Starting phenix.real_space_refine on Sat Jun 21 00:53:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dj7_46935/06_2025/9dj7_46935.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dj7_46935/06_2025/9dj7_46935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dj7_46935/06_2025/9dj7_46935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dj7_46935/06_2025/9dj7_46935.map" model { file = "/net/cci-nas-00/data/ceres_data/9dj7_46935/06_2025/9dj7_46935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dj7_46935/06_2025/9dj7_46935.cif" } resolution = 3.8 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= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 1 5.21 5 S 109 5.16 5 C 15280 2.51 5 N 4046 2.21 5 O 4406 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23851 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 18269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2338, 18269 Classifications: {'peptide': 2338} Incomplete info: {'truncation_to_alanine': 184} Link IDs: {'PTRANS': 65, 'TRANS': 2272} Chain breaks: 13 Unresolved non-hydrogen bonds: 639 Unresolved non-hydrogen angles: 793 Unresolved non-hydrogen dihedrals: 517 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 3, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 20, 'PHE:plan': 8, 'GLU:plan': 35, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 361 Chain: "B" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2769 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2700 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain breaks: 3 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 113 Unusual residues: {' MG': 1, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 14.40, per 1000 atoms: 0.60 Number of scatterers: 23851 At special positions: 0 Unit cell: (102.08, 140.36, 192.56, 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 109 16.00 P 9 15.00 Mg 1 11.99 O 4406 8.00 N 4046 7.00 C 15280 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: 6.61 Conformation dependent library (CDL) restraints added in 3.3 seconds 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5766 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 30 sheets defined 50.7% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 1433 through 1461 Processing helix chain 'A' and resid 1467 through 1470 removed outlier: 3.891A pdb=" N PHE A1470 " --> pdb=" O ILE A1467 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1467 through 1470' Processing helix chain 'A' and resid 1471 through 1494 Processing helix chain 'A' and resid 1511 through 1521 removed outlier: 3.827A pdb=" N SER A1521 " --> pdb=" O LYS A1517 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1534 Processing helix chain 'A' and resid 1535 through 1540 removed outlier: 3.537A pdb=" N PHE A1539 " --> pdb=" O ARG A1536 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1551 Processing helix chain 'A' and resid 1556 through 1567 removed outlier: 4.517A pdb=" N LYS A1560 " --> pdb=" O ASP A1556 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE A1561 " --> pdb=" O GLN A1557 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS A1563 " --> pdb=" O SER A1559 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS A1564 " --> pdb=" O LYS A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1633 removed outlier: 4.017A pdb=" N TRP A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A1616 " --> pdb=" O ASP A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1640 removed outlier: 3.847A pdb=" N VAL A1639 " --> pdb=" O ASP A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1666 removed outlier: 3.516A pdb=" N ILE A1648 " --> pdb=" O ILE A1644 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR A1666 " --> pdb=" O LYS A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1688 removed outlier: 4.216A pdb=" N ASN A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1717 Processing helix chain 'A' and resid 1721 through 1731 removed outlier: 3.684A pdb=" N VAL A1731 " --> pdb=" O LEU A1727 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1788 removed outlier: 4.080A pdb=" N GLN A1788 " --> pdb=" O ASP A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1813 Processing helix chain 'A' and resid 1827 through 1842 Processing helix chain 'A' and resid 1850 through 1853 removed outlier: 3.759A 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 1875 removed outlier: 3.804A pdb=" N SER A1862 " --> pdb=" O LEU A1858 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA A1863 " --> pdb=" O SER A1859 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASN A1864 " --> pdb=" O ALA A1860 " (cutoff:3.500A) Processing helix chain 'A' and resid 1909 through 1914 Processing helix chain 'A' and resid 1925 through 1937 Processing helix chain 'A' and resid 1942 through 1959 Processing helix chain 'A' and resid 1969 through 1981 removed outlier: 3.618A pdb=" N LEU A1973 " --> pdb=" O GLY A1969 " (cutoff:3.500A) Processing helix chain 'A' and resid 1982 through 1986 removed outlier: 3.565A pdb=" N SER A1985 " --> pdb=" O PRO A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1991 through 2003 Processing helix chain 'A' and resid 2004 through 2006 No H-bonds generated for 'chain 'A' and resid 2004 through 2006' Processing helix chain 'A' and resid 2008 through 2022 removed outlier: 3.863A pdb=" N LEU A2012 " --> pdb=" O ASP A2008 " (cutoff:3.500A) Processing helix chain 'A' and resid 2031 through 2046 Processing helix chain 'A' and resid 2050 through 2065 Processing helix chain 'A' and resid 2079 through 2096 Processing helix chain 'A' and resid 2110 through 2115 Processing helix chain 'A' and resid 2129 through 2140 Processing helix chain 'A' and resid 2159 through 2164 Processing helix chain 'A' and resid 2166 through 2171 removed outlier: 3.587A pdb=" N ASP A2171 " --> pdb=" O ASN A2167 " (cutoff:3.500A) Processing helix chain 'A' and resid 2204 through 2209 removed outlier: 3.790A pdb=" N ARG A2209 " --> pdb=" O ALA A2205 " (cutoff:3.500A) Processing helix chain 'A' and resid 2221 through 2237 removed outlier: 3.604A pdb=" N LEU A2237 " --> pdb=" O SER A2233 " (cutoff:3.500A) Processing helix chain 'A' and resid 2246 through 2257 removed outlier: 3.869A pdb=" N PHE A2257 " --> pdb=" O ILE A2253 " (cutoff:3.500A) Processing helix chain 'A' and resid 2258 through 2269 removed outlier: 3.802A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (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 2299 removed outlier: 3.704A pdb=" N ALA A2287 " --> pdb=" O LYS A2283 " (cutoff:3.500A) Processing helix chain 'A' and resid 2300 through 2302 No H-bonds generated for 'chain 'A' and resid 2300 through 2302' Processing helix chain 'A' and resid 2306 through 2327 Processing helix chain 'A' and resid 2331 through 2346 Processing helix chain 'A' and resid 2381 through 2385 removed outlier: 3.504A pdb=" N GLU A2384 " --> pdb=" O GLU A2381 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL A2385 " --> pdb=" O ALA A2382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2381 through 2385' Processing helix chain 'A' and resid 2394 through 2409 Processing helix chain 'A' and resid 2423 through 2434 removed outlier: 3.981A pdb=" N ASN A2434 " --> pdb=" O ASN A2430 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2460 removed outlier: 3.609A pdb=" N ILE A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARG A2460 " --> pdb=" O SER A2456 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2512 Processing helix chain 'A' and resid 2547 through 2552 removed outlier: 3.546A pdb=" N THR A2551 " --> pdb=" O SER A2547 " (cutoff:3.500A) Processing helix chain 'A' and resid 2563 through 2580 Processing helix chain 'A' and resid 2582 through 2587 removed outlier: 3.672A pdb=" N PHE A2585 " --> pdb=" O VAL A2582 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG A2586 " --> pdb=" O PRO A2583 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER A2587 " --> pdb=" O GLU A2584 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2582 through 2587' Processing helix chain 'A' and resid 2588 through 2607 removed outlier: 3.630A pdb=" N PHE A2592 " --> pdb=" O TYR A2588 " (cutoff:3.500A) Processing helix chain 'A' and resid 2618 through 2635 removed outlier: 3.956A pdb=" N LEU A2622 " --> pdb=" O SER A2618 " (cutoff:3.500A) Processing helix chain 'A' and resid 2640 through 2657 Processing helix chain 'A' and resid 2662 through 2681 Processing helix chain 'A' and resid 2690 through 2694 removed outlier: 3.520A pdb=" N LEU A2694 " --> pdb=" O SER A2691 " (cutoff:3.500A) Processing helix chain 'A' and resid 2709 through 2727 Processing helix chain 'A' and resid 2735 through 2751 removed outlier: 3.607A pdb=" N GLN A2751 " --> pdb=" O ARG A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2766 through 2777 Processing helix chain 'A' and resid 2791 through 2808 removed outlier: 