A4102 " ideal model delta sigma weight residual 139.87 128.25 11.62 1.00e+00 1.00e+00 1.35e+02 angle pdb=" PB ATP A4101 " pdb=" O3B ATP A4101 " pdb=" PG ATP A4101 " ideal model delta sigma weight residual 139.87 128.32 11.55 1.00e+00 1.00e+00 1.33e+02 angle pdb=" PA ATP A4103 " pdb=" O3A ATP A4103 " pdb=" PB ATP A4103 " ideal model delta sigma weight residual 136.83 129.63 7.20 1.00e+00 1.00e+00 5.19e+01 angle pdb=" PA ATP A4102 " pdb=" O3A ATP A4102 " pdb=" PB ATP A4102 " ideal model delta sigma weight residual 136.83 129.83 7.00 1.00e+00 1.00e+00 4.90e+01 ... (remaining 33298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.80: 14460 34.80 - 69.60: 281 69.60 - 104.40: 18 104.40 - 139.20: 0 139.20 - 174.00: 2 Dihedral angle restraints: 14761 sinusoidal: 6087 harmonic: 8674 Sorted by residual: dihedral pdb=" O1B ADP A4104 " pdb=" O3A ADP A4104 " pdb=" PB ADP A4104 " pdb=" PA ADP A4104 " ideal model delta sinusoidal sigma weight residual -60.00 114.00 -174.00 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP A4104 " pdb=" O5' ADP A4104 " pdb=" PA ADP A4104 " pdb=" O2A ADP A4104 " ideal model delta sinusoidal sigma weight residual 300.00 126.71 173.29 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP A4104 " pdb=" O3A ADP A4104 " pdb=" PA ADP A4104 " pdb=" PB ADP A4104 " ideal model delta sinusoidal sigma weight residual -60.00 28.57 -88.57 1 2.00e+01 2.50e-03 2.34e+01 ... (remaining 14758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2826 0.044 - 0.089: 692 0.089 - 0.133: 238 0.133 - 0.177: 7 0.177 - 0.222: 4 Chirality restraints: 3767 Sorted by residual: chirality pdb=" CA LEU A2873 " pdb=" N LEU A2873 " pdb=" C LEU A2873 " pdb=" CB LEU A2873 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA VAL A2935 " pdb=" N VAL A2935 " pdb=" C VAL A2935 " pdb=" CB VAL A2935 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C3' ADP A4104 " pdb=" C2' ADP A4104 " pdb=" C4' ADP A4104 " pdb=" O3' ADP A4104 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.20 2.00e-01 2.50e+01 9.92e-01 ... (remaining 3764 not shown) Planarity restraints: 4169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A2618 " 0.037 5.00e-02 4.00e+02 5.63e-02 5.08e+00 pdb=" N PRO A2619 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A2619 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A2619 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A2875 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C ASP A2875 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP A2875 " 0.013 2.00e-02 2.50e+03 pdb=" N TRP A2876 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP A4102 " -0.026 2.00e-02 2.50e+03 1.14e-02 3.59e+00 pdb=" C2 ATP A4102 " 0.002 2.00e-02 2.50e+03 pdb=" C4 ATP A4102 " 0.009 2.00e-02 2.50e+03 pdb=" C5 ATP A4102 " 0.007 2.00e-02 2.50e+03 pdb=" C6 ATP A4102 " 0.004 2.00e-02 2.50e+03 pdb=" C8 ATP A4102 " -0.001 2.00e-02 2.50e+03 pdb=" N1 ATP A4102 " -0.006 2.00e-02 2.50e+03 pdb=" N3 ATP A4102 " 0.007 2.00e-02 2.50e+03 pdb=" N6 ATP A4102 " -0.017 2.00e-02 2.50e+03 pdb=" N7 ATP A4102 " 0.007 2.00e-02 2.50e+03 pdb=" N9 ATP A4102 " 0.013 2.00e-02 2.50e+03 ... (remaining 4166 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 110 2.48 - 3.08: 16549 3.08 - 3.69: 34892 3.69 - 4.29: 53781 4.29 - 4.90: 90493 Nonbonded interactions: 195825 Sorted by model distance: nonbonded pdb=" O2B ATP A4103 " pdb="MG MG A4106 " model vdw 1.874 2.170 nonbonded pdb=" O2G ATP A4103 " pdb="MG MG A4106 " model vdw 1.917 2.170 nonbonded pdb=" O2B ATP A4101 " pdb="MG MG A4105 " model vdw 2.014 2.170 nonbonded pdb=" OG1 THR A1803 " pdb="MG MG A4105 " model vdw 2.016 2.170 nonbonded pdb=" OG1 THR A2081 " pdb="MG MG A4106 " model vdw 2.018 2.170 ... (remaining 195820 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 139 through 350 or resid 355 through 400 or resid 405 thro \ ugh 493 or (resid 494 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD or name NE or name CZ or name NH1 or name NH2)))) } 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.640 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 24599 Z= 0.198 Angle : 0.553 11.917 33303 Z= 0.328 Chirality : 0.043 0.222 3767 Planarity : 0.003 0.056 4169 Dihedral : 14.451 174.003 9119 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.04 % Allowed : 0.26 % Favored : 99.70 % 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: 0.78 (0.16), residues: 2922 helix: 2.19 (0.15), residues: 1315 sheet: -0.07 (0.24), residues: 482 loop : -1.29 (0.17), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2620 TYR 0.019 0.001 TYR A2874 PHE 0.019 0.001 PHE A1850 TRP 0.025 0.001 TRP B 288 HIS 0.007 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00440 (24599) covalent geometry : angle 0.55336 (33303) hydrogen