Starting phenix.real_space_refine on Fri May 23 09:48:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bms_44709/05_2025/9bms_44709.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bms_44709/05_2025/9bms_44709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bms_44709/05_2025/9bms_44709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bms_44709/05_2025/9bms_44709.map" model { file = "/net/cci-nas-00/data/ceres_data/9bms_44709/05_2025/9bms_44709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bms_44709/05_2025/9bms_44709.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 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 117 5.16 5 C 15068 2.51 5 N 4090 2.21 5 O 4421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23707 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 23593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2937, 23593 Classifications: {'peptide': 2937} Link IDs: {'PTRANS': 131, 'TRANS': 2805} 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: 12.80, per 1000 atoms: 0.54 Number of scatterers: 23707 At special positions: 0 Unit cell: (116.526, 189.741, 166.023, 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 117 16.00 P 9 15.00 Mg 2 11.99 O 4421 8.00 N 4090 7.00 C 15068 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: 5.79 Conformation dependent library (CDL) restraints added in 2.9 seconds 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5588 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 20 sheets defined 63.8% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'A' and resid 1457 through 1473 Processing helix chain 'A' and resid 1489 through 1510 removed outlier: 3.683A pdb=" N SER A1510 " --> pdb=" O ALA A1506 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1554 removed outlier: 4.024A pdb=" N PHE A1516 " --> pdb=" O TYR A1512 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLU A1518 " --> pdb=" O LYS A1514 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP A1519 " --> pdb=" O VAL A1515 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE A1538 " --> pdb=" O PHE A1534 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A1553 " --> pdb=" O GLY A1549 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER A1554 " --> pdb=" O ILE A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1561 removed outlier: 4.198A pdb=" N HIS A1559 " --> pdb=" O ALA A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1585 removed outlier: 3.558A pdb=" N THR A1565 " --> pdb=" O LEU A1561 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1593 Processing helix chain 'A' and resid 1596 through 1614 Processing helix chain 'A' and resid 1615 through 1626 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 1651 removed outlier: 3.877A pdb=" N GLN A1651 " --> pdb=" O ALA A1648 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1658 removed outlier: 3.852A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1728 removed outlier: 4.447A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE A1727 " --> pdb=" O GLU A1723 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1770 Processing helix chain 'A' and resid 1777 through 1797 Processing helix chain 'A' and resid 1801 through 1828 Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 1852 through 1855 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 Processing helix chain 'A' and resid 1937 through 1952 Processing helix chain 'A' and resid 1960 through 1963 Processing helix chain 'A' and resid 1964 through 1987 removed outlier: 3.956A pdb=" N GLN A1973 " --> pdb=" O SER A1969 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN A1974 " --> pdb=" O ALA A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2034 Processing helix chain 'A' and resid 2045 through 2057 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix 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 Processing helix chain 'A' and resid 2147 through 2149 No H-bonds generated for 'chain 'A' and resid 2147 through 2149' Processing helix chain 'A' and resid 2152 through 2165 removed outlier: 4.087A 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 removed outlier: 3.523A pdb=" N ILE A2216 " --> pdb=" O GLN A2212 " (cutoff:3.500A) Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2293 through 2297 removed outlier: 3.685A pdb=" N GLN A2296 " --> pdb=" O GLY A2293 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A2297 " --> pdb=" O GLU A2294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2293 through 2297' Processing helix chain 'A' and resid 2308 through 2313 Processing helix chain 'A' and resid 2314 through 2316 No H-bonds generated for 'chain 'A' and resid 2314 through 2316' Processing helix chain 'A' and resid 2352 through 2358 Processing helix chain 'A' and resid 2370 through 2385 Processing helix chain 'A' and resid 2411 through 2424 Processing helix chain 'A' and resid 2431 through 2441 Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.516A 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 2558 through 2562 Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.805A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2610 Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.272A 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 2740 through 2756 Processing helix chain 'A' and resid 2757 through 2764 Proline residue: A2760 - end of helix removed outlier: 4.675A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2784 removed outlier: 3.505A pdb=" N ALA A2771 " --> pdb=" O GLU A2767 " (cutoff:3.500A) Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.786A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 Processing helix chain 'A' and resid 2839 through 2858 removed outlier: 3.506A pdb=" N ARG A2843 " --> pdb=" O GLU A2839 " (cutoff:3.500A) Processing helix chain 'A' and resid 2862 through 2867 Processing helix chain 'A' and resid 2885 through 2904 Processing helix chain 'A' and resid 2912 through 2927 Processing helix chain 'A' and resid 2942 through 2955 Processing helix chain 'A' and resid 2968 through 2985 