Starting phenix.real_space_refine on Fri Sep 19 10:06:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bmw_44713/09_2025/9bmw_44713.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bmw_44713/09_2025/9bmw_44713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bmw_44713/09_2025/9bmw_44713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bmw_44713/09_2025/9bmw_44713.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bmw_44713/09_2025/9bmw_44713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bmw_44713/09_2025/9bmw_44713.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 2 5.21 5 S 122 5.16 5 C 15646 2.51 5 N 4254 2.21 5 O 4584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24617 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 24503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3043, 24503 Classifications: {'peptide': 3043} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 130, 'TRANS': 2909} Chain breaks: 3 Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 114 Unusual residues: {' MG': 2, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 6.07, per 1000 atoms: 0.25 Number of scatterers: 24617 At special positions: 0 Unit cell: (171.179, 156.742, 127.869, 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 122 16.00 P 9 15.00 Mg 2 11.99 O 4584 8.00 N 4254 7.00 C 15646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5788 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 20 sheets defined 63.6% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 1327 through 1348 Processing helix chain 'A' and resid 1350 through 1354 Processing helix chain 'A' and resid 1355 through 1372 Processing helix chain 'A' and resid 1374 through 1379 Processing helix chain 'A' and resid 1380 through 1396 Processing helix chain 'A' and resid 1396 through 1404 Processing helix chain 'A' and resid 1410 through 1421 Processing helix chain 'A' and resid 1430 through 1437 removed outlier: 3.629A pdb=" N ILE A1434 " --> pdb=" O THR A1430 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A1437 " --> pdb=" O GLN A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1472 removed outlier: 3.710A pdb=" N THR A1472 " --> pdb=" O GLU A1468 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1508 removed outlier: 3.733A pdb=" N LYS A1508 " --> pdb=" O VAL A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1509 through 1515 removed outlier: 5.087A pdb=" N TYR A1512 " --> pdb=" O LEU A1509 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A1514 " --> pdb=" O PRO A1511 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A1515 " --> pdb=" O TYR A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1553 removed outlier: 3.862A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1561 Processing helix chain 'A' and resid 1561 through 1585 Processing helix chain 'A' and resid 1587 through 1593 Processing helix chain 'A' and resid 1596 through 1626 removed outlier: 3.508A pdb=" N SER A1600 " --> pdb=" O GLY A1596 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1632 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1646 through 1652 removed outlier: 3.720A pdb=" N GLN A1651 " --> pdb=" O ALA A1648 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1658 removed outlier: 3.544A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1729 removed outlier: 3.823A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1773 removed outlier: 3.731A pdb=" N GLY A1771 " --> pdb=" O SER A1767 " (cutoff:3.500A) Processing helix chain 'A' and resid 1775 through 1798 removed outlier: 3.753A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1829 removed outlier: 3.551A pdb=" N HIS A1817 " --> pdb=" O THR A1813 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 Processing helix chain 'A' and resid 1940 through 1952 Processing helix chain 'A' and resid 1959 through 1963 removed outlier: 3.611A pdb=" N LEU A1963 " --> pdb=" O PHE A1960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1964 through 1984 Processing helix chain 'A' and resid 1985 through 1987 No H-bonds generated for 'chain 'A' and resid 1985 through 1987' Processing helix chain 'A' and resid 2029 through 2033 Processing helix chain 'A' and resid 2045 through 2056 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix removed outlier: 3.584A pdb=" N LEU A2080 " --> pdb=" O CYS A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2118 Processing helix chain 'A' and resid 2123 through 2130 Processing helix chain 'A' and resid 2132 through 2146 removed outlier: 3.619A pdb=" N ILE A2136 " --> pdb=" O PRO A2132 " (cutoff:3.500A) Processing helix chain 'A' and resid 2152 through 2165 removed outlier: 4.088A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2260 through 2266 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2293 through 2297 Processing helix chain 'A' and resid 2314 through 2320 removed outlier: 4.324A pdb=" N VAL A2318 " --> pdb=" O ASN A2314 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2358 Processing helix chain 'A' and resid 2370 through 2385 removed outlier: 3.521A pdb=" N ILE A2374 " --> pdb=" O SER A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2394 through 2400 removed outlier: 4.093A pdb=" N ARG A2398 " --> pdb=" O ALA A2394 " (cutoff:3.500A) Processing helix chain 'A' and resid 2410 through 2424 Processing helix chain 'A' and resid 2425 through 2427 No H-bonds generated for 'chain 'A' and resid 2425 through 2427' Processing helix chain 'A' and resid 2431 through 2443 removed outlier: 3.674A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.612A pdb=" N CYS A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2503 Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2549 through 2552 Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.736A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2611 removed outlier: 3.641A pdb=" N ALA A2611 " --> pdb=" O SER A2607 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.000A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2689 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2739 through 2757 removed outlier: 4.269A pdb=" N SER A2743 " --> pdb=" O PRO A2739 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 3.605A pdb=" N ARG A2763 " --> pdb=" O PRO A2760 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2784 Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.849A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2833 Processing helix chain 'A' and resid 2834 through 2837 Processing helix chain 'A' and resid 2839 through 2858 removed outlier: 3.733A pdb=" N ARG A2843 " --> pdb=" O GLU A2839 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A2851 " --> pdb=" O ASP A2847 " (cutoff:3.500A) Processing helix chain 'A' and resid 2862 through 2867 removed outlier: 3.541A pdb=" N ALA A2866 " --> pdb=" O ASP A2862 " (cutoff:3.500A) Processing helix chain 'A' and resid 2885 through 2904 Processing helix chain 'A' and resid 2912 through 2927 removed outlier: 3.555A pdb=" N LEU A2920 " --> pdb=" O LEU A2916 " (cutoff:3.500A) Processing helix chain 'A' and resid 2942 through 