bonds : bond 0.15003 ( 1205) hydrogen bonds : angle 5.91390 ( 3492) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.823 Fit side-chains REVERT: A 1741 LEU cc_start: 0.8135 (mm) cc_final: 0.7740 (tp) REVERT: A 2386 MET cc_start: 0.9024 (mmm) cc_final: 0.8742 (mmt) REVERT: A 2873 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8671 (mt) REVERT: A 3398 MET cc_start: 0.9127 (mmm) cc_final: 0.8353 (mmm) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.1515 time to fit residues: 18.6768 Evaluate side-chains 67 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2873 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2348 HIS A2931 ASN B 232 HIS B 244 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.044599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.035525 restraints weight = 120279.165| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 2.70 r_work: 0.2674 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24599 Z= 0.109 Angle : 0.459 6.744 33303 Z= 0.249 Chirality : 0.041 0.150 3767 Planarity : 0.003 0.048 4169 Dihedral : 8.327 166.897 3277 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.15 % Allowed : 2.95 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.16), residues: 2922 helix: 2.45 (0.15), residues: 1325 sheet: 0.17 (0.24), residues: 489 loop : -1.15 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 247 TYR 0.014 0.001 TYR A3330 PHE 0.014 0.001 PHE A1620 TRP 0.021 0.001 TRP A2084 HIS 0.004 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00237 (24599) covalent geometry : angle 0.45862 (33303) hydrogen bonds : bond 0.04162 ( 1205) hydrogen bonds : angle 4.32830 ( 3492) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.909 Fit side-chains REVERT: A 1741 LEU cc_start: 0.8339 (mm) cc_final: 0.7934 (tp) REVERT: A 1963 MET cc_start: 0.8296 (mtp) cc_final: 0.7822 (mtt) REVERT: A 3398 MET cc_start: 0.9285 (mmm) cc_final: 0.8999 (mmm) outliers start: 4 outliers final: 1 residues processed: 68 average time/residue: 0.1455 time to fit residues: 17.5801 Evaluate side-chains 66 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2427 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 260 optimal weight: 10.0000 chunk 221 optimal weight: 10.0000 chunk 182 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 292 optimal weight: 9.9990 chunk 278 optimal weight: 20.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3542 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.044107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.034976 restraints weight = 121921.432| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.71 r_work: 0.2651 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24599 Z= 0.160 Angle : 0.468 6.777 33303 Z= 0.251 Chirality : 0.041 0.138 3767 Planarity : 0.003 0.049 4169 Dihedral : 8.018 172.527 3275 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.33 % Allowed : 4.28 % Favored : 95.39 % 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: 1.20 (0.16), residues: 2922 helix: 2.49 (0.14), residues: 1328 sheet: 0.24 (0.24), residues: 489 loop : -1.10 (0.17), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 247 TYR 0.013 0.001 TYR A2571 PHE 0.015 0.001 PHE A1850 TRP 0.021 0.001 TRP A2084 HIS 0.003 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00376 (24599) covalent geometry : angle 0.46753 (33303) hydrogen bonds : bond 0.04321 ( 1205) hydrogen bonds : angle 4.16836 ( 3492) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.862 Fit side-chains REVERT: A 1963 MET cc_start: 0.8439 (mtp) cc_final: 0.8105 (mtt) REVERT: A 3398 MET cc_start: 0.9226 (mmm) cc_final: 0.8499 (mmm) REVERT: B 255 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8435 (mp) outliers start: 9 outliers final: 4 residues processed: 72 average time/residue: 0.1485 time to fit residues: 19.0525 Evaluate side-chains 71 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2503 VAL Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain C residue 493 MET Chi-restraints excluded: chain B residue 255 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 35 optimal weight: 0.9980 chunk 180 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 205 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 280 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3011 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.044005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.034930 restraints weight = 121637.710| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.70 r_work: 0.2650 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24599 Z= 0.160 Angle : 0.464 6.704 33303 Z= 0.249 Chirality : 0.041 0.138 3767 Planarity : 0.003 0.048 4169 Dihedral : 7.695 147.591 3275 