3.591A pdb=" N PHE A2795 " --> pdb=" O ASN A2791 " (cutoff:3.500A) Processing helix chain 'A' and resid 2820 through 2822 No H-bonds generated for 'chain 'A' and resid 2820 through 2822' Processing helix chain 'A' and resid 2824 through 2837 removed outlier: 3.806A pdb=" N LEU A2828 " --> pdb=" O GLU A2824 " (cutoff:3.500A) Processing helix chain 'A' and resid 2846 through 2864 Processing helix chain 'A' and resid 2869 through 2884 Processing helix chain 'A' and resid 2896 through 2905 Processing helix chain 'A' and resid 2905 through 2911 Processing helix chain 'A' and resid 2921 through 2934 Processing helix chain 'A' and resid 2960 through 2980 removed outlier: 3.638A pdb=" N ALA A2964 " --> pdb=" O THR A2960 " (cutoff:3.500A) Processing helix chain 'A' and resid 2989 through 3034 Processing helix chain 'A' and resid 3290 through 3298 Processing helix chain 'A' and resid 3299 through 3319 removed outlier: 4.525A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) Processing helix chain 'A' and resid 3319 through 3333 Processing helix chain 'A' and resid 3334 through 3337 removed outlier: 3.742A pdb=" N LEU A3337 " --> pdb=" O PHE A3334 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3334 through 3337' Processing helix chain 'A' and resid 3338 through 3356 removed outlier: 3.510A pdb=" N PHE A3356 " --> pdb=" O LEU A3352 " (cutoff:3.500A) 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 3398 Processing helix chain 'A' and resid 3413 through 3422 Processing helix chain 'A' and resid 3423 through 3426 removed outlier: 3.797A pdb=" N THR A3426 " --> pdb=" O GLY A3423 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3423 through 3426' Processing helix chain 'A' and resid 3435 through 3447 Processing helix chain 'A' and resid 3459 through 3461 No H-bonds generated for 'chain 'A' and resid 3459 through 3461' Processing helix chain 'A' and resid 3462 through 3467 Processing helix chain 'A' and resid 3506 through 3513 removed outlier: 3.817A pdb=" N ARG A3512 " --> pdb=" O PHE A3508 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3538 Processing helix chain 'A' and resid 3538 through 3572 Processing helix chain 'A' and resid 3583 through 3605 Processing helix chain 'A' and resid 3607 through 3639 removed outlier: 3.981A pdb=" N PHE A3611 " --> pdb=" O PHE A3607 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE A3620 " --> pdb=" O GLU A3616 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE A3621 " --> pdb=" O GLU A3617 " (cutoff:3.500A) Processing helix chain 'A' and resid 3640 through 3643 removed outlier: 3.728A 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: 3.573A pdb=" N PHE A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) Processing helix chain 'A' and resid 3670 through 3687 Processing helix chain 'A' and resid 3691 through 3711 Processing helix chain 'A' and resid 3712 through 3727 Processing helix chain 'A' and resid 3741 through 3753 removed outlier: 4.091A pdb=" N ARG A3745 " --> pdb=" O ASN A3741 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A3746 " --> pdb=" O ASP A3742 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A3753 " --> pdb=" O ASP A3749 " (cutoff:3.500A) Processing helix chain 'A' and resid 3755 through 3768 removed outlier: 4.183A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.569A 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: 3.520A pdb=" N LEU A3800 " --> pdb=" O GLY A3796 " (cutoff:3.500A) Processing helix chain 'A' and resid 3818 through 3836 Processing helix chain 'A' and resid 3844 through 3846 No H-bonds generated for 'chain 'A' and resid 3844 through 3846' Processing helix chain 'A' and resid 3847 through 3861 removed outlier: 4.161A pdb=" N LEU A3855 " --> pdb=" O VAL A3851 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N HIS A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) Processing helix chain 'A' and resid 3885 through 3892 Processing helix chain 'A' and resid 3902 through 3914 removed outlier: 3.622A pdb=" N GLN A3914 " --> pdb=" O LEU A3910 " (cutoff:3.500A) Processing helix chain 'A' and resid 3923 through 3943 Processing helix chain 'A' and resid 3945 through 3950 removed outlier: 4.076A pdb=" N PHE A3950 " --> pdb=" O VAL A3946 " (cutoff:3.500A) Processing helix chain 'A' and resid 3957 through 3975 removed outlier: 3.920A pdb=" N PHE A3961 " --> pdb=" O ASN A3957 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3992 Processing helix chain 'A' and resid 4000 through 4015 Processing helix chain 'A' and resid 4037 through 4051 Processing helix chain 'A' and resid 4057 through 4062 Processing helix chain 'A' and resid 4066 through 4090 removed outlier: 4.106A pdb=" N ILE A4070 " --> pdb=" O PRO A4066 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN A4090 " --> pdb=" O GLU A4086 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'C' and resid 355 through 359 removed outlier: 3.822A pdb=" N ARG C 358 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR C 359 " --> pdb=" O ARG C 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 355 through 359' Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'C' and resid 401 through 405 removed outlier: 3.868A pdb=" N SER C 405 " --> pdb=" O PRO C 402 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1569 through 1575 removed outlier: 3.916A pdb=" N SER A1571 " --> pdb=" O ARG A1583 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE A1575 " --> pdb=" O ILE A1579 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ILE A1579 " --> pdb=" O PHE A1575 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N SER A1578 " --> pdb=" O GLU A1594 " (cutoff:3.500A) removed outlier: 11.180A pdb=" N GLU A1594 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N THR A1580 " --> pdb=" O LEU A1592 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A1592 " --> pdb=" O THR A1580 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1733 through 1736 removed outlier: 3.511A pdb=" N PHE A1748 " --> pdb=" O TYR A1735 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1818 through 1821 removed outlier: 3.779A pdb=" N GLY A1792 " --> pdb=" O VAL A1894 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1878 through 1881 Processing sheet with id=AA5, first strand: chain 'A' and resid 2098 through 2104 removed outlier: 3.543A pdb=" N VAL A2100 " --> pdb=" O ARG A2149 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N ARG A2191 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE A2150 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU A2193 " --> pdb=" O ILE A2150 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL A2152 " --> pdb=" O LEU A2193 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N GLU A2195 " --> pdb=" O VAL A2152 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE A2154 " --> pdb=" O GLU A2195 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA A2069 " --> pdb=" O GLY A2211 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N LEU A2213 " --> pdb=" O ALA A2069 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE A2071 " --> pdb=" O LEU A2213 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2116 through 2119 Processing sheet with id=AA7, first strand: chain 'A' and resid 2175 through 2177 Processing sheet with id=AA8, first strand: chain 'A' and resid 2358 through 2360 removed outlier: 3.613A pdb=" N SER A2367 " --> pdb=" O VAL A2360 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2438 through 2444 removed outlier: 6.257A pdb=" N ASP A2439 " --> pdb=" O VAL A2483 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE A2485 " --> pdb=" O ASP A2439 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL A2441 " --> pdb=" O PHE A2485 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASP A2487 " --> pdb=" O VAL A2441 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A2443 " --> pdb=" O ASP A2487 " (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 2514 through 2517 removed outlier: 3.750A pdb=" N PHE A2515 " --> pdb=" O VAL A2524 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A2522 " --> pdb=" O LYS A2517 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2696 through 2697 removed outlier: 3.515A pdb=" N LYS A2705 " --> pdb=" O SER A2697 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2780 through 2782 removed outlier: 6.724A pdb=" N LYS A2780 " --> pdb=" O CYS A2814 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ILE A2816 " --> pdb=" O LYS A2780 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL A2782 " --> pdb=" O ILE A2816 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N ASP A2818 " --> pdb=" O VAL A2782 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR A2813 " --> pdb=" O HIS A2886 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL A2888 " --> pdb=" O THR A2813 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU A2815 " --> pdb=" O VAL A2888 