2955 Processing helix chain 'A' and resid 2968 through 2984 removed outlier: 3.547A pdb=" N PHE A2972 " --> pdb=" O THR A2968 " (cutoff:3.500A) Processing helix chain 'A' and resid 3002 through 3015 removed outlier: 3.856A pdb=" N GLU A3006 " --> pdb=" O SER A3002 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG A3007 " --> pdb=" O GLY A3003 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3040 removed outlier: 3.538A pdb=" N GLU A3035 " --> pdb=" O THR A3031 " (cutoff:3.500A) Processing helix chain 'A' and resid 3046 through 3061 Processing helix chain 'A' and resid 3071 through 3082 Processing helix chain 'A' and resid 3083 through 3088 Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3165 Processing helix chain 'A' and resid 3172 through 3221 removed outlier: 3.649A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP A3221 " --> pdb=" O GLU A3217 " (cutoff:3.500A) Processing helix chain 'A' and resid 3471 through 3516 removed outlier: 4.880A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLY A3505 " --> pdb=" O SER A3501 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3538 Processing helix chain 'A' and resid 3548 through 3553 removed outlier: 3.684A pdb=" N LEU A3553 " --> pdb=" O ARG A3549 " (cutoff:3.500A) Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3582 Processing helix chain 'A' and resid 3594 through 3604 removed outlier: 3.648A pdb=" N GLU A3598 " --> pdb=" O GLY A3594 " (cutoff:3.500A) Processing helix chain 'A' and resid 3618 through 3630 Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3651 Processing helix chain 'A' and resid 3689 through 3694 Processing helix chain 'A' and resid 3706 through 3721 Processing helix chain 'A' and resid 3721 through 3734 Processing helix chain 'A' and resid 3736 through 3755 removed outlier: 4.180A pdb=" N GLU A3755 " --> pdb=" O GLN A3751 " (cutoff:3.500A) Processing helix chain 'A' and resid 3758 through 3762 Processing helix chain 'A' and resid 3766 through 3786 removed outlier: 4.502A pdb=" N LEU A3770 " --> pdb=" O ILE A3766 " (cutoff:3.500A) Processing helix chain 'A' and resid 3786 through 3818 removed outlier: 3.712A pdb=" N VAL A3790 " --> pdb=" O GLU A3786 " (cutoff:3.500A) Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3819 through 3821 No H-bonds generated for 'chain 'A' and resid 3819 through 3821' Processing helix chain 'A' and resid 3828 through 3841 Processing helix chain 'A' and resid 3843 through 3847 Processing helix chain 'A' and resid 3851 through 3874 removed outlier: 3.582A pdb=" N ARG A3873 " --> pdb=" O ASN A3869 " (cutoff:3.500A) Processing helix chain 'A' and resid 3875 through 3878 removed outlier: 6.287A pdb=" N GLN A3878 " --> pdb=" O MET A3875 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3875 through 3878' Processing helix chain 'A' and resid 3879 through 3895 Processing helix chain 'A' and resid 3901 through 3911 Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3946 through 3954 removed outlier: 3.683A pdb=" N GLN A3952 " --> pdb=" O ILE A3948 " (cutoff:3.500A) Processing helix chain 'A' and resid 3956 through 3962 removed outlier: 3.880A pdb=" N TRP A3960 " --> pdb=" O GLN A3956 " (cutoff:3.500A) Processing helix chain 'A' and resid 3965 through 3969 Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4014 removed outlier: 3.506A pdb=" N MET A4007 " --> pdb=" O ALA A4003 " (cutoff:3.500A) Processing helix chain 'A' and resid 4015 through 4017 No H-bonds generated for 'chain 'A' and resid 4015 through 4017' Processing helix chain 'A' and resid 4018 through 4023 removed outlier: 3.641A pdb=" N GLU A4022 " --> pdb=" O MET A4018 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A4023 " --> pdb=" O SER A4019 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4018 through 4023' Processing helix chain 'A' and resid 4026 through 4033 removed outlier: 4.010A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4062 removed outlier: 3.991A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4089 removed outlier: 3.654A pdb=" N LYS A4089 " --> pdb=" O ASN A4085 " (cutoff:3.500A) Processing helix chain 'A' and resid 4098 through 4101 Processing helix chain 'A' and resid 4102 through 4115 Processing helix chain 'A' and resid 4135 through 4141 removed outlier: 3.554A pdb=" N LEU A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4171 Processing helix chain 'A' and resid 4174 through 4194 removed outlier: 4.177A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4228 removed outlier: 3.573A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 Processing helix chain 'A' and resid 4317 through 4322 Processing helix chain 'A' and resid 4326 through 4348 Processing helix chain 'A' and resid 4376 through 4391 Processing helix chain 'A' and resid 4403 through 4406 removed outlier: 3.710A pdb=" N LYS A4406 " --> pdb=" O GLU A4403 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4403 through 4406' Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4474 through 4500 Processing helix chain 'A' and resid 4501 through 4506 removed outlier: 4.094A pdb=" N LYS A4505 " --> pdb=" O ALA A4501 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN A4506 " --> pdb=" O LYS A4502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4501 through 4506' Processing helix chain 'A' and resid 4516 through 4532 Processing helix chain 'A' and resid 4535 through 4537 No H-bonds generated for 'chain 'A' and resid 4535 through 4537' Processing helix chain 'A' and resid 4631 through 4638 Processing sheet with id=AA1, first strand: chain 'A' and resid 1476 through 1480 removed outlier: 4.430A pdb=" N ASP A1476 " --> pdb=" O ARG A1488 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1661 through 1666 removed outlier: 10.461A pdb=" N VAL A1672 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 11.355A pdb=" N THR A1688 " --> pdb=" O VAL A1672 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU A1674 " --> pdb=" O PHE A1686 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1930 removed outlier: 5.951A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA7, first strand: chain 'A' and resid 2249 through 2251 removed outlier: 7.066A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLY A2219 " --> pdb=" O GLY A2360 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N VAL A2362 " --> pdb=" O GLY A2219 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N MET A2221 " --> pdb=" O VAL A2362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AA9, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB1, first strand: chain 'A' and resid 2710 through 2712 removed outlier: 6.507A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 6.672A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2643 removed outlier: 6.722A pdb=" N VAL A2648 " --> pdb=" O LYS A2702 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 6.209A pdb=" N ILE A2990 " --> pdb=" O HIS A3063 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 3.728A pdb=" N GLN A3636 " --> pdb=" O THR A3612 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3653 through 3656 Processing sheet with id=AB7, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.494A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU A4042 " --> pdb=" O PHE A4145 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N PHE A4147 " --> pdb=" O LEU A4042 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N CYS A4044 " --> pdb=" O PHE A4147 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4283 through 4285 removed outlier: 6.926A pdb=" N ILE A4294 " --> pdb=" O LEU A4284 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.297A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4583 through 4584 removed outlier: 3.569A pdb=" N ALA A4641 " --> pdb=" O GLN A4566 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4568 through 4570 1440 hydrogen bonds defined for protein. 