Processing helix chain 'A' and resid 2997 through 2999 No H-bonds generated for 'chain 'A' and resid 2997 through 2999' Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 3.908A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 Processing helix chain 'A' and resid 3046 through 3061 Processing helix chain 'A' and resid 3071 through 3082 removed outlier: 3.600A pdb=" N LEU A3075 " --> pdb=" O SER A3071 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A3076 " --> pdb=" O SER A3072 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A3080 " --> pdb=" O LYS A3076 " (cutoff:3.500A) 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 3164 Processing helix chain 'A' and resid 3172 through 3241 removed outlier: 3.633A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG A3220 " --> pdb=" O GLU A3216 " (cutoff:3.500A) Processing helix chain 'A' and resid 3450 through 3517 removed outlier: 5.245A pdb=" N ALA A3484 " --> pdb=" O LYS A3480 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLU A3485 " --> pdb=" O SER A3481 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS A3497 " --> pdb=" O SER A3493 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASN A3498 " --> pdb=" O GLU A3494 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLY A3505 " --> pdb=" O SER A3501 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 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 Processing helix chain 'A' and resid 3605 through 3608 Processing helix chain 'A' and resid 3618 through 3630 Processing helix chain 'A' and resid 3637 through 3641 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 3650 Processing helix chain 'A' and resid 3689 through 3696 Processing helix chain 'A' and resid 3704 through 3721 Processing helix chain 'A' and resid 3721 through 3756 Processing helix chain 'A' and resid 3763 through 3818 removed outlier: 3.565A pdb=" N ILE A3767 " --> pdb=" O ASP A3763 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN A3800 " --> pdb=" O THR A3796 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TYR A3801 " --> pdb=" O VAL A3797 " (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 3842 removed outlier: 3.563A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3847 removed outlier: 3.659A pdb=" N LYS A3847 " --> pdb=" O PRO A3844 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 Processing helix chain 'A' and resid 3876 through 3894 removed outlier: 3.549A pdb=" N HIS A3880 " --> pdb=" O LEU A3876 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE A3881 " --> pdb=" O HIS A3877 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR A3882 " --> pdb=" O GLN A3878 " (cutoff:3.500A) Processing helix chain 'A' and resid 3901 through 3911 Processing helix chain 'A' and resid 3912 through 3914 No H-bonds generated for 'chain 'A' and resid 3912 through 3914' Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3940 through 3945 removed outlier: 6.210A pdb=" N ALA A3943 " --> pdb=" O CYS A3940 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS A3945 " --> pdb=" O PRO A3942 " (cutoff:3.500A) Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 Processing helix chain 'A' and resid 3965 through 3970 removed outlier: 4.192A pdb=" N VAL A3970 " --> pdb=" O GLU A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4013 Processing helix chain 'A' and resid 4018 through 4023 removed outlier: 3.521A pdb=" N GLN A4023 " --> pdb=" O ILE A4020 " (cutoff:3.500A) Processing helix chain 'A' and resid 4026 through 4033 removed outlier: 3.630A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4063 Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 4.001A pdb=" N LYS A4089 " --> pdb=" O ASN A4085 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4101 No H-bonds generated for 'chain 'A' and resid 4099 through 4101' Processing helix chain 'A' and resid 4102 through 4115 removed outlier: 3.633A pdb=" N SER A4115 " --> pdb=" O LYS A4111 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4142 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.524A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4174 through 4194 removed outlier: 4.482A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) Processing helix chain 'A' and resid 4196 through 4201 removed outlier: 3.723A pdb=" N TRP A4201 " --> pdb=" O ALA A4197 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4227 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 4328 through 4346 Processing helix chain 'A' and resid 4375 through 4391 Processing helix chain 'A' and resid 4407 through 4439 removed outlier: 4.023A pdb=" N ARG A4415 " --> pdb=" O ARG A4411 " (cutoff:3.500A) Processing helix chain 'A' and resid 4445 through 4457 removed outlier: 3.502A pdb=" N LYS A4457 " --> pdb=" O ASN A4453 " (cutoff:3.500A) Processing helix chain 'A' and resid 4474 through 4498 Processing helix chain 'A' and resid 4500 through 4507 removed outlier: 3.513A pdb=" N LEU A4504 " --> pdb=" O GLY A4500 " (cutoff:3.500A) Processing helix chain 'A' and resid 4516 through 4533 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: 3.948A pdb=" N ASP A1476 " --> pdb=" O ARG A1488 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1663 through 1666 removed outlier: 3.500A pdb=" N GLY A1675 " --> pdb=" O ILE A1665 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.471A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.602A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.355A pdb=" N PHE A1686 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1842 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 removed outlier: 6.605A pdb=" N GLY A1901 " --> pdb=" O ARG A2037 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU A2039 " --> pdb=" O GLY A1901 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N SER A1903 " --> pdb=" O LEU A2039 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1931 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 2253 removed outlier: 6.513A pdb=" N VAL A2250 " --> pdb=" O TRP A2300 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL A2302 " --> pdb=" O