Starting phenix.real_space_refine on Mon Sep 30 06:51:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgm_23829/09_2024/7mgm_23829.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgm_23829/09_2024/7mgm_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgm_23829/09_2024/7mgm_23829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgm_23829/09_2024/7mgm_23829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgm_23829/09_2024/7mgm_23829.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgm_23829/09_2024/7mgm_23829.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 13.99, per 1000 atoms: 0.58 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: 6.23 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 3.63 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: 13.80 Time building geometry restraints manager: 7.31 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 59.620 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.100 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.590 ------------------------------------------------------------------------------- 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= 0.285 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 : 5.80 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (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 TRP 0.025 0.001 TRP B 288 HIS 0.007 0.001 HIS C 254 PHE 0.019 0.001 PHE A1850 TYR 0.019 0.001 TYR A2874 ARG 0.005 0.000 ARG A2620 *********************** 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 fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 2.651 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: 0.3303 time to fit residues: 41.3779 Evaluate side-chains 67 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 2.779 ------------------------------------------------------------------------------- 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 249 optimal weight: 1.9990 chunk 223 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 231 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 267 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2931 ASN B 232 HIS B 244 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.0614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 24599 Z= 0.322 Angle : 0.526 6.776 33303 Z= 0.283 Chirality : 0.043 0.148 3767 Planarity : 0.004 0.053 4169 Dihedral : 8.750 168.473 3277 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.15 % Allowed : 3.36 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.16), residues: 2922 helix: 2.30 (0.15), residues: 1319 sheet: 0.04 (0.24), residues: 494 loop : -1.24 (0.17), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A2084 HIS 0.005 0.001 HIS C 254 PHE 0.017 0.001 PHE A1850 TYR 0.016 0.001 TYR A2571 ARG 0.004 0.000 ARG B 247 *********************** 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 fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 2.657 Fit side-chains REVERT: A 1741 LEU cc_start: 0.8101 (mm) cc_final: 0.7899 (mm) REVERT: A 1963 MET cc_start: 0.8300 (mtp) cc_final: 0.7914 (mtt) REVERT: A 2386 MET cc_start: 0.9156 (mmm) cc_final: 0.8834 (mmt) REVERT: A 3398 MET cc_start: 0.9079 (mmm) cc_final: 0.8330 (mmm) REVERT: A 3722 MET cc_start: 0.8625 (mmt) cc_final: 0.8420 (mmt) outliers start: 4 outliers final: 3 residues processed: 68 average time/residue: 0.3383 time to fit residues: 41.1546 Evaluate side-chains 68 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain B residue 479 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 148 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 222 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 268 optimal weight: 0.0060 chunk 289 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 266 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24599 Z= 0.169 Angle : 0.445 6.746 33303 Z= 0.241 Chirality : 0.041 0.138 3767 Planarity : 0.003 0.047 4169 Dihedral : 8.081 178.401 3275 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.33 % Allowed : 4.98 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.16), residues: 2922 helix: 2.48 (0.14), residues: 1328 sheet: 0.22 (0.24), residues: 489 loop : -1.13 (0.17), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A2084 HIS 0.003 0.001 HIS C 254 PHE 0.014 0.001 PHE A1620 TYR 0.012 0.001 TYR A2571 ARG 0.002 0.000 ARG B 247 *********************** 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 fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 2.754 Fit side-chains REVERT: A 1963 MET cc_start: 0.8304 (mtp) cc_final: 0.7949 (mtt) REVERT: A 2386 MET cc_start: 0.9127 (mmm) cc_final: 0.8771 (mmt) REVERT: A 3398 MET cc_start: 0.9030 (mmm) cc_final: 0.8352 (mmm) REVERT: A 3722 MET cc_start: 0.8606 (mmt) cc_final: 0.8268 (mmt) REVERT: B 255 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8401 (mp) outliers start: 9 outliers final: 4 residues processed: 72 average time/residue: 0.3126 time to fit residues: 41.0112 Evaluate side-chains 71 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 2.