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N THR A2890 " --> pdb=" O LEU A2815 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE A2817 " --> pdb=" O THR A2890 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N HIS A2755 " --> pdb=" O ILE A2913 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASN A2915 " --> pdb=" O HIS A2755 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N MET A2757 " --> pdb=" O ASN A2915 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3427 through 3430 removed outlier: 6.415A pdb=" N VAL A3427 " --> pdb=" O ILE A3451 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N GLN A3453 " --> pdb=" O VAL A3427 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A3429 " --> pdb=" O GLN A3453 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE A3406 " --> pdb=" O VAL A3516 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3471 through 3473 removed outlier: 4.499A pdb=" N VAL A3477 " --> pdb=" O VAL A3488 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A3481 " --> pdb=" O HIS A3484 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS A3484 " --> pdb=" O ILE A3481 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3813 through 3815 removed outlier: 3.682A pdb=" N GLN A3842 " --> pdb=" O ILE A3814 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS A3872 " --> pdb=" O GLY A3837 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A3790 " --> pdb=" O CYS A3877 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N TYR A3785 " --> pdb=" O ASP A3893 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL A3895 " --> pdb=" O TYR A3785 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N THR A3787 " --> pdb=" O VAL A3895 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 150 through 153 removed outlier: 4.348A pdb=" N LYS B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS B 463 " --> pdb=" O GLY B 483 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 158 through 163 removed outlier: 4.072A pdb=" N SER B 160 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS B 178 " --> pdb=" O THR B 174 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 201 through 208 removed outlier: 7.095A pdb=" N ALA B 225 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N MET B 204 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 223 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL B 206 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL B 221 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU B 220 " --> pdb=" O TRP B 236 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER B 226 " --> pdb=" O GLN B 230 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLN B 230 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE B 231 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER B 248 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL B 233 " --> pdb=" O ILE B 246 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 256 through 263 removed outlier: 6.807A pdb=" N CYS B 273 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL B 259 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA B 271 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE B 261 " --> pdb=" O HIS B 269 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N HIS B 269 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP B 283 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N SER B 289 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 300 through 306 removed outlier: 6.754A pdb=" N HIS B 323 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY B 329 " --> pdb=" O HIS B 323 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 340 through 346 removed outlier: 7.167A pdb=" N ALA B 376 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL B 343 " --> pdb=" O VAL B 374 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL B 374 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N PHE B 345 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N TYR B 372 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER B 377 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE B 382 " --> pdb=" O THR B 412 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR B 412 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE B 384 " --> pdb=" O VAL B 410 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 420 through 426 removed outlier: 4.063A pdb=" N ASP B 422 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS B 433 " --> pdb=" O ASP B 422 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 439 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL B 452 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS B 441 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 150 through 153 removed outlier: 3.565A pdb=" N VAL C 491 " --> pdb=" O CYS C 150 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 161 through 163 removed outlier: 3.833A pdb=" N LEU C 194 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 201 through 208 removed outlier: 4.164A pdb=" N SER C 203 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU C 220 " --> pdb=" O TRP C 236 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP C 236 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE C 231 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER C 248 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL C 233 " --> pdb=" O ILE C 246 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 256 through 262 removed outlier: 3.696A pdb=" N ALA C 258 " --> pdb=" O CYS C 273 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS C 280 " --> pdb=" O SER C 272 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE C 293 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS C 291 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASP C 283 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N SER C 289 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 300 through 306 removed outlier: 7.075A pdb=" N GLY C 313 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE C 303 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE C 311 " --> pdb=" O ILE C 303 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL C 305 " --> pdb=" O TYR C 309 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG C 320 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU C 319 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL C 332 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU C 321 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN C 328 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 340 through 346 removed outlier: 4.792A pdb=" N TYR C 372 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS C 373 " --> pdb=" O TRP C 385 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER C 377 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU C 386 " --> pdb=" O CYS C 409 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N CYS C 409 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 420 through 426 removed outlier: 3.592A pdb=" N ASP C 422 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N SER C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C 439 " --> pdb=" O TRP C 453 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS C 441 " --> pdb=" O HIS C 451 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N HIS C 451 " --> pdb=" O CYS C 441 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASP C 443 " --> pdb=" O CYS C 449 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS C 449 " --> pdb=" O ASP C 443 " (cutoff:3.500A) 1267 hydrogen bonds defined for protein. 3708 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.02 Time building geometry restraints manager: 7.