VAL A2250 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N HIS A2252 " --> pdb=" O VAL A2302 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY A2219 " --> pdb=" O GLY A2360 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL A2362 " --> pdb=" O GLY A2219 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N MET A2221 " --> pdb=" O VAL A2362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2266 through 2268 Processing sheet with id=AA9, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AB1, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2620 removed outlier: 6.261A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N CYS A2712 " --> pdb=" O LEU A2591 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU A2593 " --> pdb=" O CYS A2712 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2644 removed outlier: 6.840A pdb=" N VAL A2648 " --> pdb=" O LYS A2702 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2873 through 2874 Processing sheet with id=AB5, first strand: chain 'A' and resid 2957 through 2959 removed outlier: 6.236A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU A2935 " --> pdb=" O MET A3068 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N HIS A2932 " --> pdb=" O VAL A3090 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ASN A3092 " --> pdb=" O HIS A2932 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU A2934 " --> pdb=" O ASN A3092 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE A3094 " --> pdb=" O LEU A2934 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ILE A2936 " --> pdb=" O PHE A3094 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.744A pdb=" N LEU A3633 " --> pdb=" O PHE A3678 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N SER A3680 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL A3635 " --> pdb=" O SER A3680 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3654 through 3656 Processing sheet with id=AB8, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.134A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL A4041 " --> pdb=" O LEU A4126 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N MET A4128 " --> pdb=" O VAL A4041 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N MET A4043 " --> pdb=" O MET A4128 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU A4042 " --> pdb=" O PHE A4145 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N PHE A4147 " --> pdb=" O LEU A4042 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS A4044 " --> pdb=" O PHE A4147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4283 through 4285 removed outlier: 6.670A pdb=" N ILE A4294 " --> pdb=" O LEU A4284 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.374A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4568 through 4571 1430 hydrogen bonds defined for protein. 4167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.20 Time building geometry restraints manager: 6.76 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: 5711 1.33 - 1.45: 4645 1.45 - 1.57: 13647 1.57 - 1.69: 14 1.69 - 1.81: 196 Bond restraints: 24213 Sorted by residual: bond pdb=" C4 ADP A4703 " pdb=" C5 ADP A4703 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C4 ADP A4701 " pdb=" C5 ADP A4701 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C4 ADP A4704 " pdb=" C5 ADP A4704 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" CA SER A1915 " pdb=" CB SER A1915 " ideal model delta sigma weight residual 1.528 1.457 0.071 1.56e-02 4.11e+03 2.09e+01 bond pdb=" C5 ADP A4703 " pdb=" C6 ADP A4703 " ideal model delta sigma weight residual 1.490 1.403 0.087 2.00e-02 2.50e+03 1.89e+01 ... (remaining 24208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 32548 2.77 - 5.53: 247 5.53 - 8.30: 29 8.30 - 11.07: 10 11.07 - 13.84: 4 Bond angle restraints: 32838 Sorted by residual: angle pdb=" PB ATP A4702 " pdb=" O3B ATP A4702 " pdb=" PG ATP A4702 " ideal model delta sigma weight residual 139.87 126.03 13.84 1.00e+00 1.00e+00 1.91e+02 angle pdb=" N ASN A2322 " pdb=" CA ASN A2322 " pdb=" C ASN A2322 " ideal model delta sigma weight residual 112.23 103.72 8.51 1.26e+00 6.30e-01 4.56e+01 angle pdb=" N THR A1885 " pdb=" CA THR A1885 " pdb=" C THR A1885 " ideal model delta sigma weight residual 113.23 104.99 8.24 1.24e+00 6.50e-01 4.42e+01 angle pdb=" N PRO A1883 " pdb=" CA PRO A1883 " pdb=" CB PRO A1883 " ideal model delta sigma weight residual 103.39 97.65 5.74 1.08e+00 8.57e-01 2.83e+01 angle pdb=" N LEU A2093 " pdb=" CA LEU A2093 " pdb=" C LEU A2093 " ideal model delta sigma weight residual 111.69 105.23 6.46 1.23e+00 6.61e-01 2.76e+01 ... (remaining 32833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.28: 14005 27.28 - 54.55: 577 54.55 - 81.83: 101 81.83 - 109.10: 7 109.10 - 136.38: 3 Dihedral angle restraints: 14693 sinusoidal: 6090 harmonic: 8603 Sorted by residual: dihedral pdb=" O1B ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PB ADP A4701 " pdb=" PA ADP A4701 " ideal model delta sinusoidal sigma weight residual 300.00 163.62 136.38 1 2.00e+01 2.50e-03 4.14e+01 dihedral pdb=" C5' ADP A4701 " pdb=" O5' ADP A4701 " pdb=" PA ADP A4701 " pdb=" O2A ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 61.13 -121.12 1 2.00e+01 2.50e-03 3.64e+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 -173.73 113.73 1 2.00e+01 2.50e-03 3.37e+01 ... (remaining 14690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3141 0.053 - 0.107: 466 0.107 - 0.160: 78 0.160 - 0.214: 6 0.214 - 0.267: 1 Chirality restraints: 3692 Sorted by residual: chirality pdb=" CA VAL A1880 " pdb=" N VAL A1880 " pdb=" C VAL A1880 " pdb=" CB VAL A1880 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA LEU A1879 " pdb=" N LEU A1879 " pdb=" C LEU A1879 " pdb=" CB LEU A1879 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" C3' ADP A4701 " pdb=" C2' ADP A4701 " pdb=" C4' ADP A4701 " pdb=" O3' ADP A4701 " both_signs ideal model delta sigma weight residual False -2.51 -2.70 0.19 2.00e-01 2.50e+01 9.06e-01 ... (remaining 3689 not shown) Planarity restraints: 