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2503 VAL Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 480 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 265 optimal weight: 5.9990 chunk 201 optimal weight: 0.0980 chunk 139 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 269 optimal weight: 10.0000 chunk 285 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 255 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3011 GLN A3542 GLN C 176 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24599 Z= 0.301 Angle : 0.489 6.708 33303 Z= 0.262 Chirality : 0.042 0.146 3767 Planarity : 0.003 0.050 4169 Dihedral : 7.886 155.189 3275 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.48 % Allowed : 5.76 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.16), residues: 2922 helix: 2.48 (0.14), residues: 1321 sheet: 0.22 (0.24), residues: 489 loop : -1.10 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A2084 HIS 0.003 0.001 HIS A2201 PHE 0.015 0.001 PHE A1620 TYR 0.016 0.001 TYR A2571 ARG 0.002 0.000 ARG B 247 *********************** 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 fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 2.958 Fit side-chains REVERT: A 1963 MET cc_start: 0.8357 (mtp) cc_final: 0.8104 (mtt) REVERT: A 2386 MET cc_start: 0.9161 (mmm) cc_final: 0.8884 (mmt) REVERT: A 3398 MET cc_start: 0.9041 (mmm) cc_final: 0.8390 (mmm) REVERT: A 3722 MET cc_start: 0.8634 (mmt) cc_final: 0.8305 (mmt) outliers start: 13 outliers final: 7 residues processed: 73 average time/residue: 0.3219 time to fit residues: 42.8773 Evaluate side-chains 73 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1655 MET 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 370 MET Chi-restraints excluded: chain C residue 493 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 237 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 145 optimal weight: 9.9990 chunk 255 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.0970 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= 0.210 Angle : 0.450 7.364 33303 Z= 0.242 Chirality : 0.041 0.138 3767 Planarity : 0.003 0.046 4169 Dihedral : 7.546 135.571 3275 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.44 % Allowed : 6.64 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.16), residues: 2922 helix: 2.57 (0.14), residues: 1323 sheet: 0.29 (0.24), residues: 489 loop : -1.06 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A2084 HIS 0.004 0.001 HIS C 254 PHE 0.014 0.001 PHE A1620 TYR 0.012 0.001 TYR A2571 ARG 0.002 0.000 ARG A1905 *********************** 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 fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 2.766 Fit side-chains REVERT: A 1963 MET cc_start: 0.8355 (mtp) cc_final: 0.8144 (mtt) REVERT: A 2386 MET cc_start: 0.9150 (mmm) cc_final: 0.8834 (mmt) REVERT: A 3722 MET cc_start: 0.8621 (mmt) cc_final: 0.8268 (mmt) outliers start: 12 outliers final: 8 residues processed: 74 average time/residue: 0.3644 time to fit residues: 47.7217 Evaluate side-chains 73 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1655 MET 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 370 MET Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 480 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 95 optimal weight: 2.9990 chunk 256 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 285 optimal weight: 7.9990 chunk 236 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24599 Z= 0.280 Angle : 0.476 6.679 33303 Z= 0.254 Chirality : 0.042 0.142 3767 Planarity : 0.003 0.048 4169 Dihedral : 7.529 124.463 3275 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.59 % Allowed : 7.42 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.16), residues: 2922 helix: 2.53 (0.14), residues: 1323 sheet: 0.30 (0.24), residues: 487 loop : -1.07 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A2084 HIS 0.002 0.001 HIS A2201 PHE 0.014 0.001 PHE A1620 TYR 0.015 0.001 TYR A2571 ARG 0.002 0.000 ARG A1905 *********************** 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 83 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 67 time to evaluate : 3.113 Fit side-chains REVERT: A 1518 MET cc_start: 0.6604 (ptp) cc_final: 0.6378 (ptp) REVERT: A 2386 MET cc_start: 0.9164 (mmm) cc_final: 0.8864 (mmt) REVERT: A 3722 MET cc_start: 0.8625 (mmt) cc_final: 0.8281 (mmt) outliers start: 16 outliers final: 12 residues processed: 76 average time/residue: 0.3289 time to fit residues: 44.7921 Evaluate side-chains 77 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 2.938 ------------------------------------------------------------------------------- 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 2432 LEU 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 C residue 480 MET Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 479 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 275 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 162 optimal weight: 4.9990 chunk 208 optimal weight: 0.6980 chunk 161 optimal weight: 5.9990 chunk 240 optimal weight: 0.7980 chunk 159 optimal weight: 0.7980 chunk 284 optimal weight: 7.9990 chunk 177 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2598 HIS ** A3387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1213 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= 0.129 Angle : 0.415 7.023 33303 Z= 0.224 Chirality : 0.040 0.137 3767 Planarity : 0.003 0.044 4169 Dihedral : 7.014 93.010 3275 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.48 % Allowed : 7.97 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.16), residues: 2922 helix: 2.74 (0.14), residues: 1323 sheet: 0.40 (0.24), residues: 493 loop : -0.95 (0.17), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A2084 HIS 0.003 0.000 HIS A2735 PHE 0.014 0.001 PHE A2877 TYR 0.010 0.001 TYR A2571 ARG 0.001 0.000 ARG A1905 *********************** 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 fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 3.156 Fit side-chains REVERT: A 2386 MET cc_start: 0.9089 (mmm) cc_final: 0.8767 (mmt) REVERT: A 3722 MET cc_start: 0.8559 (mmt) cc_final: 0.8169 (mmt) outliers start: 13 outliers final: 8 residues processed: 73 average time/residue: 0.3585 time to fit residues: 46.6355 Evaluate side-chains 73 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 2.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1655 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 2932 MET Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain B residue 480 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 175 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 180 optimal weight: 10.0000 chunk 193 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 258 optimal weight: 4.