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7647 1.34 - 1.46: 5721 1.46 - 1.58: 10820 1.58 - 1.70: 11 1.70 - 1.82: 166 Bond restraints: 24365 Sorted by residual: bond pdb=" C TRP B 324 " pdb=" N PRO B 325 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.40e+00 bond pdb=" CG1 ILE A2573 " pdb=" CD1 ILE A2573 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.37e+00 bond pdb=" C4 ADP A4104 " pdb=" C5 ADP A4104 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.34e+00 bond pdb=" CG1 ILE A3674 " pdb=" CD1 ILE A3674 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.22e+00 bond pdb=" CG MET A3414 " pdb=" SD MET A3414 " ideal model delta sigma weight residual 1.803 1.776 0.027 2.50e-02 1.60e+03 1.16e+00 ... (remaining 24360 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 32196 1.63 - 3.25: 695 3.25 - 4.88: 111 4.88 - 6.50: 52 6.50 - 8.13: 11 Bond angle restraints: 33065 Sorted by residual: angle pdb=" C ASP C 276 " pdb=" N GLN C 277 " pdb=" CA GLN C 277 " ideal model delta sigma weight residual 121.54 127.22 -5.68 1.91e+00 2.74e-01 8.85e+00 angle pdb=" CA MET A3414 " pdb=" CB MET A3414 " pdb=" CG MET A3414 " ideal model delta sigma weight residual 114.10 108.29 5.81 2.00e+00 2.50e-01 8.45e+00 angle pdb=" N PHE A3608 " pdb=" CA PHE A3608 " pdb=" C PHE A3608 " ideal model delta sigma weight residual 109.81 116.22 -6.41 2.21e+00 2.05e-01 8.42e+00 angle pdb=" CA LYS B 260 " pdb=" CB LYS B 260 " pdb=" CG LYS B 260 " ideal model delta sigma weight residual 114.10 119.70 -5.60 2.00e+00 2.50e-01 7.84e+00 angle pdb=" C LEU A3590 " pdb=" N LYS A3591 " pdb=" CA LYS A3591 " ideal model delta sigma weight residual 121.14 116.40 4.74 1.75e+00 3.27e-01 7.35e+00 ... (remaining 33060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.38: 13564 23.38 - 46.76: 861 46.76 - 70.14: 59 70.14 - 93.52: 22 93.52 - 116.90: 1 Dihedral angle restraints: 14507 sinusoidal: 5649 harmonic: 8858 Sorted by residual: dihedral pdb=" C2' ADP A4104 " pdb=" C1' ADP A4104 " pdb=" N9 ADP A4104 " pdb=" C4 ADP A4104 " ideal model delta sinusoidal sigma weight residual 91.55 -151.56 -116.90 1 2.00e+01 2.50e-03 3.49e+01 dihedral pdb=" CA MET A1963 " pdb=" C MET A1963 " pdb=" N ASN A1964 " pdb=" CA ASN A1964 " ideal model delta harmonic sigma weight residual -180.00 -162.04 -17.96 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" C2' ADP A4102 " pdb=" C1' ADP A4102 " pdb=" N9 ADP A4102 " pdb=" C4 ADP A4102 " ideal model delta sinusoidal sigma weight residual 91.55 148.38 -56.84 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 14504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2502 0.036 - 0.072: 903 0.072 - 0.108: 282 0.108 - 0.144: 99 0.144 - 0.180: 11 Chirality restraints: 3797 Sorted by residual: chirality pdb=" CA LEU A2491 " pdb=" N LEU A2491 " pdb=" C LEU A2491 " pdb=" CB LEU A2491 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.12e-01 chirality pdb=" CA MET A3414 " pdb=" N MET A3414 " pdb=" C MET A3414 " pdb=" CB MET A3414 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.65e-01 chirality pdb=" CB ILE C 310 " pdb=" CA ILE C 310 " pdb=" CG1 ILE C 310 " pdb=" CG2 ILE C 310 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.60e-01 ... (remaining 3794 not shown) Planarity restraints: 4148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A3768 " 0.010 2.00e-02 2.50e+03 2.06e-02 7.43e+00 pdb=" CG PHE A3768 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE A3768 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE A3768 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A3768 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A3768 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A3768 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A2936 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO A2937 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A2937 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A2937 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 164 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO C 165 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 165 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 165 " -0.025 5.00e-02 4.00e+02 ... (remaining 4145 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 207 2.60 - 3.17: 19352 3.17 - 3.75: 38048 3.75 - 4.32: 49016 4.32 - 4.90: 82804 Nonbonded interactions: 189427 Sorted by model distance: nonbonded pdb=" O2B ADP A4104 " pdb="MG MG A4105 " model vdw 2.023 2.170 nonbonded pdb=" OD2 ASP A1848 " pdb="MG MG A4105 " model vdw 2.063 2.170 nonbonded pdb=" OG1 THR A2081 " pdb=" OE2 GLU A2195 " model vdw 2.244 3.040 nonbonded pdb=" O GLY A1988 " pdb=" OG1 THR A1993 " model vdw 2.282 3.040 nonbonded pdb=" O ILE A2253 " pdb=" OG SER A2256 " model vdw 2.291 3.040 ... (remaining 189422 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 139 through 154 or (resid 155 and (name N or name CA or na \ me C or name O or name CB )) or resid 156 through 183 or (resid 184 and (name N \ or name CA or name C or name O or name CB )) or resid 185 or (resid 186 and (nam \ e N or name CA or name C or name O or name CB )) or resid 187 or (resid 188 thro \ ugh 189 and (name N or name CA or name C or name O or name CB )) or resid 190 th \ rough 207 or (resid 208 and (name N or name CA or name C or name O or name CB )) \ or resid 209 through 211 or (resid 212 through 213 and (name N or name CA or na \ me C or name O or name CB )) or resid 218 through 238 or (resid 239 and (name N \ or name CA or name C or name O or name CB )) or resid 240 through 243 or (resid \ 244 and (name N or name CA or name C or name O or name CB )) or resid 245 throug \ h 262 or (resid 263 through 267 and (name N or name CA or name C or name O or na \ me CB )) or resid 268 through 289 or (resid 290 and (name N or name CA or name C \ or name O or name CB )) or resid 291 through 307 or (resid 308 and (name N or n \ ame CA or name C or name O or name CB )) or resid 309 through 362 or (resid 363 \ and (name N or name CA or name C or name O or name CB )) or resid 364 through 36 \ 5 or (resid 366 and (name N or name CA or name C or name O or name CB )) or resi \ d 367 or (resid 368 and (name N or name CA or name C or name O or name CB )) or \ resid 369 through 388 or (resid 389 and (name N or name CA or name C or name O o \ r name CB )) or resid 390 or (resid 391 through 397 and (name N or name CA or na \ me C or name O or name CB )) or resid 398 through 407 or (resid 408 and (name N \ or name CA or name C or name O or name CB )) or resid 409 or (resid 410 and (nam \ e N or name CA or name C or name O or name CB )) or resid 411 through 466 or (re \ sid 467 through 468 and (name N or name CA or name C or name O or name CB )) or \ resid 469 through 470 or (resid 471 through 473 and (name N or name CA or name C \ or name O or name CB )) or resid 474 or (resid 475 and (name N or name CA or na \ me C or name O or name CB )) or resid 476 through 494)) selection = (chain 'C' and (resid 139 through 350 or resid 355 through 400 or resid 405 thro \ ugh 454 or (resid 455 and (name N or name CA or name C or name O or name CB )) o \ r resid 456 through 493 or (resid 494 and (name N or name CA or name C or name O \ or name CB or name 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.590 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: 1.020 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 62.840 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.110 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24365 Z= 0.132 Angle : 0.614 8.128 33065 Z= 0.309 Chirality : 0.044 0.180 3797 Planarity : 0.004 0.050 4148 Dihedral : 14.382 116.895 8741 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: 0.04 (0.15), residues: 2980 helix: 1.12 (0.13), residues: 1385 sheet: -0.19 (0.24), residues: 488 loop : -1.24 (0.17), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 282 HIS 0.006 0.001 HIS C 254 PHE 0.044 0.001 PHE A3768 TYR 0.017 0.001 TYR A2571 ARG 0.007 0.000 ARG A3510 Details of bonding type rmsd hydrogen bonds : bond 0.14016 ( 1267) hydrogen bonds : angle 5.88364 ( 3708) covalent geometry : bond 0.00289 (24365) covalent geometry : angle 0.61362 (33065) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2105 ASP cc_start: 0.7680 (m-30) cc_final: 0.7477 (m-30) REVERT: A 2200 ASP cc_start: 0.8494 (p0) cc_final: 0.8098 (p0) REVERT: A 2428 MET cc_start: 0.8163 (ttm) cc_final: 0.7821 (tmm) REVERT: A 2508 GLN cc_start: 0.8865 (tt0) cc_final: 0.8220 (tt0) REVERT: A 2680 TYR cc_start: 0.6792 (m-10) cc_final: 0.6589 (m-10) REVERT: A 2738 MET cc_start: 0.8103 (tmm) cc_final: 0.7628 (tmm) REVERT: A 2915 ASN cc_start: 0.8751 (t0) cc_final: 0.8366 (t0) REVERT: A 3341 GLU cc_start: 0.7897 (tt0) cc_final: 0.7477 (tp30) REVERT: A 3377 MET cc_start: 0.8773 (tpp) cc_final: 0.8424 (mmm) REVERT: A 3386 LYS cc_start: 0.8839 (mtpp) cc_final: 0.8328 (ttpp) REVERT: A 3438 LYS cc_start: 0.9081 (tptp) cc_final: 0.8694 (tppt) REVERT: A 3565 ARG cc_start: 0.8068 (tpt90) cc_final: 0.7503 (tpm170) REVERT: A 3631 MET cc_start: 0.9235 (ttp) cc_final: 0.8968 (ttt) REVERT: A 3846 MET cc_start: 0.8882 (mmm) cc_final: 0.8550 (mmm) REVERT: A 4059 LEU cc_start: 0.9127 (tp) cc_final: 0.8885 (tt) REVERT: A 4079 LYS cc_start: 0.8532 (tptp) cc_final: 0.7823 (tttt) REVERT: B 253 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8360 (mm-30) REVERT: B 281 ILE cc_start: 0.8249 (mp) cc_final: 0.7986 (mt) REVERT: B 304 ASP cc_start: 0.7451 (t70) cc_final: 0.6703 (t70) REVERT: C 187 TYR cc_start: 0.8517 (p90) cc_final: 0.7600 (p90) REVERT: C 260 LYS cc_start: 0.8563 (mmmt) cc_final: 0.8290 (tptt) REVERT: C 273 CYS cc_start: 0.8319 (p) cc_final: 0.8037 (p) REVERT: C 436 ASP cc_start: 0.7765 (t0) cc_final: 0.7337 (t0) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.3504 time to fit residues: 142.1096 Evaluate side-chains 178 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 254 optimal weight: 0.0570 chunk 228 optimal weight: 0.0010 chunk 126 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 235 optimal weight: 0.6980 chunk 91 optimal weight: 0.0270 chunk 143 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 273 optimal weight: 3.9990 overall best weight: 0.