4206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A2358 " -0.321 9.50e-02 1.11e+02 1.44e-01 1.28e+01 pdb=" NE ARG A2358 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A2358 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A2358 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A2358 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A2091 " 0.297 9.50e-02 1.11e+02 1.33e-01 1.09e+01 pdb=" NE ARG A2091 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A2091 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A2091 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A2091 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A2318 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.61e+00 pdb=" C VAL A2318 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL A2318 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A2319 " 0.017 2.00e-02 2.50e+03 ... (remaining 4203 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 4 2.04 - 2.76: 3599 2.76 - 3.47: 33785 3.47 - 4.19: 58088 4.19 - 4.90: 106795 Nonbonded interactions: 202271 Sorted by model distance: nonbonded pdb=" OG SER A2231 " pdb="MG MG A4706 " model vdw 1.330 2.170 nonbonded pdb=" OG1 THR A1913 " pdb="MG MG A4705 " model vdw 1.422 2.170 nonbonded pdb=" O3B ADP A4701 " pdb="MG MG A4705 " model vdw 1.762 2.170 nonbonded pdb=" OE2 GLU A2344 " pdb="MG MG A4706 " model vdw 1.918 2.170 nonbonded pdb=" O2B ATP A4702 " pdb="MG MG A4706 " model vdw 2.087 2.170 ... (remaining 202266 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 55.790 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 24213 Z= 0.198 Angle : 0.603 13.836 32838 Z= 0.329 Chirality : 0.040 0.267 3692 Planarity : 0.005 0.144 4206 Dihedral : 15.122 136.380 9105 Min Nonbonded Distance : 1.330 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.12 % Allowed : 0.27 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.16), residues: 2929 helix: 2.00 (0.13), residues: 1709 sheet: -0.33 (0.33), residues: 247 loop : 0.53 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1701 HIS 0.008 0.001 HIS A3188 PHE 0.013 0.001 PHE A3109 TYR 0.019 0.001 TYR A1546 ARG 0.016 0.000 ARG A4633 Details of bonding type rmsd hydrogen bonds : bond 0.12034 ( 1430) hydrogen bonds : angle 5.44614 ( 4167) covalent geometry : bond 0.00371 (24213) covalent geometry : angle 0.60280 (32838) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 581 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2901 TYR cc_start: 0.8182 (m-10) cc_final: 0.7697 (m-10) REVERT: A 3627 LEU cc_start: 0.8398 (mt) cc_final: 0.8122 (mt) REVERT: A 4325 ASN cc_start: 0.8166 (m-40) cc_final: 0.7879 (m-40) outliers start: 3 outliers final: 0 residues processed: 583 average time/residue: 0.4349 time to fit residues: 375.3532 Evaluate side-chains 278 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 2.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 247 optimal weight: 0.7980 chunk 222 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 chunk 229 optimal weight: 8.9990 chunk 88 optimal weight: 0.0470 chunk 139 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 266 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1643 ASN A1646 ASN A1784 ASN A1939 GLN A1985 HIS A2187 GLN A2713 ASN A2752 ASN A3038 GLN A3104 GLN ** A3233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3523 GLN A3602 ASN A3650 ASN A3754 ASN ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4079 GLN A4249 GLN A4381 HIS A4566 GLN A4573 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.146150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.114014 restraints weight = 35224.522| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.45 r_work: 0.3259 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24213 Z= 0.128 Angle : 0.531 7.869 32838 Z= 0.266 Chirality : 0.040 0.192 3692 Planarity : 0.004 0.047 4206 Dihedral : 6.789 134.943 3261 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.15 % Allowed : 7.64 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.16), residues: 2929 helix: 2.27 (0.13), residues: 1721 sheet: -0.48 (0.33), residues: 237 loop : 0.59 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1701 HIS 0.010 0.001 HIS A1653 PHE 0.018 0.001 PHE A1629 TYR 0.022 0.001 TYR A1546 ARG 0.007 0.000 ARG A4591 Details of bonding type rmsd hydrogen bonds : bond 0.04277 ( 1430) hydrogen bonds : angle 4.19772 ( 4167) covalent geometry : bond 0.00278 (24213) covalent geometry : angle 0.53100 (32838) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 305 time to evaluate : 2.660 Fit side-chains revert: symmetry clash REVERT: A 1646 ASN cc_start: 0.8048 (t0) cc_final: 0.7728 (t0) REVERT: A 1649 LYS cc_start: 0.7904 (mttt) cc_final: 0.6832 (tptp) REVERT: A 1997 ILE cc_start: 0.7212 (mm) cc_final: 0.6818 (tp) REVERT: A 2012 MET cc_start: 0.8466 (ppp) cc_final: 0.8144 (ppp) REVERT: A 2181 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7795 (mm-30) REVERT: A 2331 GLU cc_start: 0.8252 (tt0) cc_final: 0.8040 (tt0) REVERT: A 2542 SER cc_start: 0.8378 (p) cc_final: 0.8012 (p) REVERT: A 2839 GLU cc_start: 0.8154 (mp0) cc_final: 0.7865 (mp0) REVERT: A 2901 TYR cc_start: 0.8284 (m-10) cc_final: 0.7623 (m-10) REVERT: A 3024 ASP cc_start: 0.7818 (p0) cc_final: 0.7180 (t0) REVERT: A 3506 ASP cc_start: 0.7896 (m-30) cc_final: 0.7675 (m-30) REVERT: A 3729 SER cc_start: 0.8635 (m) cc_final: 0.8423 (t) REVERT: A 3783 LYS cc_start: 0.8371 (mppt) cc_final: 0.8116 (mtmm) REVERT: A 3956 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8175 (mt0) REVERT: A 4082 LYS cc_start: 0.8296 (mmmt) cc_final: 0.8081 (mtmm) REVERT: A 4213 ARG cc_start: 0.7835 (mtt90) cc_final: 0.7625 (mtm110) REVERT: A 4287 LYS cc_start: 0.8162 (ptmt) cc_final: 0.7645 (mptt) REVERT: A 4325 ASN cc_start: 0.9070 (m-40) cc_final: 0.8816 (m-40) outliers start: 30 outliers final: 14 residues processed: 324 average time/residue: 0.4047 time to fit residues: 203.2137 Evaluate side-chains 269 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 255 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1855 