4197 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: 7.41 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6741 1.33 - 1.45: 4325 1.45 - 1.58: 13856 1.58 - 1.70: 14 1.70 - 1.82: 206 Bond restraints: 25142 Sorted by residual: bond pdb=" N ILE A1611 " pdb=" CA ILE A1611 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 9.04e+00 bond pdb=" N VAL A1563 " pdb=" CA VAL A1563 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.77e+00 bond pdb=" N ILE A1571 " pdb=" CA ILE A1571 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.44e+00 bond pdb=" N ASP A1606 " pdb=" CA ASP A1606 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.17e-02 7.31e+03 6.26e+00 bond pdb=" N PHE A1568 " pdb=" CA PHE A1568 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.17e+00 ... (remaining 25137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 33451 2.14 - 4.27: 550 4.27 - 6.41: 76 6.41 - 8.54: 9 8.54 - 10.68: 3 Bond angle restraints: 34089 Sorted by residual: angle pdb=" C LYS A1409 " pdb=" CA LYS A1409 " pdb=" CB LYS A1409 " ideal model delta sigma weight residual 117.23 110.39 6.84 1.36e+00 5.41e-01 2.53e+01 angle pdb=" CA LYS A1409 " pdb=" C LYS A1409 " pdb=" N ASP A1410 " ideal model delta sigma weight residual 119.98 116.90 3.08 8.50e-01 1.38e+00 1.31e+01 angle pdb=" CB MET A2953 " pdb=" CG MET A2953 " pdb=" SD MET A2953 " ideal model delta sigma weight residual 112.70 102.02 10.68 3.00e+00 1.11e-01 1.27e+01 angle pdb=" C THR A3031 " pdb=" N GLN A3032 " pdb=" CA GLN A3032 " ideal model delta sigma weight residual 121.14 115.09 6.05 1.75e+00 3.27e-01 1.20e+01 angle pdb=" CB MET A3885 " pdb=" CG MET A3885 " pdb=" SD MET A3885 " ideal model delta sigma weight residual 112.70 102.66 10.04 3.00e+00 1.11e-01 1.12e+01 ... (remaining 34084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 13626 17.96 - 35.92: 1311 35.92 - 53.88: 230 53.88 - 71.84: 69 71.84 - 89.80: 22 Dihedral angle restraints: 15258 sinusoidal: 6348 harmonic: 8910 Sorted by residual: dihedral pdb=" CA ARG A2507 " pdb=" C ARG A2507 " pdb=" N LEU A2508 " pdb=" CA LEU A2508 " ideal model delta harmonic sigma weight residual 180.00 -158.18 -21.82 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA TRP A3093 " pdb=" C TRP A3093 " pdb=" N PHE A3094 " pdb=" CA PHE A3094 " ideal model delta harmonic sigma weight residual 180.00 159.46 20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" C5' ADP A4703 " pdb=" O5' ADP A4703 " pdb=" PA ADP A4703 " pdb=" O2A ADP A4703 " ideal model delta sinusoidal sigma weight residual -60.00 -123.58 63.59 1 2.00e+01 2.50e-03 1.33e+01 ... (remaining 15255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2949 0.045 - 0.090: 664 0.090 - 0.135: 191 0.135 - 0.180: 16 0.180 - 0.225: 1 Chirality restraints: 3821 Sorted by residual: chirality pdb=" CA ILE A1571 " pdb=" N ILE A1571 " pdb=" C ILE A1571 " pdb=" CB ILE A1571 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE A1466 " pdb=" CA ILE A1466 " pdb=" CG1 ILE A1466 " pdb=" CG2 ILE A1466 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CB THR A3685 " pdb=" CA THR A3685 " pdb=" OG1 THR A3685 " pdb=" CG2 THR A3685 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.29e-01 ... (remaining 3818 not shown) Planarity restraints: 4367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A3093 " 0.017 2.00e-02 2.50e+03 1.83e-02 8.38e+00 pdb=" CG TRP A3093 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP A3093 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A3093 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A3093 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A3093 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A3093 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A3093 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A3093 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A3093 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A2907 " -0.046 5.00e-02 4.00e+02 6.98e-02 7.79e+00 pdb=" N PRO A2908 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A2908 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A2908 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A2825 " -0.015 2.00e-02 2.50e+03 1.23e-02 3.79e+00 pdb=" CG TRP A2825 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A2825 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A2825 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A2825 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A2825 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A2825 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2825 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2825 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A2825 " 0.001 2.00e-02 2.50e+03 ... (remaining 4364 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 164 2.55 - 3.14: 19892 3.14 - 3.73: 39987 3.73 - 4.31: 52072 4.31 - 4.90: 88691 Nonbonded interactions: 200806 Sorted by model distance: nonbonded pdb=" O1B ATP A4702 " pdb="MG MG A4706 " model vdw 1.967 2.170 nonbonded pdb=" OG SER A2231 " pdb="MG MG A4706 " model vdw 1.986 2.170 nonbonded pdb=" OG SER A3593 " pdb=" OE1 GLN A3595 " model vdw 2.127 3.040 nonbonded pdb=" O ASP A4631 " pdb=" OG SER A4634 " model vdw 2.163 3.040 nonbonded pdb=" O THR A3028 " pdb=" OG1 THR A3031 " model vdw 2.179 3.040 ... (remaining 200801 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.910 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 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 0.052 25142 Z= 0.163 Angle : 0.637 10.680 34089 Z= 0.335 Chirality : 0.041 0.225 3821 Planarity : 0.004 0.070 4367 Dihedral : 14.817 89.799 9470 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.16), residues: 3035 helix: 1.90 (0.12), residues: 1748 sheet: -0.32 (0.38), residues: 213 loop : 0.29 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A2965 TYR 0.025 0.002 TYR A2748 PHE 0.027 0.002 PHE A1629 TRP 0.047 0.002 TRP A3093 HIS 0.009 0.001 HIS A4119 Details of bonding type rmsd covalent geometry : bond 0.00337 (25142) covalent geometry : angle 0.63738 (34089) hydrogen bonds : bond 0.12766 ( 1440) hydrogen bonds : angle 5.54818 ( 4197) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1533 LEU cc_start: 0.8226 (tp) cc_final: 0.7984 (tp) REVERT: A 2222 MET cc_start: 0.8077 (mpp) cc_final: 0.7846 (mtm) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.1649 time to fit residues: 93.9460 Evaluate side-chains 262 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1481 GLN A1566 GLN A1863 ASN ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2187 GLN ** A2263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2377 ASN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2588 HIS ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3014 ASN A3837 HIS A4023 GLN A4063 ASN A4466 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.151708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.110482 restraints weight = 45769.537| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.83 r_work: 0.3383 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 25142 Z= 0.206 Angle : 0.614 8.078 34089 Z= 0.309 Chirality : 0.043 0.226 3821 Planarity : 0.004 0.055 4367 Dihedral : 5.948 78.157 3377 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.24 % Favored : 97.73 % Rotamer: Outliers : 1.07 % Allowed : 7.06 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.16), residues: 3035 helix: 1.88 (0.12), residues: 1771 sheet: -0.75 (0.36), residues: 227 loop : 0.30 (0.20), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2610 TYR 0.016 0.002 TYR A3836 PHE 0.025 0.002 PHE A3529 TRP 0.023 0.002 TRP A2825 HIS 0.006 0.001 HIS A2857 Details of bonding type rmsd covalent geometry : bond 0.00482 (25142) covalent geometry : angle 0.61438 (34089) hydrogen bonds : bond 0.04180 ( 1440) hydrogen bonds : angle 4.49579 ( 4197) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 299 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1814 GLU cc_start: 0.8376 (tp30) cc_final: 0.8132 (tp30) REVERT: A 1937 ASP cc_start: 0.7889 (t70) cc_final: 0.7236 (p0) REVERT: A 2643 ARG cc_start: 0.8160 (mmm160) cc_final: 0.7799 (tpp80) REVERT: A 2779 MET cc_start: 0.8342 (mtm) cc_final: 0.7880 (tpt) REVERT: A 2994 MET cc_start: 0.7847 (ptp) cc_final: 0.7546 (ptp) REVERT: A 3108 GLU cc_start: 0.8356 (tp30) cc_final: 0.8077 (tp30) REVERT: A 4281 GLU cc_start: 0.8416 (pm20) cc_final: 0.8129 (pp20) REVERT: A 4346 MET cc_start: 0.8639 (mmm) cc_final: 0.8421 (mmm) outliers start: 29 outliers final: 22 residues processed: 318 average time/residue: 0.1553 time to fit residues: 80.3805 Evaluate side-chains 267 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 245 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1768 SER Chi-restraints excluded: chain A residue 1999 CYS Chi-restraints excluded: chain A residue 2318 VAL Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2483 ILE Chi-restraints excluded: chain A residue 2531 ASN Chi-restraints excluded: chain A residue 2695 THR Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2799 MET Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3032 GLN Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3560 LEU Chi-restraints excluded: chain A residue 3717 LEU Chi-restraints excluded: chain A residue 3970 VAL Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4226 THR Chi-restraints excluded: chain A residue 4516 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 215 optimal weight: 0.9990 chunk 190 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 47 optimal weight: 0.0170 chunk 147 optimal weight: 4.9990 chunk 213 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 206 optimal weight: 3.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1566 GLN A1863 ASN ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2187 GLN ** A2263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2430 ASN ** A2998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3047 HIS A3197 GLN A3994 GLN A4023 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.150542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.108990 restraints weight = 45300.095| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.86 r_work: 0.3351 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 25142 Z= 0.202 Angle : 0.584 8.436 34089 Z= 0.292 Chirality : 0.042 0.184 3821 Planarity : 0.004 0.052 4367 Dihedral : 5.905 86.372 3377 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.66 % Rotamer: Outliers : 1.66 % Allowed : 10.24 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.16), residues: 3035 helix: 1.86 (0.12), residues: 1772 sheet: -0.87 (0.36), residues: 218 loop : 0.26 (0.20), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A2921 TYR 0.027 0.002 TYR A1745 PHE 0.027 0.002 PHE A4077 TRP 0.019 0.002 TRP A2825 HIS 0.006 0.001 HIS A4119 Details of bonding type rmsd covalent geometry : bond 0.00477 (25142) covalent geometry : angle 0.58367 (34089) hydrogen bonds : bond 0.04083 ( 1440) hydrogen bonds : angle 4.40200 ( 4197) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 277 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1610 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7621 (mptt) REVERT: A 1679 ARG cc_start: 0.8710 (tmm-80) cc_final: 0.8489 (ttp-170) REVERT: A 1872 TYR cc_start: 0.8948 (t80) cc_final: 0.8723 (t80) REVERT: A 2367 ASP cc_start: 0.9004 (t0) cc_final: 0.8654 (t0) REVERT: A 2643 ARG cc_start: 0.8341 (mmm160) cc_final: 0.8004 (tpp80) REVERT: A 2779 MET cc_start: 0.8506 (mtm) cc_final: 0.8067 (tpt) REVERT: A 2936 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8505 (mm) REVERT: A 3054 PHE cc_start: 0.6349 (t80) cc_final: 0.6146 (t80) REVERT: A 3108 GLU cc_start: 0.8510 (tp30) cc_final: 0.8246 (tp30) REVERT: A 3135 GLN cc_start: 0.7646 (mt0) cc_final: 0.7254 (tp-100) REVERT: A 3526 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8205 (tm-30) REVERT: A 3682 ARG cc_start: 0.8359 (ttm-80) cc_final: 0.7993 (ttm-80) REVERT: A 4022 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8135 (mp0) REVERT: A 4281 GLU cc_start: 0.8238 (pm20) cc_final: 0.7951 (pp20) outliers start: 45 outliers final: 25 residues processed: 304 average time/residue: 0.1620 time to fit residues: 79.7041 Evaluate side-chains 273 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 246 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1610 LYS Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1768 SER Chi-restraints excluded: chain A residue 1999 CYS Chi-restraints excluded: chain A residue 2318 VAL Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2483 ILE Chi-restraints excluded: chain A residue 2571 THR Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2623 SER Chi-restraints excluded: chain A residue 2695 THR Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2897 LEU Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3032 GLN Chi-restraints excluded: chain A residue 3047 HIS Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 96 optimal weight: 6.9990 chunk 9 optimal weight: 0.1980 chunk 88 optimal weight: 2.9990 chunk 263 optimal weight: 0.9990 chunk 128 optimal weight: 0.0050 chunk 236 optimal weight: 0.7980 chunk 159 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 211 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1566 GLN A1863 ASN ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2187 GLN ** A2263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3047 HIS A4023 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.150486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.108230 restraints weight = 44842.068| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.89 r_work: 0.3406 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25142 Z= 0.111 Angle : 0.527 9.320 34089 Z= 0.261 Chirality : 0.039 0.206 3821 Planarity : 0.004 0.049 4367 Dihedral : 5.680 86.722 3377 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.14 % Favored : 97.83 % Rotamer: Outliers : 1.40 % Allowed : 11.75 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.16), residues: 3035 helix: 2.02 (0.12), residues: 1771 sheet: -0.82 (0.36), residues: 218 loop : 0.41 (0.21), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2863 TYR 0.017 0.001 TYR A2748 PHE 0.017 0.001 PHE A3813 TRP 0.017 0.001 TRP A2234 HIS 0.011 0.001 HIS A3047 Details of bonding type rmsd covalent geometry : bond 0.00243 (25142) covalent geometry : angle 0.52677 (34089) hydrogen bonds : bond 0.03624 ( 1440) hydrogen bonds : angle 4.19562 ( 4197) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 287 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1417 MET cc_start: 0.0467 (ppp) cc_final: -0.0324 (mtm) REVERT: A 1485 ARG cc_start: 0.7660 (tpt170) cc_final: 0.7259 (tpp80) REVERT: A 1610 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7756 (mptt) REVERT: A 1829 LYS cc_start: 0.8884 (mmtt) cc_final: 0.8592 (mtmt) REVERT: A 2367 ASP cc_start: 0.8998 (t0) cc_final: 0.8616 (t0) REVERT: A 2643 ARG cc_start: 0.8263 (mmm160) cc_final: 0.7906 (tpt170) REVERT: A 2779 MET cc_start: 0.8412 (mtm) cc_final: 0.7971 (tpt) REVERT: A 2855 LEU cc_start: 0.7659 (pp) cc_final: 0.7142 (mt) REVERT: A 3153 THR cc_start: 0.8246 (t) cc_final: 0.7950 (p) REVERT: A 3526 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8167 (tm-30) REVERT: A 4030 ILE cc_start: 0.8859 (tt) cc_final: 0.8612 (tt) REVERT: A 4511 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9061 (mt) outliers start: 38 outliers final: 24 residues processed: 312 average time/residue: 0.1696 time to fit residues: 85.3291 Evaluate side-chains 287 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 261 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1610 LYS Chi-restraints excluded: chain A residue 1768 SER Chi-restraints excluded: chain A residue 2349 LYS Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2510 MET Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 2897 LEU Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3032 GLN Chi-restraints excluded: chain A residue 3047 HIS Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3196 GLU Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3768 THR Chi-restraints excluded: chain A residue 4033 THR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4226 THR Chi-restraints excluded: chain A residue 4377 MET Chi-restraints excluded: chain A residue 4511 LEU Chi-restraints excluded: chain A residue 4516 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 240 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 187 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 265 optimal weight: 5.9990 chunk 126 optimal weight: 0.0570 chunk 209 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1566 GLN ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2187 GLN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3047 HIS A4023 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.152126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.111012 restraints weight = 44617.347| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.84 r_work: 0.3370 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25142 Z= 0.127 Angle : 0.533 9.572 34089 Z= 0.263 Chirality : 0.039 0.296 3821 Planarity : 0.004 0.050 4367 Dihedral : 5.597 84.867 3377 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.17 % Favored : 97.79 % Rotamer: Outliers : 1.70 % Allowed : 12.53 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.16), residues: 3035 helix: 2.02 (0.12), residues: 1779 sheet: -0.92 (0.35), residues: 225 loop : 0.48 (0.21), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3682 TYR 0.019 0.001 TYR A2748 PHE 0.027 0.001 PHE A4077 TRP 0.016 0.001 TRP A2234 HIS 0.010 0.001 HIS A3047 Details of bonding type rmsd covalent geometry : bond 0.00292 (25142) covalent geometry : angle 0.53293 (34089) hydrogen bonds : bond 0.03551 ( 1440) hydrogen bonds : angle 4.13962 ( 4197) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 277 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1417 MET cc_start: 0.0316 (ppp) cc_final: -0.0376 (mtm) REVERT: A 1485 ARG cc_start: 0.7630 (tpt170) cc_final: 0.7308 (tpp80) REVERT: A 1610 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7691 (mptt) REVERT: A 1677 SER cc_start: 0.8668 (t) cc_final: 0.8062 (p) REVERT: A 1829 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8618 (mtmt) REVERT: A 2367 ASP cc_start: 0.9041 (t0) cc_final: 0.8643 (t0) REVERT: A 2643 ARG cc_start: 0.8300 (mmm160) cc_final: 0.7917 (tpt170) REVERT: A 2779 MET cc_start: 0.8426 (mtm) cc_final: 0.7999 (tpt) REVERT: A 2855 LEU cc_start: 0.7663 (pp) cc_final: 0.7159 (mt) REVERT: A 2936 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8510 (mm) REVERT: A 3078 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7121 (mpp80) REVERT: A 3153 THR cc_start: 0.8268 (t) cc_final: 0.7959 (p) REVERT: A 3510 SER cc_start: 0.9080 (m) cc_final: 0.8576 (p) REVERT: A 3526 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8185 (tm-30) REVERT: A 4030 ILE cc_start: 0.8868 (tt) cc_final: 0.8595 (tt) REVERT: A 4511 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9096 (mt) outliers start: 46 outliers final: 25 residues processed: 304 average time/residue: 0.1678 time to fit residues: 82.8276 Evaluate side-chains 289 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 260 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1610 LYS Chi-restraints excluded: chain A residue 1768 SER Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2709 VAL Chi-restraints excluded: chain A residue 2799 MET Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 2897 LEU Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3032 GLN Chi-restraints excluded: chain A residue 3078 ARG Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3768 THR Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4033 THR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4226 THR Chi-restraints excluded: chain A residue 4377 MET Chi-restraints excluded: chain A residue 4511 LEU Chi-restraints excluded: chain A residue 4516 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 88 optimal weight: 0.9990 chunk 188 optimal weight: 6.9990 chunk 225 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 297 optimal weight: 0.7980 chunk 257 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 199 optimal weight: 10.0000 chunk 255 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1566 GLN A1961 ASN A2187 GLN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2752 