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1554 HIS A1899 ASN A2832 ASN B 197 HIS C 153 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.104327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.086471 restraints weight = 57790.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.089051 restraints weight = 29317.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.090758 restraints weight = 18748.193| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24365 Z= 0.097 Angle : 0.508 12.423 33065 Z= 0.258 Chirality : 0.041 0.161 3797 Planarity : 0.003 0.043 4148 Dihedral : 5.209 114.696 3284 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.74 % Allowed : 8.30 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.63 (0.15), residues: 2980 helix: 1.79 (0.14), residues: 1404 sheet: -0.10 (0.24), residues: 486 loop : -1.17 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2084 HIS 0.007 0.001 HIS B 197 PHE 0.022 0.001 PHE A3313 TYR 0.014 0.001 TYR C 429 ARG 0.003 0.000 ARG A2433 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 1267) hydrogen bonds : angle 4.39076 ( 3708) covalent geometry : bond 0.00205 (24365) covalent geometry : angle 0.50814 (33065) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 210 time to evaluate : 2.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2200 ASP cc_start: 0.8268 (p0) cc_final: 0.7998 (p0) REVERT: A 2508 GLN cc_start: 0.8811 (tt0) cc_final: 0.8057 (tt0) REVERT: A 2573 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8527 (mp) REVERT: A 2680 TYR cc_start: 0.6551 (m-10) cc_final: 0.6191 (m-10) REVERT: A 2875 ASP cc_start: 0.8153 (m-30) cc_final: 0.7876 (m-30) REVERT: A 3341 GLU cc_start: 0.7698 (tt0) cc_final: 0.7034 (tp30) REVERT: A 3345 MET cc_start: 0.7612 (mpp) cc_final: 0.6617 (mpp) REVERT: A 3377 MET cc_start: 0.8644 (tpp) cc_final: 0.8250 (mmm) REVERT: A 3438 LYS cc_start: 0.9117 (tptp) cc_final: 0.8737 (tppt) REVERT: A 3631 MET cc_start: 0.9224 (ttp) cc_final: 0.8922 (ttp) REVERT: A 3696 MET cc_start: 0.8023 (mtm) cc_final: 0.7792 (mtm) REVERT: A 3722 MET cc_start: 0.9128 (mmp) cc_final: 0.8784 (mmt) REVERT: A 4059 LEU cc_start: 0.9165 (tp) cc_final: 0.8942 (tt) REVERT: A 4079 LYS cc_start: 0.8573 (tptp) cc_final: 0.7936 (tttt) REVERT: B 253 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8330 (mm-30) REVERT: B 304 ASP cc_start: 0.7435 (t70) cc_final: 0.6743 (t0) REVERT: C 273 CYS cc_start: 0.8163 (p) cc_final: 0.7878 (p) REVERT: C 436 ASP cc_start: 0.7684 (t0) cc_final: 0.7383 (t0) REVERT: C 478 GLN cc_start: 0.7679 (pt0) cc_final: 0.7473 (pt0) outliers start: 19 outliers final: 7 residues processed: 220 average time/residue: 0.3505 time to fit residues: 127.0492 Evaluate side-chains 184 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1554 HIS Chi-restraints excluded: chain A residue 1963 MET Chi-restraints excluded: chain A residue 2226 ILE Chi-restraints excluded: chain A residue 2573 ILE Chi-restraints excluded: chain A residue 2582 VAL Chi-restraints excluded: chain A residue 3362 VAL Chi-restraints excluded: chain A residue 3650 LEU Chi-restraints excluded: chain B residue 463 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 213 optimal weight: 6.9990 chunk 240 optimal weight: 0.0010 chunk 281 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 258 optimal weight: 0.5980 chunk 248 optimal weight: 3.9990 chunk 275 optimal weight: 0.5980 chunk 108 optimal weight: 0.2980 chunk 103 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1554 HIS A1951 HIS ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.104098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.086447 restraints weight = 57631.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.088942 restraints weight = 29845.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.090568 restraints weight = 19308.385| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24365 Z= 0.094 Angle : 0.483 7.946 33065 Z= 0.245 Chirality : 0.040 0.156 3797 Planarity : 0.003 0.044 4148 Dihedral : 5.094 113.230 3284 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.63 % Allowed : 10.96 % Favored : 88.41 % 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: 0.95 (0.16), residues: 2980 helix: 2.12 (0.14), residues: 1403 sheet: -0.09 (0.24), residues: 485 loop : -1.03 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2084 HIS 0.011 0.001 HIS A1554 PHE 0.012 0.001 PHE A3313 TYR 0.013 0.001 TYR A2571 ARG 0.003 0.000 ARG A3510 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 1267) hydrogen bonds : angle 4.10836 ( 3708) covalent geometry : bond 0.00203 (24365) covalent geometry : angle 0.48254 (33065) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 3.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1454 TRP cc_start: 0.6982 (t-100) cc_final: 0.6524 (t-100) REVERT: A 2200 ASP cc_start: 0.8225 (p0) cc_final: 0.7889 (p0) REVERT: A 2573 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8445 (mp) REVERT: A 2680 TYR cc_start: 0.6519 (m-10) cc_final: 0.6178 (m-10) REVERT: A 2738 MET cc_start: 0.8437 (tmm) cc_final: 0.8051 (tmm) REVERT: A 2875 ASP cc_start: 0.8107 (m-30) cc_final: 0.7811 (m-30) REVERT: A 3341 GLU cc_start: 0.7762 (tt0) cc_final: 0.7080 (tp30) REVERT: A 3345 MET cc_start: 0.7709 (mpp) cc_final: 0.6731 (mpp) REVERT: A 3377 MET cc_start: 0.8591 (tpp) cc_final: 0.8232 (mmm) REVERT: A 3438 LYS cc_start: 0.9115 (tptp) cc_final: 0.8745 (tppt) REVERT: A 3565 ARG cc_start: 0.8453 (tpp80) cc_final: 0.8024 (tpp-160) REVERT: A 3631 MET cc_start: 0.9235 (ttp) cc_final: 0.8938 (ttp) REVERT: A 3696 MET cc_start: 0.8001 (mtm) cc_final: 0.7724 (mtt) REVERT: A 3722 MET cc_start: 0.9134 (mmp) cc_final: 0.8799 (mmt) REVERT: A 4079 LYS cc_start: 0.8575 (tptp) cc_final: 0.7933 (ttpt) REVERT: B 253 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8339 (mm-30) REVERT: B 304 ASP cc_start: 0.7509 (t70) cc_final: 0.6841 (t0) REVERT: B 324 TRP cc_start: 0.8034 (t60) cc_final: 0.7833 (t60) REVERT: B 429 TYR cc_start: 0.8005 (m-10) cc_final: 0.7747 (m-80) REVERT: C 436 ASP cc_start: 0.7585 (t0) cc_final: 0.7299 (t0) outliers start: 16 outliers final: 7 residues processed: 210 average time/residue: 0.3460 time to fit residues: 121.3421 Evaluate side-chains 181 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 173 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1554 HIS Chi-restraints excluded: chain A residue 1951 HIS Chi-restraints excluded: chain A residue 1963 MET Chi-restraints excluded: chain A residue 2284 LEU Chi-restraints excluded: chain A residue 2573 ILE Chi-restraints excluded: chain A residue 2878 VAL Chi-restraints excluded: chain A residue 3650 LEU Chi-restraints excluded: chain B residue 463 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 114 optimal weight: 0.9980 chunk 204 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 265 optimal weight: 10.0000 chunk 211 optimal weight: 0.7980 chunk 182 optimal weight: 8.9990 chunk 295 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 chunk 258 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 276 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1554 HIS A1867 GLN A1951 HIS A2282 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.102610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.084535 restraints weight = 58809.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.087063 restraints weight = 30126.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.088727 restraints weight = 19443.433| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24365 Z= 0.121 Angle : 0.489 9.668 33065 Z= 0.248 Chirality : 0.040 0.155 3797 Planarity : 0.003 0.041 4148 Dihedral : 5.123 112.846 3284 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.94 % Allowed : 12.88 % Favored : 86.18 % 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: 1.08 (0.16), residues: 2980 helix: 2.27 (0.14), residues: 1408 sheet: -0.10 (0.24), residues: 485 loop : -1.00 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2084 HIS 0.010 0.001 HIS A1951 PHE 0.037 0.001 PHE A2281 TYR 0.013 0.001 TYR A2571 ARG 0.004 0.000 ARG A3510 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 1267) hydrogen bonds : angle 4.00767 ( 3708) covalent geometry : bond 0.00278 (24365) covalent geometry : angle 0.48912 (33065) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 2.