GLN Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2591 LEU Chi-restraints excluded: chain A residue 2780 SER Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3199 MET Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3631 ASN Chi-restraints excluded: chain A residue 3734 LEU Chi-restraints excluded: chain A residue 3912 ASN Chi-restraints excluded: chain A residue 4081 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 106 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 257 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 237 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1784 ASN A1810 HIS A1876 GLN ** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2187 GLN A2439 HIS A3540 ASN ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4062 GLN ** A4100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4381 HIS A4573 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.136048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.102923 restraints weight = 35183.574| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.41 r_work: 0.3103 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 24213 Z= 0.202 Angle : 0.573 12.392 32838 Z= 0.287 Chirality : 0.042 0.156 3692 Planarity : 0.004 0.048 4206 Dihedral : 6.494 125.773 3261 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.69 % Allowed : 9.64 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.16), residues: 2929 helix: 2.13 (0.12), residues: 1727 sheet: -0.59 (0.33), residues: 226 loop : 0.48 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A2234 HIS 0.017 0.001 HIS A1985 PHE 0.021 0.002 PHE A3996 TYR 0.023 0.002 TYR A3812 ARG 0.007 0.001 ARG A2763 Details of bonding type rmsd hydrogen bonds : bond 0.04493 ( 1430) hydrogen bonds : angle 4.09316 ( 4167) covalent geometry : bond 0.00479 (24213) covalent geometry : angle 0.57292 (32838) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 289 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1589 MET cc_start: 0.6585 (ttp) cc_final: 0.6230 (tmm) REVERT: A 1649 LYS cc_start: 0.8250 (mttt) cc_final: 0.6683 (tptp) REVERT: A 1805 ARG cc_start: 0.8435 (ttp-110) cc_final: 0.7639 (ttm110) REVERT: A 2117 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: A 2202 MET cc_start: 0.8580 (mtp) cc_final: 0.8357 (mtp) REVERT: A 2331 GLU cc_start: 0.8440 (tt0) cc_final: 0.8224 (tt0) REVERT: A 2542 SER cc_start: 0.8875 (p) cc_final: 0.8640 (p) REVERT: A 2544 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7965 (pm20) REVERT: A 2632 LEU cc_start: 0.8706 (mt) cc_final: 0.8408 (mt) REVERT: A 3016 GLU cc_start: 0.8708 (pp20) cc_final: 0.8202 (pp20) REVERT: A 3503 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8196 (tt) REVERT: A 3506 ASP cc_start: 0.8082 (m-30) cc_final: 0.7784 (m-30) REVERT: A 3540 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8285 (m110) REVERT: A 3761 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7224 (mt) REVERT: A 3816 GLU cc_start: 0.8245 (tp30) cc_final: 0.7997 (tp30) REVERT: A 3944 PHE cc_start: 0.7565 (m-10) cc_final: 0.7066 (m-10) REVERT: A 3956 GLN cc_start: 0.8331 (mm-40) cc_final: 0.8019 (pt0) REVERT: A 4020 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8695 (mt) REVERT: A 4213 ARG cc_start: 0.8134 (mtt90) cc_final: 0.7896 (mtm110) REVERT: A 4287 LYS cc_start: 0.8247 (ptmt) cc_final: 0.7754 (mptt) REVERT: A 4325 ASN cc_start: 0.9210 (m-40) cc_final: 0.8857 (m-40) REVERT: A 4453 ASN cc_start: 0.8395 (t0) cc_final: 0.7962 (t0) REVERT: A 4509 VAL cc_start: 0.8607 (t) cc_final: 0.8329 (p) REVERT: A 4542 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7414 (pt0) outliers start: 44 outliers final: 16 residues processed: 312 average time/residue: 0.3726 time to fit residues: 183.0287 Evaluate side-chains 265 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 242 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1693 THR Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1740 THR Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2544 GLU Chi-restraints excluded: chain A residue 2780 SER Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3540 ASN Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3631 ASN Chi-restraints excluded: chain A residue 3734 LEU Chi-restraints excluded: chain A residue 3761 LEU Chi-restraints excluded: chain A residue 3912 ASN Chi-restraints excluded: chain A residue 4020 ILE Chi-restraints excluded: chain A residue 4199 LEU Chi-restraints excluded: chain A residue 4542 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 259 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 282 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 140 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN A1985 HIS A2187 GLN ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4100 HIS A4381 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.103788 restraints weight = 35061.799| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.31 r_work: 0.3135 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24213 Z= 0.121 Angle : 0.490 8.210 32838 Z= 0.245 Chirality : 0.039 0.148 3692 Planarity : 0.004 0.047 4206 Dihedral : 6.285 127.977 3261 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.57 % Allowed : 10.94 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.16), residues: 2929 helix: 2.37 (0.12), residues: 1722 sheet: -0.60 (0.33), residues: 231 loop : 0.49 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2234 HIS 0.009 0.001 HIS A1985 PHE 0.013 0.001 PHE A4260 TYR 0.023 0.001 TYR A1546 ARG 0.005 0.000 ARG A2060 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 1430) hydrogen bonds : angle 3.92475 ( 4167) covalent geometry : bond 0.00269 (24213) covalent geometry : angle 0.49046 (32838) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 268 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1589 MET cc_start: 0.6634 (ttp) cc_final: 0.6228 (tmm) REVERT: A 1649 LYS cc_start: 0.8127 (mttt) cc_final: 0.7758 (mttp) REVERT: A 1805 ARG cc_start: 0.8395 (ttp-110) cc_final: 0.7723 (ttm110) REVERT: A 2117 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6974 (mp0) REVERT: A 2202 MET cc_start: 0.8588 (mtp) cc_final: 0.8342 (mtp) REVERT: A 2331 GLU cc_start: 0.8343 (tt0) cc_final: 0.8119 (tt0) REVERT: A 2632 LEU cc_start: 0.8621 (mt) cc_final: 0.8374 (mt) REVERT: A 2762 LEU cc_start: 0.8823 (mt) cc_final: 0.8617 (mp) REVERT: A 2786 GLN cc_start: 0.8940 (mt0) cc_final: 0.8680 (mm-40) REVERT: A 2901 TYR cc_start: 0.8469 (m-10) cc_final: 0.7598 (m-10) REVERT: A 3016 GLU cc_start: 0.8690 (pp20) cc_final: 0.8233 (pp20) REVERT: A 3503 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8268 (tt) REVERT: A 3506 ASP cc_start: 0.8061 (m-30) cc_final: 0.7823 (m-30) REVERT: A 4063 ASN cc_start: 0.8320 (t0) cc_final: 0.8108 (t0) REVERT: A 4287 LYS cc_start: 0.8147 (ptmt) cc_final: 0.7820 (mptt) REVERT: A 4419 MET cc_start: 0.8442 (mtm) cc_final: 0.8120 (mtm) REVERT: A 4453 ASN cc_start: 0.8433 (t0) cc_final: 0.8033 (t0) REVERT: A 4462 ARG cc_start: 0.8829 (mmm-85) cc_final: 0.8538 (ttm170) outliers start: 41 outliers final: 19 residues processed: 295 average time/residue: 0.3743 time to fit residues: 174.0164 Evaluate side-chains 265 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 244 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1780 SER Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 3038 GLN Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3631 ASN Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3734 LEU Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 3912 ASN Chi-restraints excluded: chain A residue 3962 ASP Chi-restraints excluded: chain A residue 4137 ASN Chi-restraints excluded: chain A residue 4199 LEU Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 114 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 275 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN A1817 HIS A1985 HIS A2187 GLN ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4381 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.134342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.102277 restraints weight = 35325.778| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.32 r_work: 0.3112 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24213 Z= 0.152 Angle : 0.508 7.549 32838 Z= 0.252 Chirality : 0.040 0.175 3692 Planarity : 0.004 0.049 4206 Dihedral : 6.118 127.192 3261 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.31 % Allowed : 12.21 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.16), residues: 2929 helix: 2.40 (0.12), residues: 1722 sheet: -0.73 (0.31), residues: 246 loop : 0.51 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.016 0.001 HIS A1985 PHE 0.014 0.001 PHE A4260 TYR 0.024 0.001 TYR A1546 ARG 0.004 0.000 ARG A2060 Details of bonding type rmsd hydrogen bonds : bond 0.03963 ( 1430) hydrogen bonds : angle 3.90250 ( 4167) covalent geometry : bond 0.00356 (24213) covalent geometry : angle 0.50811 (32838) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 271 time to evaluate : 2.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1547 LEU cc_start: 0.8019 (mt) cc_final: 0.7628 (mt) REVERT: A 1589 MET cc_start: 0.6674 (ttp) cc_final: 0.6215 (tmm) REVERT: A 1805 ARG cc_start: 0.8419 (ttp-110) cc_final: 0.7750 (ttm110) REVERT: A 2041 MET cc_start: 0.8912 (mtp) cc_final: 0.8614 (mtp) REVERT: A 2074 LYS cc_start: 0.8330 (mmmm) cc_final: 0.7949 (mptt) REVERT: A 2202 MET cc_start: 0.8632 (mtp) cc_final: 0.8405 (mtp) REVERT: A 2694 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8511 (ttp-170) REVERT: A 2762 LEU cc_start: 0.8824 (mt) cc_final: 0.8606 (mp) REVERT: A 2777 TYR cc_start: 0.9138 (t80) cc_final: 0.8709 (t80) REVERT: A 2901 TYR cc_start: 0.8506 (m-10) cc_final: 0.7670 (m-10) REVERT: A 3503 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8289 (tt) REVERT: A 3506 ASP cc_start: 0.8080 (m-30) cc_final: 0.7835 (m-30) REVERT: A 3944 PHE cc_start: 0.7505 (m-10) cc_final: 0.7242 (m-10) REVERT: A 4063 ASN cc_start: 0.8329 (t0) cc_final: 0.8114 (t0) REVERT: A 4287 LYS cc_start: 0.8124 (ptmt) cc_final: 0.7828 (mptt) REVERT: A 4377 MET cc_start: 0.7319 (tpp) cc_final: 0.7097 (tpp) REVERT: A 4453 ASN cc_start: 0.8445 (t0) cc_final: 0.8060 (t0) REVERT: A 4462 ARG cc_start: 0.8923 (mmm-85) cc_final: 0.8621 (ttm170) REVERT: A 4542 GLU cc_start: 0.7518 (pt0) cc_final: 0.7236 (mp0) outliers start: 34 outliers final: 23 residues processed: 295 average time/residue: 0.3949 time to fit residues: 181.7497 Evaluate side-chains 263 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 238 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2080 LEU Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2321 ASP Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2449 LEU Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2694 ARG Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3631 ASN Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 3734 LEU Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 3962 ASP Chi-restraints excluded: chain A residue 4081 ASP Chi-restraints excluded: chain A residue 4199 LEU Chi-restraints excluded: chain A residue 4225 ASP Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 144 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 275 optimal weight: 8.9990 chunk 249 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 288 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN A1985 HIS ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.131857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.099848 restraints weight = 35117.206| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.40 r_work: 0.3071 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 24213 Z= 0.190 Angle : 0.532 8.544 32838 Z= 0.265 Chirality : 0.041 0.146 3692 Planarity : 0.004 0.049 4206 Dihedral : 6.073 127.727 3261 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.88 % Allowed : 12.28 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.16), residues: 2929 helix: 2.33 (0.12), residues: 1721 sheet: -0.88 (0.31), residues: 243 loop : 0.44 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.014 0.001 HIS A1985 PHE 0.020 0.002 PHE A3957 TYR 0.023 0.001 TYR A1546 ARG 0.007 0.000 ARG A2060 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 1430) hydrogen bonds : angle 3.94839 ( 4167) covalent geometry : bond 0.00450 (24213) covalent geometry : angle 0.53222 (32838) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 263 time to evaluate : 2.