ASN A3540 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.151678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.110450 restraints weight = 44699.085| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.85 r_work: 0.3377 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25142 Z= 0.130 Angle : 0.536 10.916 34089 Z= 0.262 Chirality : 0.040 0.283 3821 Planarity : 0.004 0.051 4367 Dihedral : 5.504 81.118 3377 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.27 % Favored : 97.69 % Rotamer: Outliers : 1.88 % Allowed : 13.23 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.16), residues: 3035 helix: 2.04 (0.12), residues: 1779 sheet: -0.92 (0.35), residues: 237 loop : 0.54 (0.21), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3682 TYR 0.019 0.001 TYR A2748 PHE 0.023 0.001 PHE A3513 TRP 0.016 0.001 TRP A2234 HIS 0.005 0.001 HIS A2445 Details of bonding type rmsd covalent geometry : bond 0.00301 (25142) covalent geometry : angle 0.53551 (34089) hydrogen bonds : bond 0.03500 ( 1440) hydrogen bonds : angle 4.08986 ( 4197) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 271 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1417 MET cc_start: 0.0267 (ppp) cc_final: -0.0340 (mtm) REVERT: A 1485 ARG cc_start: 0.7522 (tpt170) cc_final: 0.7213 (tpp80) REVERT: A 1610 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7625 (mptt) REVERT: A 1679 ARG cc_start: 0.8795 (tmm-80) cc_final: 0.8483 (ttp-170) REVERT: A 1829 LYS cc_start: 0.8887 (mmtt) cc_final: 0.8630 (mtmt) REVERT: A 1937 ASP cc_start: 0.8253 (t70) cc_final: 0.7524 (p0) REVERT: A 2018 MET cc_start: 0.8677 (mmm) cc_final: 0.8418 (mmm) REVERT: A 2367 ASP cc_start: 0.9066 (t0) cc_final: 0.8709 (t0) REVERT: A 2643 ARG cc_start: 0.8297 (mmm160) cc_final: 0.7918 (tpt170) REVERT: A 2779 MET cc_start: 0.8461 (mtm) cc_final: 0.8044 (tpt) REVERT: A 2855 LEU cc_start: 0.7687 (pp) cc_final: 0.7188 (mt) REVERT: A 2936 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8548 (mm) REVERT: A 3078 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.7115 (mpp80) REVERT: A 3153 THR cc_start: 0.8234 (t) cc_final: 0.7936 (p) REVERT: A 3178 ASP cc_start: 0.8759 (t0) cc_final: 0.8362 (t0) REVERT: A 3510 SER cc_start: 0.9127 (m) cc_final: 0.8639 (p) REVERT: A 3526 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8171 (tm-30) REVERT: A 4030 ILE cc_start: 0.8910 (tt) cc_final: 0.8641 (tt) REVERT: A 4346 MET cc_start: 0.8557 (mmp) cc_final: 0.8209 (mmm) outliers start: 51 outliers final: 30 residues processed: 305 average time/residue: 0.1706 time to fit residues: 84.2930 Evaluate side-chains 287 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 254 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1610 LYS Chi-restraints excluded: chain A residue 1768 SER Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2455 LEU Chi-restraints excluded: chain A residue 2510 MET Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2709 VAL Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2799 MET Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3032 GLN Chi-restraints excluded: chain A residue 3047 HIS Chi-restraints excluded: chain A residue 3078 ARG Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3768 THR Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4033 THR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4226 THR Chi-restraints excluded: chain A residue 4377 MET Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4645 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 82 optimal weight: 0.6980 chunk 136 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 225 optimal weight: 1.9990 chunk 296 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 251 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 214 optimal weight: 0.9980 chunk 301 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1566 GLN A1961 ASN A2187 GLN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2677 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.152367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.111515 restraints weight = 44764.361| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.83 r_work: 0.3396 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25142 Z= 0.112 Angle : 0.529 10.580 34089 Z= 0.257 Chirality : 0.039 0.198 3821 Planarity : 0.003 0.051 4367 Dihedral : 5.398 76.037 3377 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.11 % Favored : 97.86 % Rotamer: Outliers : 1.70 % Allowed : 14.19 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.16), residues: 3035 helix: 2.10 (0.12), residues: 1777 sheet: -0.85 (0.35), residues: 241 loop : 0.61 (0.21), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3682 TYR 0.020 0.001 TYR A2748 PHE 0.026 0.001 PHE A4077 TRP 0.016 0.001 TRP A2234 HIS 0.006 0.001 HIS A4119 Details of bonding type rmsd covalent geometry : bond 0.00253 (25142) covalent geometry : angle 0.52897 (34089) hydrogen bonds : bond 0.03399 ( 1440) hydrogen bonds : angle 4.02482 ( 4197) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 277 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1417 MET cc_start: 0.0365 (ppp) cc_final: -0.0321 (mtm) REVERT: A 1485 ARG cc_start: 0.7545 (tpt170) cc_final: 0.7187 (tpp80) REVERT: A 1610 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7681 (mptt) REVERT: A 1829 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8635 (mtmt) REVERT: A 1937 ASP cc_start: 0.8131 (t70) cc_final: 0.7452 (p0) REVERT: A 2018 MET cc_start: 0.8687 (mmm) cc_final: 0.8415 (mmm) REVERT: A 2170 TYR cc_start: 0.7559 (t80) cc_final: 0.7348 (t80) REVERT: A 2367 ASP cc_start: 0.9066 (t0) cc_final: 0.8704 (t0) REVERT: A 2643 ARG cc_start: 0.8300 (mmm160) cc_final: 0.7912 (tpt170) REVERT: A 2779 MET cc_start: 0.8461 (mtm) cc_final: 0.8057 (tpt) REVERT: A 2936 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8547 (mm) REVERT: A 3043 MET cc_start: 0.5615 (tpp) cc_final: 0.4648 (ptp) REVERT: A 3078 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7329 (mpp80) REVERT: A 3178 ASP cc_start: 0.8731 (t0) cc_final: 0.8350 (t0) REVERT: A 3510 SER cc_start: 0.9142 (m) cc_final: 0.8651 (p) REVERT: A 3526 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8188 (tm-30) REVERT: A 3833 LEU cc_start: 0.8516 (mm) cc_final: 0.8238 (mt) REVERT: A 4030 ILE cc_start: 0.8886 (tt) cc_final: 0.8612 (tt) REVERT: A 4346 MET cc_start: 0.8554 (mmp) cc_final: 0.8294 (mmm) outliers start: 46 outliers final: 35 residues processed: 308 average time/residue: 0.1655 time to fit residues: 82.7927 Evaluate side-chains 295 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 257 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1610 LYS Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1768 SER Chi-restraints excluded: chain A residue 1880 VAL Chi-restraints excluded: chain A residue 1961 ASN Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2510 MET Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2709 VAL Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2799 MET Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 2960 