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1454 TRP cc_start: 0.7052 (t-100) cc_final: 0.6621 (t-100) REVERT: A 2200 ASP cc_start: 0.8279 (p0) cc_final: 0.7956 (p0) REVERT: A 2428 MET cc_start: 0.8236 (tmm) cc_final: 0.7533 (tmm) REVERT: A 2573 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8512 (mp) REVERT: A 2738 MET cc_start: 0.8513 (tmm) cc_final: 0.8046 (tmm) REVERT: A 2875 ASP cc_start: 0.8159 (m-30) cc_final: 0.7882 (m-30) REVERT: A 3341 GLU cc_start: 0.7807 (tt0) cc_final: 0.7083 (tp30) REVERT: A 3345 MET cc_start: 0.7890 (mpp) cc_final: 0.6901 (mpp) REVERT: A 3377 MET cc_start: 0.8654 (tpp) cc_final: 0.8299 (mmm) REVERT: A 3438 LYS cc_start: 0.9156 (tptp) cc_final: 0.8793 (tppt) REVERT: A 3565 ARG cc_start: 0.8419 (tpp80) cc_final: 0.7987 (tpp-160) REVERT: A 3631 MET cc_start: 0.9256 (ttp) cc_final: 0.8944 (ttp) REVERT: A 3696 MET cc_start: 0.8053 (mtm) cc_final: 0.7777 (mtt) REVERT: A 3722 MET cc_start: 0.9141 (mmp) cc_final: 0.8835 (mmt) REVERT: A 4079 LYS cc_start: 0.8601 (tptp) cc_final: 0.7979 (tttt) REVERT: B 253 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8250 (mm-30) REVERT: B 304 ASP cc_start: 0.7570 (t70) cc_final: 0.6870 (t0) REVERT: C 436 ASP cc_start: 0.7643 (t0) cc_final: 0.7374 (t0) REVERT: C 480 MET cc_start: 0.8472 (ttp) cc_final: 0.8219 (ttt) outliers start: 24 outliers final: 16 residues processed: 201 average time/residue: 0.3362 time to fit residues: 113.3631 Evaluate side-chains 186 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1554 HIS Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1963 MET Chi-restraints excluded: chain A residue 2284 LEU Chi-restraints excluded: chain A residue 2573 ILE Chi-restraints excluded: chain A residue 2582 VAL Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2878 VAL Chi-restraints excluded: chain A residue 2945 VAL Chi-restraints excluded: chain A residue 3362 VAL Chi-restraints excluded: chain A residue 3650 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 273 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 62 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 187 optimal weight: 5.9990 chunk 192 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1468 GLN A1554 HIS ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.102337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.084219 restraints weight = 58763.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.086741 restraints weight = 30128.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.088418 restraints weight = 19456.477| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24365 Z= 0.114 Angle : 0.483 6.954 33065 Z= 0.245 Chirality : 0.040 0.155 3797 Planarity : 0.003 0.042 4148 Dihedral : 5.119 111.992 3284 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.21 % Allowed : 13.98 % Favored : 84.81 % 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: 1.20 (0.16), residues: 2980 helix: 2.37 (0.14), residues: 1405 sheet: -0.06 (0.24), residues: 487 loop : -0.93 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2084 HIS 0.008 0.001 HIS A1554 PHE 0.024 0.001 PHE A2281 TYR 0.013 0.001 TYR A2571 ARG 0.008 0.000 ARG A2594 Details of bonding type rmsd hydrogen bonds : bond 0.03169 ( 1267) hydrogen bonds : angle 3.92076 ( 3708) covalent geometry : bond 0.00262 (24365) covalent geometry : angle 0.48284 (33065) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 2.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1454 TRP cc_start: 0.7009 (t-100) cc_final: 0.6642 (t-100) REVERT: A 2200 ASP cc_start: 0.8284 (p0) cc_final: 0.7962 (p0) REVERT: A 2428 MET cc_start: 0.8363 (tmm) cc_final: 0.7514 (tmm) REVERT: A 2573 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8522 (mp) REVERT: A 2875 ASP cc_start: 0.8169 (m-30) cc_final: 0.7884 (m-30) REVERT: A 3002 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8757 (tt) REVERT: A 3341 GLU cc_start: 0.7803 (tt0) cc_final: 0.7047 (tp30) REVERT: A 3345 MET cc_start: 0.7987 (mpp) cc_final: 0.6753 (mpp) REVERT: A 3377 MET cc_start: 0.8869 (tpp) cc_final: 0.8540 (mmm) REVERT: A 3438 LYS cc_start: 0.9192 (tptp) cc_final: 0.8840 (tppt) REVERT: A 3565 ARG cc_start: 0.8490 (tpp80) cc_final: 0.8101 (tpp-160) REVERT: A 3631 MET cc_start: 0.9244 (ttp) cc_final: 0.8927 (ttp) REVERT: A 3696 MET cc_start: 0.8024 (mtm) cc_final: 0.7696 (mtt) REVERT: A 3722 MET cc_start: 0.9147 (mmp) cc_final: 0.8758 (mmt) REVERT: A 3846 MET cc_start: 0.8965 (mmm) cc_final: 0.8714 (mmm) REVERT: A 4079 LYS cc_start: 0.8606 (tptp) cc_final: 0.7970 (ttpt) REVERT: B 253 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8226 (mm-30) REVERT: B 304 ASP cc_start: 0.7571 (t70) cc_final: 0.6827 (t0) REVERT: C 436 ASP cc_start: 0.7619 (t0) cc_final: 0.7376 (t0) REVERT: C 480 MET cc_start: 0.8519 (ttp) cc_final: 0.8267 (ttt) outliers start: 31 outliers final: 21 residues processed: 204 average time/residue: 0.3270 time to fit residues: 111.6696 Evaluate side-chains 190 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1554 HIS Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1836 VAL Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1963 MET Chi-restraints excluded: chain A residue 2284 LEU Chi-restraints excluded: chain A residue 2544 ILE Chi-restraints excluded: chain A residue 2573 ILE Chi-restraints excluded: chain A residue 2582 VAL Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2730 VAL Chi-restraints excluded: chain A residue 2878 VAL Chi-restraints excluded: chain A residue 2945 VAL Chi-restraints excluded: chain A residue 3002 LEU Chi-restraints excluded: chain A residue 3362 VAL Chi-restraints excluded: chain A residue 3534 LEU Chi-restraints excluded: chain A residue 3650 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 273 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 31 optimal weight: 0.9980 chunk 288 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 28 optimal weight: 0.0060 chunk 98 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 6 optimal weight: 40.0000 chunk 270 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1554 HIS A2971 HIS B 263 GLN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.102098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.084049 restraints weight = 58189.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.086578 restraints weight = 29838.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.088256 restraints weight = 19209.622| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24365 Z= 0.113 Angle : 0.491 8.171 33065 Z= 0.247 Chirality : 0.040 0.173 3797 Planarity : 0.003 0.040 4148 Dihedral : 5.083 111.467 3284 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.33 % Allowed : 14.41 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.16), residues: 2980 helix: 2.41 (0.14), residues: 1410 sheet: -0.11 (0.24), residues: 492 loop : -0.90 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2084 HIS 0.007 0.001 HIS A1554 PHE 0.020 0.001 PHE A2281 TYR 0.014 0.001 TYR A2571 ARG 0.004 0.000 ARG A3510 Details of bonding type rmsd hydrogen bonds : bond 0.03134 ( 1267) hydrogen bonds : angle 3.87615 ( 3708) covalent geometry : bond 0.00259 (24365) covalent geometry : angle 0.49141 (33065) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 2.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1454 TRP cc_start: 0.7025 (t-100) cc_final: 0.6702 (t-100) REVERT: A 2200 ASP cc_start: 0.8302 (p0) cc_final: 0.7981 (p0) REVERT: A 2428 MET cc_start: 0.8445 (tmm) cc_final: 0.7664 (tmm) REVERT: A 2573 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8511 (mp) REVERT: A 2875 ASP cc_start: 0.8158 (m-30) cc_final: 0.7875 (m-30) REVERT: A 3002 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8754 (tt) REVERT: A 3341 GLU cc_start: 0.7829 (tt0) cc_final: 0.7030 (tp30) REVERT: A 3345 MET cc_start: 0.8006 (mpp) cc_final: 0.6778 (mpp) REVERT: A 3377 MET cc_start: 0.8847 (tpp) cc_final: 0.8532 (mmm) REVERT: A 3384 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7807 (tt) REVERT: A 3438 LYS cc_start: 0.9189 (tptp) cc_final: 0.8872 (tppt) REVERT: A 3565 ARG cc_start: 0.8496 (tpp80) cc_final: 0.8133 (tpp-160) REVERT: A 3631 MET cc_start: 0.9223 (ttp) cc_final: 0.8909 (ttp) REVERT: A 3722 MET cc_start: 0.9138 (mmp) cc_final: 0.8756 (mmt) REVERT: A 3846 MET cc_start: 0.8970 (mmm) cc_final: 0.8714 (mmm) REVERT: A 4079 LYS cc_start: 0.8636 (tptp) cc_final: 0.7992 (ttpt) REVERT: B 253 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8225 (mm-30) REVERT: B 304 ASP cc_start: 0.7568 (t70) cc_final: 0.6807 (t0) REVERT: C 436 ASP cc_start: 0.7626 (t0) cc_final: 0.7392 (t0) outliers start: 34 outliers final: 23 residues processed: 207 average time/residue: 0.3374 time to fit residues: 116.6947 Evaluate side-chains 192 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1554 HIS Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 1836 VAL Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1963 MET Chi-restraints excluded: chain A residue 2284 LEU Chi-restraints excluded: chain A residue 2544 ILE Chi-restraints excluded: chain A residue 2573 ILE Chi-restraints excluded: chain A residue 2582 VAL Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2730 VAL Chi-restraints excluded: chain A residue 2878 VAL Chi-restraints excluded: chain A residue 2945 VAL Chi-restraints excluded: chain A residue 3002 LEU Chi-restraints excluded: chain A residue 3362 VAL Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3650 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 282 TRP Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 273 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 183 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 194 optimal weight: 0.7980 chunk 178 optimal weight: 0.2980 chunk 112 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 259 optimal weight: 5.9990 chunk 296 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1554 HIS ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.102504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.084425 restraints weight = 58414.