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.48 % Allowed : 5.35 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.16), residues: 2922 helix: 2.52 (0.14), residues: 1329 sheet: 0.28 (0.24), residues: 489 loop : -1.07 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1905 TYR 0.014 0.001 TYR A2571 PHE 0.014 0.001 PHE A1620 TRP 0.021 0.001 TRP A2084 HIS 0.003 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00377 (24599) covalent geometry : angle 0.46370 (33303) hydrogen bonds : bond 0.04186 ( 1205) hydrogen bonds : angle 4.08239 ( 3492) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.997 Fit side-chains REVERT: A 1963 MET cc_start: 0.8456 (mtp) cc_final: 0.8195 (mtt) REVERT: A 3345 MET cc_start: 0.9218 (mmm) cc_final: 0.8923 (mmm) REVERT: A 3398 MET cc_start: 0.9228 (mmm) cc_final: 0.8590 (mmm) REVERT: B 255 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8546 (mp) outliers start: 13 outliers final: 8 residues processed: 73 average time/residue: 0.1423 time to fit residues: 18.6740 Evaluate side-chains 75 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 2348 HIS Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2503 VAL Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 493 MET Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 479 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 250 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 196 optimal weight: 9.9990 chunk 135 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 258 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 231 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.044302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.035250 restraints weight = 120452.951| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.71 r_work: 0.2662 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24599 Z= 0.127 Angle : 0.437 6.713 33303 Z= 0.235 Chirality : 0.041 0.137 3767 Planarity : 0.003 0.046 4169 Dihedral : 7.335 121.491 3275 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.41 % Allowed : 6.31 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.16), residues: 2922 helix: 2.61 (0.14), residues: 1329 sheet: 0.33 (0.24), residues: 489 loop : -1.02 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1905 TYR 0.012 0.001 TYR A2571 PHE 0.013 0.001 PHE A1620 TRP 0.021 0.001 TRP A2084 HIS 0.003 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00296 (24599) covalent geometry : angle 0.43652 (33303) hydrogen bonds : bond 0.03862 ( 1205) hydrogen bonds : angle 3.96657 ( 3492) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.856 Fit side-chains REVERT: A 1963 MET cc_start: 0.8480 (mtp) cc_final: 0.8218 (mtt) REVERT: A 3345 MET cc_start: 0.9189 (mmm) cc_final: 0.8893 (mmm) REVERT: A 3398 MET cc_start: 0.9221 (mmm) cc_final: 0.8619 (mmm) REVERT: B 240 GLU cc_start: 0.8851 (mp0) cc_final: 0.8371 (mp0) outliers start: 11 outliers final: 5 residues processed: 75 average time/residue: 0.1414 time to fit residues: 18.9560 Evaluate side-chains 72 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 2166 MET Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2503 VAL Chi-restraints excluded: chain C residue 324 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 164 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 243 optimal weight: 10.0000 chunk 256 optimal weight: 6.9990 chunk 178 optimal weight: 6.9990 chunk 106 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.044340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.035242 restraints weight = 120861.361| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.71 r_work: 0.2665 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24599 Z= 0.122 Angle : 0.432 6.710 33303 Z= 0.232 Chirality : 0.040 0.136 3767 Planarity : 0.003 0.045 4169 Dihedral : 7.162 101.097 3275 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.41 % Allowed : 6.94 % Favored : 92.66 % 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: 1.43 (0.16), residues: 2922 helix: 2.67 (0.14), residues: 1329 sheet: 0.33 (0.24), residues: 494 loop : -0.96 (0.17), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1905 TYR 0.012 0.001 TYR A2571 PHE 0.013 0.001 PHE A2877 TRP 0.021 0.001 TRP A2084 HIS 0.003 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00284 (24599) covalent geometry : angle 0.43157 (33303) hydrogen bonds : bond 0.03771 ( 1205) hydrogen bonds : angle 3.91364 ( 3492) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.968 Fit side-chains REVERT: A 1963 MET cc_start: 0.8493 (mtp) cc_final: 0.8248 (mtt) REVERT: A 3398 MET cc_start: 0.9218 (mmm) cc_final: 0.8751 (mmm) REVERT: B 240 GLU cc_start: 0.8796 (mp0) cc_final: 0.8309 (mp0) outliers start: 11 outliers final: 8 residues processed: 74 average time/residue: 