GLN Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3032 GLN Chi-restraints excluded: chain A residue 3047 HIS Chi-restraints excluded: chain A residue 3078 ARG Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3196 GLU Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3589 ILE Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3768 THR Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4033 THR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4377 MET Chi-restraints excluded: chain A residue 4425 GLN Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4645 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 147 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 233 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 209 optimal weight: 0.0000 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1566 GLN A1863 ASN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2445 HIS A3182 HIS A4023 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.152888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.113607 restraints weight = 44735.488| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 3.30 r_work: 0.3377 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25142 Z= 0.115 Angle : 0.539 13.484 34089 Z= 0.259 Chirality : 0.039 0.317 3821 Planarity : 0.003 0.051 4367 Dihedral : 5.348 74.055 3377 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.66 % Rotamer: Outliers : 1.85 % Allowed : 14.56 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.16), residues: 3035 helix: 2.10 (0.12), residues: 1778 sheet: -0.75 (0.35), residues: 237 loop : 0.58 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1962 TYR 0.023 0.001 TYR A1745 PHE 0.026 0.001 PHE A3513 TRP 0.016 0.001 TRP A2234 HIS 0.006 0.001 HIS A4119 Details of bonding type rmsd covalent geometry : bond 0.00261 (25142) covalent geometry : angle 0.53863 (34089) hydrogen bonds : bond 0.03386 ( 1440) hydrogen bonds : angle 4.00547 ( 4197) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 263 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1417 MET cc_start: 0.0253 (ppp) cc_final: -0.0338 (mtm) REVERT: A 1478 VAL cc_start: 0.6367 (p) cc_final: 0.5950 (m) REVERT: A 1485 ARG cc_start: 0.7680 (tpt170) cc_final: 0.7296 (tpp80) REVERT: A 1610 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7729 (mptt) REVERT: A 1829 LYS cc_start: 0.8876 (mmtt) cc_final: 0.8578 (mtmm) REVERT: A 1937 ASP cc_start: 0.8118 (t70) cc_final: 0.7520 (p0) REVERT: A 2018 MET cc_start: 0.8753 (mmm) cc_final: 0.8548 (mmm) REVERT: A 2170 TYR cc_start: 0.7589 (t80) cc_final: 0.7375 (t80) REVERT: A 2367 ASP cc_start: 0.9056 (t0) cc_final: 0.8691 (t0) REVERT: A 2643 ARG cc_start: 0.8249 (mmm160) cc_final: 0.7847 (tpt170) REVERT: A 2779 MET cc_start: 0.8482 (mtm) cc_final: 0.8060 (tpt) REVERT: A 2799 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8371 (mpp) REVERT: A 2855 LEU cc_start: 0.7622 (pp) cc_final: 0.7188 (mt) REVERT: A 2936 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8563 (mm) REVERT: A 3043 MET cc_start: 0.6373 (tpp) cc_final: 0.5140 (ptp) REVERT: A 3077 ASP cc_start: 0.8714 (t0) cc_final: 0.8362 (t0) REVERT: A 3153 THR cc_start: 0.8108 (t) cc_final: 0.7827 (p) REVERT: A 3178 ASP cc_start: 0.8840 (t0) cc_final: 0.8437 (t0) REVERT: A 3510 SER cc_start: 0.9140 (m) cc_final: 0.8658 (p) REVERT: A 3526 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8172 (tm-30) REVERT: A 3833 LEU cc_start: 0.8500 (mm) cc_final: 0.8212 (mt) REVERT: A 4030 ILE cc_start: 0.8892 (tt) cc_final: 0.8615 (tt) outliers start: 50 outliers final: 32 residues processed: 294 average time/residue: 0.1641 time to fit residues: 78.9576 Evaluate side-chains 288 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 253 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1610 LYS Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1768 SER Chi-restraints excluded: chain A residue 1880 VAL Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2510 MET Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2799 MET Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 2960 GLN Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3032 GLN Chi-restraints excluded: chain A residue 3047 HIS Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3196 GLU Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3768 THR Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4033 THR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4377 MET Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4645 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 6 optimal weight: 30.0000 chunk 289 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 225 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 302 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1566 GLN A1863 ASN A1961 ASN A2187 GLN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3838 ASN ** A3952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4023 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.149909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.108369 restraints weight = 44854.767| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.84 r_work: 0.3340 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25142 Z= 0.182 Angle : 0.590 12.699 34089 Z= 0.285 Chirality : 0.041 0.291 3821 Planarity : 0.004 0.052 4367 Dihedral : 5.519 79.368 3377 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.64 % Favored : 97.33 % Rotamer: Outliers : 1.81 % Allowed : 14.86 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.16), residues: 3035 helix: 1.98 (0.12), residues: 1780 sheet: -0.95 (0.35), residues: 226 loop : 0.51 (0.21), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1488 TYR 0.024 0.001 TYR A1745 PHE 0.021 0.002 PHE A3513 TRP 0.016 0.001 TRP A1701 HIS 0.004 0.001 HIS A4119 Details of bonding type rmsd covalent geometry : bond 0.00429 (25142) covalent geometry : angle 0.59033 (34089) hydrogen bonds : bond 0.03709 ( 1440) hydrogen bonds : angle 4.14170 ( 4197) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 255 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1417 MET cc_start: 0.0125 (ppp) cc_final: -0.0445 (mtm) REVERT: A 1610 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7712 (mptt) REVERT: A 1829 LYS cc_start: 0.8895 (mmtt) cc_final: 0.8670 (mtmt) REVERT: A 1937 ASP cc_start: 0.8150 (t70) cc_final: 0.7760 (p0) REVERT: A 2018 MET cc_start: 0.8823 (mmm) cc_final: 0.8543 (mmm) REVERT: A 2297 LYS cc_start: 0.8762 (mtpt) cc_final: 0.8471 (mttm) REVERT: A 2367 ASP cc_start: 0.9026 (t0) cc_final: 0.8693 (t0) REVERT: A 2643 ARG cc_start: 0.8364 (mmm160) cc_final: 0.7959 (tpt170) REVERT: A 2779 MET cc_start: 0.8580 (mtm) cc_final: 0.8114 (tpt) REVERT: A 2799 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8465 (mpp) REVERT: A 2855 LEU cc_start: 0.7738 (pp) cc_final: 0.7212 (mt) REVERT: A 2936 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8658 (mm) REVERT: A 3043 MET cc_start: 0.6382 (tpp) cc_final: 0.5240 (ptp) REVERT: A 3077 ASP cc_start: 0.8696 (t0) cc_final: 0.8344 (t0) REVERT: A 3178 ASP cc_start: 0.8838 (t0) cc_final: 0.8402 (t0) REVERT: A 3510 SER cc_start: 0.9144 (m) cc_final: 0.8685 (p) REVERT: A 3526 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8165 (tm-30) REVERT: A 4287 LYS cc_start: 0.7687 (mtpp) cc_final: 0.7399 (tmtt) outliers start: 49 outliers final: 35 residues processed: 287 average time/residue: 0.1711 time to fit residues: 79.4648 Evaluate side-chains 283 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 245 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1610 LYS Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1768 SER Chi-restraints excluded: chain A residue 2006 VAL Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2510 MET Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2709 VAL Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2799 MET Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 2960 GLN Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3032 GLN Chi-restraints excluded: chain A residue 3047 HIS Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3196 GLU Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3716 VAL Chi-restraints excluded: chain A residue 3768 THR Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4033 THR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4581 ILE Chi-restraints excluded: chain A residue 4645 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 122 optimal weight: 0.0370 chunk 146 optimal weight: 0.6980 chunk 242 optimal weight: 0.6980 chunk 201 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 154 optimal weight: 4.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1863 ASN ** A1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1961 ASN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4023 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.152578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.111521 restraints weight = 44562.709| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.85 r_work: 0.3390 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25142 Z= 0.108 Angle : 0.549 12.854 34089 Z= 0.263 Chirality : 0.039 0.306 3821 Planarity : 0.003 0.049 4367 Dihedral : 5.371 69.425 3377 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.08 % Favored : 97.89 % Rotamer: Outliers : 1.33 % Allowed : 15.30 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.16), residues: 3035 helix: 2.07 (0.12), residues: 1778 sheet: -0.74 (0.37), residues: 216 loop : 0.57 (0.21), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3682 TYR 0.020 0.001 TYR A2748 PHE 0.023 0.001 PHE A3513 TRP 0.018 0.001 TRP A2234 HIS 0.005 0.001 HIS A4119 Details of bonding type rmsd covalent geometry : bond 0.00241 (25142) covalent geometry : angle 0.54927 (34089) hydrogen bonds : bond 0.03386 ( 1440) hydrogen bonds : angle 4.01336 ( 4197) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 263 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1417 MET cc_start: 0.0294 (ppp) cc_final: -0.0313 (mtm) REVERT: A 1610 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7739 (mptt) REVERT: A 1814 GLU cc_start: 0.8138 (tp30) cc_final: 0.7700 (tp30) REVERT: A 1829 LYS cc_start: 0.8839 (mmtt) cc_final: 0.8558 (mtmm) REVERT: A 1937 ASP cc_start: 0.7940 (t70) cc_final: 0.7670 (p0) REVERT: A 2003 ASN cc_start: 0.8447 (m-40) cc_final: 0.8146 (p0) REVERT: A 2297 LYS cc_start: 0.8729 (mtpt) cc_final: 0.8426 (mttm) REVERT: A 2367 ASP cc_start: 0.9004 (t0) cc_final: 0.8659 (t0) REVERT: A 2643 ARG cc_start: 0.8217 (mmm160) cc_final: 0.7825 (tpt170) REVERT: A 2779 MET cc_start: 0.8553 (mtm) cc_final: 0.8123 (tpt) REVERT: A 2799 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8462 (mpp) REVERT: A 2936 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8591 (mm) REVERT: A 3043 MET cc_start: 0.6704 (tpp) cc_final: 0.5505 (ptp) REVERT: A 3077 ASP cc_start: 0.8669 (t0) cc_final: 0.8342 (t0) REVERT: A 3153 THR cc_start: 0.8005 (t) cc_final: 0.7738 (p) REVERT: A 3178 ASP cc_start: 0.8811 (t0) cc_final: 0.8407 (t0) REVERT: A 3510 SER cc_start: 0.9100 (m) cc_final: 0.8629 (p) REVERT: A 4287 LYS cc_start: 0.7565 (mtpp) cc_final: 0.7346 (tmtt) outliers start: 36 outliers final: 32 residues processed: 288 average time/residue: 0.1678 time to fit residues: 78.3680 Evaluate side-chains 285 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 250 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1486 LEU Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1610 LYS Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1768 SER Chi-restraints excluded: chain A residue 1961 ASN Chi-restraints excluded: chain A residue 2006 VAL Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2716 THR Chi-restraints excluded: chain A residue 2799 MET Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2839 GLU Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 2960 GLN Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3017 VAL Chi-restraints excluded: chain A residue 3032 GLN Chi-restraints excluded: chain A residue 3047 HIS Chi-restraints excluded: chain A residue 3090 VAL Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3194 LEU Chi-restraints excluded: chain A residue 3196 GLU Chi-restraints excluded: chain A residue 3201 LEU Chi-restraints excluded: chain A residue 3590 ILE Chi-restraints excluded: chain A residue 3716 VAL Chi-restraints excluded: chain A residue 3768 THR Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4033 THR Chi-restraints excluded: chain A residue 4046 VAL Chi-restraints excluded: chain A residue 4516 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 172 optimal weight: 0.9990 chunk 134 optimal weight: 0.0070 chunk 298 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 279 optimal weight: 10.0000 chunk 69 optimal weight: 0.0570 chunk 285 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 290 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1961 ASN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3838 ASN A4023 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.152864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.113422 restraints weight = 44628.018| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.25 r_work: 0.3381 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25142 Z= 0.109 Angle : 0.554 12.507 34089 Z= 0.266 Chirality : 0.039 0.294 3821 Planarity : 0.004 0.049 4367 Dihedral : 5.326 68.557 3377 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.41 % Favored : 97.56 % Rotamer: Outliers : 1.40 % Allowed : 15.56 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.16), residues: 3035 helix: 2.10 (0.12), residues: 1777 sheet: -0.77 (0.36), residues: 222 loop : 0.60 (0.21), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3682 TYR 0.024 0.001 TYR A4447 PHE 0.029 0.001 PHE A1960 TRP 0.016 0.001 TRP A2234 HIS 0.005 0.001 HIS A4119 Details of bonding type rmsd covalent geometry : bond 0.00243 (25142) covalent geometry : angle 0.55419 (34089) hydrogen bonds : bond 0.03353 ( 1440) hydrogen bonds : angle 3.98683 ( 4197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7131.68 seconds wall clock time: 122 minutes 37.33 seconds (7357.33 seconds total)