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.086958 restraints weight = 29867.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.088636 restraints weight = 19236.400| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24365 Z= 0.101 Angle : 0.489 8.990 33065 Z= 0.245 Chirality : 0.040 0.156 3797 Planarity : 0.003 0.040 4148 Dihedral : 5.033 110.873 3284 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.33 % Allowed : 15.00 % Favored : 83.67 % 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: 1.27 (0.16), residues: 2980 helix: 2.43 (0.14), residues: 1409 sheet: -0.09 (0.24), residues: 492 loop : -0.87 (0.19), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2084 HIS 0.004 0.001 HIS A1555 PHE 0.018 0.001 PHE A2281 TYR 0.018 0.001 TYR A3715 ARG 0.003 0.000 ARG A3510 Details of bonding type rmsd hydrogen bonds : bond 0.03051 ( 1267) hydrogen bonds : angle 3.82403 ( 3708) covalent geometry : bond 0.00229 (24365) covalent geometry : angle 0.48876 (33065) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1454 TRP cc_start: 0.6983 (t-100) cc_final: 0.6668 (t-100) REVERT: A 1934 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7944 (mt) REVERT: A 2200 ASP cc_start: 0.8293 (p0) cc_final: 0.7969 (p0) REVERT: A 2428 MET cc_start: 0.8501 (tmm) cc_final: 0.7680 (tmm) REVERT: A 2573 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8493 (mp) REVERT: A 2875 ASP cc_start: 0.8142 (m-30) cc_final: 0.7858 (m-30) REVERT: A 3002 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8751 (tt) REVERT: A 3341 GLU cc_start: 0.7852 (tt0) cc_final: 0.6981 (tp30) REVERT: A 3345 MET cc_start: 0.8020 (mpp) cc_final: 0.6738 (mpp) REVERT: A 3377 MET cc_start: 0.8833 (tpp) cc_final: 0.8522 (mmm) REVERT: A 3384 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.7895 (tt) REVERT: A 3438 LYS cc_start: 0.9179 (tptp) cc_final: 0.8870 (tppt) REVERT: A 3631 MET cc_start: 0.9209 (ttp) cc_final: 0.8934 (ttp) REVERT: A 3696 MET cc_start: 0.7969 (mtm) cc_final: 0.7734 (mtt) REVERT: A 3722 MET cc_start: 0.9138 (mmp) cc_final: 0.8778 (mmt) REVERT: A 3793 ASP cc_start: 0.4942 (OUTLIER) cc_final: 0.4545 (t70) REVERT: A 4079 LYS cc_start: 0.8622 (tptp) cc_final: 0.7973 (ttpt) REVERT: B 253 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8226 (mm-30) REVERT: B 304 ASP cc_start: 0.7541 (t70) cc_final: 0.6775 (t0) REVERT: C 436 ASP cc_start: 0.7627 (t0) cc_final: 0.7419 (t70) outliers start: 34 outliers final: 24 residues processed: 207 average time/residue: 0.3407 time to fit residues: 119.2164 Evaluate side-chains 198 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1554 HIS Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 1836 VAL Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1934 LEU Chi-restraints excluded: chain A residue 1963 MET Chi-restraints excluded: chain A residue 2284 LEU Chi-restraints excluded: chain A residue 2391 VAL Chi-restraints excluded: chain A residue 2544 ILE Chi-restraints excluded: chain A residue 2573 ILE Chi-restraints excluded: chain A residue 2582 VAL Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2730 VAL Chi-restraints excluded: chain A residue 2878 VAL Chi-restraints excluded: chain A residue 2945 VAL Chi-restraints excluded: chain A residue 2969 LEU Chi-restraints excluded: chain A residue 3002 LEU Chi-restraints excluded: chain A residue 3362 VAL Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3650 LEU Chi-restraints excluded: chain A residue 3793 ASP Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 273 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 268 optimal weight: 5.9990 chunk 289 optimal weight: 0.0770 chunk 161 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 217 optimal weight: 2.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1554 HIS ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.102640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.084605 restraints weight = 58228.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.087148 restraints weight = 29728.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.088825 restraints weight = 19082.589| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24365 Z= 0.102 Angle : 0.497 11.031 33065 Z= 0.248 Chirality : 0.040 0.155 3797 Planarity : 0.003 0.040 4148 Dihedral : 4.998 110.519 3284 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.37 % Allowed : 15.11 % Favored : 83.52 % 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: 1.30 (0.16), residues: 2980 helix: 2.45 (0.14), residues: 1409 sheet: -0.02 (0.24), residues: 487 loop : -0.87 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 288 HIS 0.005 0.001 HIS A1555 PHE 0.017 0.001 PHE A3457 TYR 0.013 0.001 TYR A3715 ARG 0.003 0.000 ARG A3510 Details of bonding type rmsd hydrogen bonds : bond 0.03029 ( 1267) hydrogen bonds : angle 3.79525 ( 3708) covalent geometry : bond 0.00231 (24365) covalent geometry : angle 0.49661 (33065) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1454 TRP cc_start: 0.6958 (t-100) cc_final: 0.6697 (t-100) REVERT: A 2200 ASP cc_start: 0.8382 (p0) cc_final: 0.8084 (p0) REVERT: A 2428 MET cc_start: 0.8504 (tmm) cc_final: 0.7689 (tmm) REVERT: A 2573 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8486 (mp) REVERT: A 2658 ASP cc_start: 0.8491 (m-30) cc_final: 0.8127 (m-30) REVERT: A 2875 ASP cc_start: 0.8181 (m-30) cc_final: 0.7956 (m-30) REVERT: A 3002 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8741 (tt) REVERT: A 3341 GLU cc_start: 0.7846 (tt0) cc_final: 0.7096 (tp30) REVERT: A 3345 MET cc_start: 0.8080 (mpp) cc_final: 0.6892 (mpp) REVERT: A 3377 MET cc_start: 0.8834 (tpp) cc_final: 0.8516 (mmm) REVERT: A 3384 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.7941 (tt) REVERT: A 3438 LYS cc_start: 0.9171 (tptp) cc_final: 0.8867 (tppt) REVERT: A 3464 ARG cc_start: 0.8306 (mmm-85) cc_final: 0.7728 (mmt90) REVERT: A 3631 MET cc_start: 0.9183 (ttp) cc_final: 0.8917 (ttp) REVERT: A 3696 MET cc_start: 0.7953 (mtm) cc_final: 0.7702 (mtt) REVERT: A 3722 MET cc_start: 0.9137 (mmp) cc_final: 0.8793 (mmt) REVERT: A 3793 ASP cc_start: 0.4945 (OUTLIER) cc_final: 0.4549 (t70) REVERT: A 3846 MET cc_start: 0.8958 (mmm) cc_final: 0.8701 (mmm) REVERT: A 4079 LYS cc_start: 0.8605 (tptp) cc_final: 0.7974 (ttpt) REVERT: B 253 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8237 (mm-30) REVERT: B 304 ASP cc_start: 0.7523 (t70) cc_final: 0.6759 (t0) REVERT: C 341 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8559 (mm-30) REVERT: C 436 ASP cc_start: 0.7650 (t0) cc_final: 0.7404 (t0) outliers start: 35 outliers final: 25 residues processed: 206 average time/residue: 0.3276 time to fit residues: 113.8892 Evaluate side-chains 200 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 1836 VAL Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1963 MET Chi-restraints excluded: chain A residue 2284 LEU Chi-restraints excluded: chain A residue 2391 VAL Chi-restraints excluded: chain A residue 2544 ILE Chi-restraints excluded: chain A residue 2573 ILE Chi-restraints excluded: chain A residue 2582 VAL Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2730 VAL Chi-restraints excluded: chain A residue 2878 VAL Chi-restraints excluded: chain A residue 2915 ASN Chi-restraints excluded: chain A residue 2945 VAL Chi-restraints excluded: chain A residue 3002 LEU Chi-restraints excluded: chain A residue 3362 VAL Chi-restraints excluded: chain A residue 3372 THR Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3650 LEU Chi-restraints excluded: chain A residue 3793 ASP Chi-restraints excluded: chain A residue 3834 ILE Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 273 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 85 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 181 optimal weight: 0.9980 chunk 195 optimal weight: 0.5980 chunk 185 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 chunk 268 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2274 HIS A3018 ASN ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.093590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.075502 restraints weight = 60362.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.077860 restraints weight = 31284.