0.1481 time to fit residues: 19.6057 Evaluate side-chains 75 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 2166 MET Chi-restraints excluded: chain A residue 2348 HIS Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2503 VAL Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 468 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 234 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 184 optimal weight: 0.5980 chunk 247 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 206 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.044410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.035376 restraints weight = 119995.980| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 2.70 r_work: 0.2670 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24599 Z= 0.113 Angle : 0.425 6.727 33303 Z= 0.229 Chirality : 0.040 0.137 3767 Planarity : 0.003 0.044 4169 Dihedral : 6.980 81.698 3275 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.37 % Allowed : 7.27 % Favored : 92.36 % 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: 1.51 (0.16), residues: 2922 helix: 2.70 (0.14), residues: 1336 sheet: 0.42 (0.24), residues: 498 loop : -0.92 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1905 TYR 0.012 0.001 TYR A2571 PHE 0.013 0.001 PHE A2877 TRP 0.021 0.001 TRP A2084 HIS 0.003 0.000 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00263 (24599) covalent geometry : angle 0.42548 (33303) hydrogen bonds : bond 0.03643 ( 1205) hydrogen bonds : angle 3.86478 ( 3492) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.694 Fit side-chains REVERT: A 1963 MET cc_start: 0.8500 (mtp) cc_final: 0.8267 (mtt) REVERT: A 3345 MET cc_start: 0.9205 (mmp) cc_final: 0.8955 (mmm) REVERT: A 3398 MET cc_start: 0.9221 (mmm) cc_final: 0.8759 (mmm) REVERT: B 240 GLU cc_start: 0.8779 (mp0) cc_final: 0.8292 (mp0) outliers start: 10 outliers final: 8 residues processed: 75 average time/residue: 0.1408 time to fit residues: 18.8455 Evaluate side-chains 75 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 2348 HIS Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2503 VAL Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain B residue 324 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 3 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 250 optimal weight: 4.9990 chunk 239 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 190 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.044687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.035642 restraints weight = 119845.848| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.70 r_work: 0.2680 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24599 Z= 0.103 Angle : 0.417 6.708 33303 Z= 0.224 Chirality : 0.040 0.137 3767 Planarity : 0.003 0.044 4169 Dihedral : 6.764 80.037 3275 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.48 % Allowed : 7.23 % Favored : 92.29 % 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: 1.58 (0.16), residues: 2922 helix: 2.75 (0.14), residues: 1336 sheet: 0.43 (0.24), residues: 500 loop : -0.89 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1905 TYR 0.013 0.001 TYR B 372 PHE 0.013 0.001 PHE A2877 TRP 0.021 0.001 TRP A2084 HIS 0.003 0.000 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00237 (24599) covalent geometry : angle 0.41725 (33303) hydrogen bonds : bond 0.03517 ( 1205) hydrogen bonds : angle 3.81933 ( 3492) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.966 Fit side-chains REVERT: A 1963 MET cc_start: 0.8492 (mtp) cc_final: 0.8256 (mtt) REVERT: A 2386 MET cc_start: 0.9394 (mmm) cc_final: 0.9006 (mmt) REVERT: A 3345 MET cc_start: 0.9199 (mmp) cc_final: 0.8956 (mmm) REVERT: A 3398 MET cc_start: 0.9215 (mmm) cc_final: 0.8742 (mmm) REVERT: B 240 GLU cc_start: 0.8760 (mp0) cc_final: 0.8256 (mp0) outliers start: 13 outliers final: 9 residues processed: 75 average time/residue: 0.1341 time to fit residues: 18.2395 Evaluate side-chains 76 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 2166 MET Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2503 VAL Chi-restraints excluded: chain A residue 2738 MET Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain B residue 324 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 93 optimal weight: 0.9980 chunk 156 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.044648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.035575 restraints weight = 121158.966| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.71 r_work: 0.2676 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24599 Z= 0.111 Angle : 0.424 7.589 33303 Z= 0.226 Chirality : 0.040 0.136 3767 Planarity : 0.003 0.044 4169 Dihedral : 6.721 78.926 3275 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.41 % Allowed : 7.31 % Favored : 92.29 % 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: 1.62 (0.16), residues: 2922 helix: 2.78 (0.14), residues: 1336 sheet: 0.48 (0.24), residues: 498 loop : -0.87 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1905 TYR 0.012 0.001 TYR B 372 PHE 0.013 0.001 PHE A2877 TRP 0.020 0.001 TRP A2084 HIS 0.003 0.000 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00257 (24599) covalent geometry : angle 0.42414 (33303) hydrogen bonds : bond 0.03558 ( 1205) hydrogen bonds : angle 3.81244 ( 3492) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 1.228 Fit side-chains REVERT: A 2386 MET cc_start: 0.9358 (mmm) cc_final: 0.8958 (mmt) REVERT: A 3345 MET cc_start: 0.9193 (mmp) cc_final: 0.8959 (mmm) REVERT: A 3398 MET cc_start: 0.9226 (mmm) cc_final: 0.8755 (mmm) REVERT: B 240 GLU cc_start: 0.8747 (mp0) cc_final: 0.8232 (mp0) outliers start: 11 outliers final: 10 residues processed: 73 average time/residue: 0.1488 time to fit residues: 19.7333 Evaluate side-chains 77 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 2166 MET Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2432 LEU Chi-restraints excluded: chain A residue 2503 VAL Chi-restraints excluded: chain A residue 2738 MET Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain B residue 324 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 221 optimal weight: 0.9990 chunk 271 optimal weight: 6.9990 chunk 242 optimal weight: 0.9990 chunk 257 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 255 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 177 optimal weight: 1.9990 chunk 202 optimal weight: 0.8980 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2598 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.044858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.035771 restraints weight = 120754.131| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.73 r_work: 0.2685 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24599 Z= 0.097 Angle : 0.414 7.464 33303 Z= 0.221 Chirality : 0.040 0.136 3767 Planarity : 0.003 0.043 4169 Dihedral : 6.608 78.970 3275 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.41 % Allowed : 7.45 % Favored : 92.14 % 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 (0.16), residues: 2922 helix: 2.82 (0.14), residues: 1336 sheet: 0.53 (0.24), residues: 498 loop : -0.84 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1905 TYR 0.012 0.001 TYR A2571 PHE 0.013 0.001 PHE A2877 TRP 0.021 0.001 TRP A2084 HIS 0.003 0.000 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00221 (24599) covalent geometry : angle 0.41401 (33303) hydrogen bonds : bond 0.03391 ( 1205) hydrogen bonds : angle 3.77123 ( 3492) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.959 Fit side-chains REVERT: A 2386 MET cc_start: 0.9352 (mmm) cc_final: 0.8936 (mmt) REVERT: A 3345 MET cc_start: 0.9179 (mmp) cc_final: 0.8953 (mmm) REVERT: A 3398 MET cc_start: 0.9250 (mmm) cc_final: 0.8807 (mmm) REVERT: B 240 GLU cc_start: 0.8730 (mp0) cc_final: 0.8217 (mp0) outliers start: 11 outliers final: 10 residues processed: 75 average time/residue: 0.1524 time to fit residues: 20.1994 Evaluate side-chains 77 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 2166 MET Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2432 LEU Chi-restraints excluded: chain A residue 2503 VAL Chi-restraints excluded: chain A residue 2738 MET Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain B residue 324 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 120 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 202 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.044809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.035746 restraints weight = 118787.195| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.76 r_work: 0.2689 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24599 Z= 0.125 Angle : 0.430 7.575 33303 Z= 0.229 Chirality : 0.040 0.180 3767 Planarity : 0.003 0.044 4169 Dihedral : 6.674 78.926 3275 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.37 % Allowed : 7.56 % Favored : 92.07 % 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: 1.65 (0.16), residues: 2922 helix: 2.79 (0.14), residues: 1337 sheet: 0.52 (0.24), residues: 498 loop : -0.86 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1905 TYR 0.012 0.001 TYR A2571 PHE 0.013 0.001 PHE A2877 TRP 0.020 0.001 TRP A2084 HIS 0.002 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00294 (24599) covalent geometry : angle 0.42998 (33303) hydrogen bonds : bond 0.03617 ( 1205) hydrogen bonds : angle 3.80716 ( 3492) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4151.97 seconds wall clock time: 72 minutes 43.38 seconds (4363.38 seconds total)