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1547 LEU cc_start: 0.7972 (mt) cc_final: 0.7546 (mt) REVERT: A 1589 MET cc_start: 0.6690 (ttp) cc_final: 0.6227 (tmm) REVERT: A 1649 LYS cc_start: 0.8313 (mtpt) cc_final: 0.7846 (mttp) REVERT: A 2074 LYS cc_start: 0.8345 (mmmm) cc_final: 0.8019 (mptt) REVERT: A 2113 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6655 (mmp80) REVERT: A 2632 LEU cc_start: 0.8646 (mt) cc_final: 0.8378 (mt) REVERT: A 2901 TYR cc_start: 0.8561 (m-10) cc_final: 0.7828 (m-10) REVERT: A 3503 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8299 (tt) REVERT: A 3506 ASP cc_start: 0.8124 (m-30) cc_final: 0.7871 (m-30) REVERT: A 3785 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: A 4287 LYS cc_start: 0.8173 (ptmt) cc_final: 0.7446 (mptt) REVERT: A 4462 ARG cc_start: 0.8924 (mmm-85) cc_final: 0.8615 (ttm170) REVERT: A 4492 ILE cc_start: 0.8334 (mt) cc_final: 0.8078 (mt) outliers start: 49 outliers final: 34 residues processed: 298 average time/residue: 0.3856 time to fit residues: 179.6590 Evaluate side-chains 268 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 231 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1780 SER Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2080 LEU Chi-restraints excluded: chain A residue 2113 ARG Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2176 THR Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2321 ASP Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2449 LEU Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 3038 GLN Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3631 ASN Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 3734 LEU Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 3912 ASN Chi-restraints excluded: chain A residue 4038 ASN Chi-restraints excluded: chain A residue 4081 ASP Chi-restraints excluded: chain A residue 4137 ASN Chi-restraints excluded: chain A residue 4199 LEU Chi-restraints excluded: chain A residue 4225 ASP Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4556 CYS Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 180 optimal weight: 10.0000 chunk 113 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 204 optimal weight: 0.6980 chunk 179 optimal weight: 10.0000 chunk 247 optimal weight: 0.8980 chunk 224 optimal weight: 3.9990 chunk 218 optimal weight: 0.7980 chunk 233 optimal weight: 0.5980 chunk 215 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1653 HIS A1755 GLN A1985 HIS A2827 HIS ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.133821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.101655 restraints weight = 35184.351| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.28 r_work: 0.3105 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24213 Z= 0.113 Angle : 0.484 7.314 32838 Z= 0.241 Chirality : 0.039 0.143 3692 Planarity : 0.003 0.046 4206 Dihedral : 5.944 128.245 3261 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.42 % Allowed : 13.05 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.16), residues: 2929 helix: 2.50 (0.12), residues: 1720 sheet: -0.85 (0.31), residues: 243 loop : 0.49 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2234 HIS 0.012 0.001 HIS A1985 PHE 0.013 0.001 PHE A3957 TYR 0.023 0.001 TYR A1546 ARG 0.006 0.000 ARG A2060 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 1430) hydrogen bonds : angle 3.83410 ( 4167) covalent geometry : bond 0.00250 (24213) covalent geometry : angle 0.48450 (32838) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 260 time to evaluate : 3.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1547 LEU cc_start: 0.8009 (mt) cc_final: 0.7569 (mt) REVERT: A 1589 MET cc_start: 0.6693 (ttp) cc_final: 0.6240 (tmm) REVERT: A 1649 LYS cc_start: 0.8275 (mtpt) cc_final: 0.6743 (tptp) REVERT: A 1861 MET cc_start: 0.8851 (ttt) cc_final: 0.8646 (ttt) REVERT: A 2074 LYS cc_start: 0.8334 (mmmm) cc_final: 0.7969 (mptt) REVERT: A 2077 ASP cc_start: 0.8292 (t0) cc_final: 0.8070 (t0) REVERT: A 2777 TYR cc_start: 0.9117 (t80) cc_final: 0.8738 (t80) REVERT: A 2901 TYR cc_start: 0.8481 (m-10) cc_final: 0.7698 (m-10) REVERT: A 3206 ARG cc_start: 0.8141 (mtm110) cc_final: 0.7807 (ttm-80) REVERT: A 3503 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8293 (tt) REVERT: A 3506 ASP cc_start: 0.8157 (m-30) cc_final: 0.7941 (m-30) REVERT: A 3540 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8498 (m-40) REVERT: A 3785 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: A 4213 ARG cc_start: 0.8282 (mtt90) cc_final: 0.8069 (mtm110) REVERT: A 4287 LYS cc_start: 0.8025 (ptmt) cc_final: 0.7713 (mptt) REVERT: A 4377 MET cc_start: 0.7587 (tpp) cc_final: 0.6952 (tpp) REVERT: A 4462 ARG cc_start: 0.8921 (mmm-85) cc_final: 0.8587 (ttm170) REVERT: A 4492 ILE cc_start: 0.8356 (mt) cc_final: 0.8113 (mt) outliers start: 37 outliers final: 27 residues processed: 287 average time/residue: 0.3889 time to fit residues: 175.9506 Evaluate side-chains 271 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1780 SER Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2321 ASP Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2449 LEU Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2780 SER Chi-restraints excluded: chain A residue 3038 GLN Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3540 ASN Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3631 ASN Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 3734 LEU Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 3912 ASN Chi-restraints excluded: chain A residue 3962 ASP Chi-restraints excluded: chain A residue 4081 ASP Chi-restraints excluded: chain A residue 4199 LEU Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4556 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 