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24599 Z= 0.320 Angle : 0.491 6.715 33303 Z= 0.261 Chirality : 0.042 0.146 3767 Planarity : 0.003 0.047 4169 Dihedral : 7.267 86.436 3275 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.59 % Allowed : 8.34 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.16), residues: 2922 helix: 2.64 (0.14), residues: 1323 sheet: 0.36 (0.24), residues: 487 loop : -1.01 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2084 HIS 0.003 0.001 HIS A2201 PHE 0.014 0.001 PHE A1620 TYR 0.017 0.001 TYR A2571 ARG 0.002 0.000 ARG A2507 *********************** 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 81 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 3.001 Fit side-chains REVERT: A 2386 MET cc_start: 0.9179 (mmm) cc_final: 0.8883 (mmt) outliers start: 16 outliers final: 12 residues processed: 74 average time/residue: 0.3310 time to fit residues: 44.3754 Evaluate side-chains 77 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 3.088 ------------------------------------------------------------------------------- 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 2432 LEU 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 370 MET Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 479 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 272 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 264 optimal weight: 0.9980 chunk 159 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 239 optimal weight: 0.9990 chunk 250 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 chunk 280 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1867 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24599 Z= 0.162 Angle : 0.431 6.903 33303 Z= 0.231 Chirality : 0.040 0.136 3767 Planarity : 0.003 0.045 4169 Dihedral : 6.935 82.748 3275 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.41 % Allowed : 8.52 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.16), residues: 2922 helix: 2.71 (0.14), residues: 1330 sheet: 0.39 (0.24), residues: 492 loop : -0.95 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A2084 HIS 0.003 0.000 HIS C 254 PHE 0.013 0.001 PHE A1620 TYR 0.012 0.001 TYR A2571 ARG 0.002 0.000 ARG A1905 *********************** 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 76 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 3.076 Fit side-chains REVERT: A 2386 MET cc_start: 0.9113 (mmm) cc_final: 0.8806 (mmt) REVERT: A 3398 MET cc_start: 0.9060 (mmm) cc_final: 0.8578 (mmm) REVERT: A 3722 MET cc_start: 0.8571 (mmt) cc_final: 0.8196 (mmt) outliers start: 11 outliers final: 9 residues processed: 73 average time/residue: 0.3437 time to fit residues: 45.4089 Evaluate side-chains 74 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1655 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 2532 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 480 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 171 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 293 optimal weight: 6.9990 chunk 270 optimal weight: 6.9990 chunk 234 optimal weight: 3.9990 chunk 24 optimal weight: 0.0030 chunk 180 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 185 optimal weight: 1.9990 chunk 249 optimal weight: 0.8980 overall best weight: 2.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1867 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24599 Z= 0.225 Angle : 0.452 7.481 33303 Z= 0.241 Chirality : 0.041 0.135 3767 Planarity : 0.003 0.045 4169 Dihedral : 6.970 82.237 3275 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.44 % Allowed : 8.49 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.16), residues: 2922 helix: 2.68 (0.14), residues: 1330 sheet: 0.39 (0.24), residues: 492 loop : -0.95 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A2084 HIS 0.002 0.001 HIS C 254 PHE 0.013 0.001 PHE A2877 TYR 0.013 0.001 TYR A2571 ARG 0.002 0.000 ARG A2620 ********************** 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 77 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 3.028 Fit side-chains REVERT: A 2386 MET cc_start: 0.9167 (mmm) cc_final: 0.8853 (mmt) REVERT: A 3398 MET cc_start: 0.9067 (mmm) cc_final: 0.8573 (mmm) REVERT: A 3722 MET cc_start: 0.8571 (mmt) cc_final: 0.8192 (mmt) outliers start: 12 outliers final: 12 residues processed: 73 average time/residue: 0.3195 time to fit residues: 42.4049 Evaluate side-chains 77 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1655 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 2532 VAL Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 480 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 71 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 234 optimal weight: 0.0020 chunk 98 optimal weight: 4.9990 chunk 240 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1867 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.044659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.035664 restraints weight = 120035.454| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.68 r_work: 0.2681 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24599 Z= 0.145 Angle : 0.423 8.607 33303 Z= 0.226 Chirality : 0.040 0.136 3767 Planarity : 0.003 0.044 4169 Dihedral : 6.710 80.362 3275 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.41 % Allowed : 8.52 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.16), residues: 2922 helix: 2.78 (0.14), residues: 1330 sheet: 0.48 (0.24), residues: 492 loop : -0.90 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A2084 HIS 0.003 0.000 HIS A2735 PHE 0.013 0.001 PHE A2877 TYR 0.012 0.001 TYR A2571 ARG 0.002 0.000 ARG A2830 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3337.39 seconds wall clock time: 62 minutes 19.55 seconds (3739.55 seconds total)