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.079437 restraints weight = 20229.516| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24365 Z= 0.166 Angle : 0.544 11.636 33065 Z= 0.275 Chirality : 0.042 0.156 3797 Planarity : 0.003 0.042 4148 Dihedral : 5.193 110.861 3284 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.45 % Allowed : 15.04 % Favored : 83.52 % 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: 1.25 (0.16), residues: 2980 helix: 2.41 (0.14), residues: 1411 sheet: -0.14 (0.24), residues: 493 loop : -0.86 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2084 HIS 0.004 0.001 HIS C 254 PHE 0.016 0.001 PHE A3457 TYR 0.014 0.001 TYR A2571 ARG 0.003 0.000 ARG A3510 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 1267) hydrogen bonds : angle 3.91349 ( 3708) covalent geometry : bond 0.00390 (24365) covalent geometry : angle 0.54392 (33065) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 3.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1454 TRP cc_start: 0.7059 (t-100) cc_final: 0.6770 (t-100) REVERT: A 1934 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8219 (mt) REVERT: A 2091 MET cc_start: 0.8809 (ttm) cc_final: 0.8385 (mtt) REVERT: A 2200 ASP cc_start: 0.8427 (p0) cc_final: 0.8126 (p0) REVERT: A 2428 MET cc_start: 0.8490 (tmm) cc_final: 0.7793 (tmm) REVERT: A 2658 ASP cc_start: 0.8564 (m-30) cc_final: 0.8120 (m-30) REVERT: A 3002 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8790 (tt) REVERT: A 3341 GLU cc_start: 0.7890 (tt0) cc_final: 0.6988 (tp30) REVERT: A 3345 MET cc_start: 0.8185 (mpp) cc_final: 0.7058 (mpp) REVERT: A 3377 MET cc_start: 0.8930 (tpp) cc_final: 0.8698 (mmm) REVERT: A 3384 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.7955 (tt) REVERT: A 3438 LYS cc_start: 0.9225 (tptp) cc_final: 0.8933 (tppt) REVERT: A 3631 MET cc_start: 0.9191 (ttp) cc_final: 0.8844 (ttp) REVERT: A 3696 MET cc_start: 0.8113 (mtm) cc_final: 0.7850 (mtt) REVERT: A 3722 MET cc_start: 0.9157 (mmp) cc_final: 0.8822 (mmt) REVERT: A 3793 ASP cc_start: 0.5098 (OUTLIER) cc_final: 0.4704 (t70) REVERT: A 3846 MET cc_start: 0.9135 (mmm) cc_final: 0.8854 (mmm) REVERT: B 253 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8287 (mm-30) REVERT: C 436 ASP cc_start: 0.7806 (t0) cc_final: 0.7549 (t0) REVERT: C 493 MET cc_start: 0.8571 (mmm) cc_final: 0.7958 (mtm) outliers start: 37 outliers final: 25 residues processed: 205 average time/residue: 0.3275 time to fit residues: 114.8489 Evaluate side-chains 193 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 1836 VAL Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1934 LEU Chi-restraints excluded: chain A residue 1963 MET Chi-restraints excluded: chain A residue 2284 LEU Chi-restraints excluded: chain A residue 2582 VAL Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2730 VAL Chi-restraints excluded: chain A residue 2878 VAL Chi-restraints excluded: chain A residue 2915 ASN Chi-restraints excluded: chain A residue 2945 VAL Chi-restraints excluded: chain A residue 3002 LEU Chi-restraints excluded: chain A residue 3018 ASN Chi-restraints excluded: chain A residue 3362 VAL Chi-restraints excluded: chain A residue 3372 THR Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3650 LEU Chi-restraints excluded: chain A residue 3793 ASP Chi-restraints excluded: chain A residue 3834 ILE Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 282 TRP Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 273 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 216 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.094928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.076887 restraints weight = 60161.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.079285 restraints weight = 30935.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.080870 restraints weight = 19899.778| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24365 Z= 0.114 Angle : 0.531 13.219 33065 Z= 0.263 Chirality : 0.041 0.158 3797 Planarity : 0.003 0.040 4148 Dihedral : 5.124 110.434 3284 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.14 % Allowed : 15.62 % Favored : 83.24 % 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: 1.28 (0.16), residues: 2980 helix: 2.43 (0.14), residues: 1412 sheet: -0.16 (0.24), residues: 493 loop : -0.83 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2084 HIS 0.004 0.001 HIS C 254 PHE 0.028 0.001 PHE A2404 TYR 0.015 0.001 TYR A2571 ARG 0.005 0.000 ARG A3510 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 1267) hydrogen bonds : angle 3.86372 ( 3708) covalent geometry : bond 0.00262 (24365) covalent geometry : angle 0.53067 (33065) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1454 TRP cc_start: 0.6989 (t-100) cc_final: 0.6734 (t-100) REVERT: A 1934 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8155 (mt) REVERT: A 2200 ASP cc_start: 0.8405 (p0) cc_final: 0.8106 (p0) REVERT: A 2428 MET cc_start: 0.8474 (tmm) cc_final: 0.7621 (tmm) REVERT: A 2658 ASP cc_start: 0.8577 (m-30) cc_final: 0.8142 (m-30) REVERT: A 3002 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8664 (tt) REVERT: A 3341 GLU cc_start: 0.7985 (tt0) cc_final: 0.7075 (tp30) REVERT: A 3345 MET cc_start: 0.8201 (mpp) cc_final: 0.7103 (mpp) REVERT: A 3377 MET cc_start: 0.8898 (tpp) cc_final: 0.8679 (mmm) REVERT: A 3384 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.7889 (tt) REVERT: A 3438 LYS cc_start: 0.9198 (tptp) cc_final: 0.8918 (tppt) REVERT: A 3631 MET cc_start: 0.9208 (ttp) cc_final: 0.8945 (ttp) REVERT: A 3696 MET cc_start: 0.8086 (mtm) cc_final: 0.7828 (mtt) REVERT: A 3722 MET cc_start: 0.9089 (mmp) cc_final: 0.8734 (mmt) REVERT: A 3793 ASP cc_start: 0.4820 (OUTLIER) cc_final: 0.4467 (t70) REVERT: A 3846 MET cc_start: 0.9089 (mmm) cc_final: 0.8817 (mmm) REVERT: A 3992 ILE cc_start: 0.9471 (mm) cc_final: 0.9242 (mt) REVERT: B 253 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8296 (mm-30) REVERT: B 304 ASP cc_start: 0.8467 (t0) cc_final: 0.8165 (t70) REVERT: B 345 PHE cc_start: 0.8686 (m-80) cc_final: 0.8365 (m-10) REVERT: C 341 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8583 (mm-30) REVERT: C 436 ASP cc_start: 0.7777 (t0) cc_final: 0.7491 (t0) REVERT: C 493 MET cc_start: 0.8581 (mmm) cc_final: 0.7962 (mtm) outliers start: 29 outliers final: 24 residues processed: 203 average time/residue: 0.3329 time to fit residues: 114.6253 Evaluate side-chains 201 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1819 VAL Chi-restraints excluded: chain A residue 1836 VAL Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1934 LEU Chi-restraints excluded: chain A residue 1963 MET Chi-restraints excluded: chain A residue 2284 LEU Chi-restraints excluded: chain A residue 2582 VAL Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2730 VAL Chi-restraints excluded: chain A residue 2878 VAL Chi-restraints excluded: chain A residue 2915 ASN Chi-restraints excluded: chain A residue 2945 VAL Chi-restraints excluded: chain A residue 3002 LEU Chi-restraints excluded: chain A residue 3362 VAL Chi-restraints excluded: chain A residue 3372 THR Chi-restraints excluded: chain A residue 3384 LEU Chi-restraints excluded: chain A residue 3478 THR Chi-restraints excluded: chain A residue 3650 LEU Chi-restraints excluded: chain A residue 3793 ASP Chi-restraints excluded: chain A residue 3834 ILE Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 282 TRP Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 273 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 41 optimal weight: 1.9990 chunk 185 optimal weight: 0.1980 chunk 78 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 204 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.095815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.077827 restraints weight = 59215.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.080223 restraints weight = 30540.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.081837 restraints weight = 19655.938| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24365 Z= 0.102 Angle : 0.513 12.052 33065 Z= 0.254 Chirality : 0.040 0.157 3797 Planarity : 0.003 0.040 4148 Dihedral : 4.987 109.614 3284 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.14 % Allowed : 15.90 % Favored : 82.97 % 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: 1.34 (0.16), residues: 2980 helix: 2.48 (0.14), residues: 1412 sheet: -0.11 (0.24), residues: 491 loop : -0.81 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2084 HIS 0.004 0.001 HIS C 254 PHE 0.025 0.001 PHE A2404 TYR 0.013 0.001 TYR A2571 ARG 0.005 0.000 ARG A3510 Details of bonding type rmsd hydrogen bonds : bond 0.03050 ( 1267) hydrogen bonds : angle 3.77813 ( 3708) covalent geometry : bond 0.00233 (24365) covalent geometry : angle 0.51322 (33065) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6793.61 seconds wall clock time: 119 minutes 22.70 seconds (7162.70 seconds total)