48 optimal weight: 0.0980 chunk 286 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 213 optimal weight: 1.9990 chunk 236 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 263 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN A1985 HIS ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.133764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.101442 restraints weight = 35125.381| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.24 r_work: 0.3105 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24213 Z= 0.122 Angle : 0.488 8.151 32838 Z= 0.242 Chirality : 0.039 0.146 3692 Planarity : 0.004 0.047 4206 Dihedral : 5.878 127.337 3261 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.34 % Allowed : 13.63 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.16), residues: 2929 helix: 2.53 (0.12), residues: 1720 sheet: -0.86 (0.31), residues: 243 loop : 0.51 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.011 0.001 HIS A1985 PHE 0.013 0.001 PHE A4260 TYR 0.023 0.001 TYR A1546 ARG 0.007 0.000 ARG A2060 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 1430) hydrogen bonds : angle 3.82370 ( 4167) covalent geometry : bond 0.00278 (24213) covalent geometry : angle 0.48809 (32838) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 250 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1589 MET cc_start: 0.6656 (ttp) cc_final: 0.6216 (tmm) REVERT: A 1649 LYS cc_start: 0.8273 (mtpt) cc_final: 0.7834 (mttp) REVERT: A 1861 MET cc_start: 0.8847 (ttt) cc_final: 0.8646 (ttt) REVERT: A 2074 LYS cc_start: 0.8279 (mmmm) cc_final: 0.7877 (mptt) REVERT: A 2077 ASP cc_start: 0.8288 (t0) cc_final: 0.8053 (t0) REVERT: A 2113 ARG cc_start: 0.6845 (mmp80) cc_final: 0.6629 (mpt180) REVERT: A 2777 TYR cc_start: 0.9124 (t80) cc_final: 0.8731 (t80) REVERT: A 2901 TYR cc_start: 0.8501 (m-10) cc_final: 0.7699 (m-10) REVERT: A 3030 MET cc_start: 0.7932 (mmm) cc_final: 0.7507 (mmm) REVERT: A 3503 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8281 (tt) REVERT: A 3506 ASP cc_start: 0.8163 (m-30) cc_final: 0.7930 (m-30) REVERT: A 3540 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8436 (m-40) REVERT: A 3785 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: A 4287 LYS cc_start: 0.8067 (ptmt) cc_final: 0.7719 (mptt) REVERT: A 4308 TRP cc_start: 0.9128 (t60) cc_final: 0.8918 (t60) REVERT: A 4377 MET cc_start: 0.7541 (tpp) cc_final: 0.7103 (tpp) REVERT: A 4462 ARG cc_start: 0.8891 (mmm-85) cc_final: 0.8563 (ttm170) REVERT: A 4492 ILE cc_start: 0.8359 (mt) cc_final: 0.8115 (mt) outliers start: 35 outliers final: 26 residues processed: 275 average time/residue: 0.3802 time to fit residues: 165.0900 Evaluate side-chains 269 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1780 SER Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2321 ASP Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2448 ASP Chi-restraints excluded: chain A residue 2449 LEU Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2780 SER Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 3038 GLN Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3540 ASN Chi-restraints excluded: chain A residue 3550 THR Chi-restraints excluded: chain A residue 3631 ASN Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 3734 LEU Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 3912 ASN Chi-restraints excluded: chain A residue 4038 ASN Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4556 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 4 optimal weight: 0.8980 chunk 208 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 287 optimal weight: 0.0270 chunk 71 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 254 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 174 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN A1985 HIS ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.134876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.103102 restraints weight = 34979.111| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.30 r_work: 0.3127 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 24213 Z= 0.109 Angle : 0.479 8.225 32838 Z= 0.237 Chirality : 0.039 0.200 3692 Planarity : 0.003 0.048 4206 Dihedral : 5.765 127.369 3261 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.19 % Allowed : 14.05 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.16), residues: 2929 helix: 2.59 (0.12), residues: 1727 sheet: -0.82 (0.31), residues: 241 loop : 0.52 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.012 0.001 HIS A1985 PHE 0.022 0.001 PHE A2088 TYR 0.024 0.001 TYR A1546 ARG 0.007 0.000 ARG A2060 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 1430) hydrogen bonds : angle 3.78299 ( 4167) covalent geometry : bond 0.00245 (24213) covalent geometry : angle 0.47886 (32838) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 257 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1589 MET cc_start: 0.6702 (ttp) cc_final: 0.6276 (tmm) REVERT: A 1649 LYS cc_start: 0.8302 (mtpt) cc_final: 0.7343 (tptp) REVERT: A 1820 ASP cc_start: 0.8451 (m-30) cc_final: 0.8236 (m-30) REVERT: A 1861 MET cc_start: 0.8808 (ttt) cc_final: 0.8592 (ttt) REVERT: A 2074 LYS cc_start: 0.8343 (mmmm) cc_final: 0.7911 (mptt) REVERT: A 2077 ASP cc_start: 0.8322 (t0) cc_final: 0.8108 (t0) REVERT: A 2113 ARG cc_start: 0.6906 (mmp80) cc_final: 0.6673 (mpt180) REVERT: A 2777 TYR cc_start: 0.9072 (t80) cc_final: 0.8696 (t80) REVERT: A 2901 TYR cc_start: 0.8451 (m-10) cc_final: 0.7645 (m-10) REVERT: A 3500 MET cc_start: 0.8673 (mmm) cc_final: 0.8435 (tpt) REVERT: A 3503 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8288 (tt) REVERT: A 3506 ASP cc_start: 0.8146 (m-30) cc_final: 0.7925 (m-30) REVERT: A 3595 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7893 (mp10) REVERT: A 3785 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: A 3791 MET cc_start: 0.7432 (tpt) cc_final: 0.7086 (mmm) REVERT: A 4213 ARG cc_start: 0.8276 (mtt90) cc_final: 0.8034 (mtm110) REVERT: A 4287 LYS cc_start: 0.8016 (ptmt) cc_final: 0.7788 (mmtm) REVERT: A 4308 TRP cc_start: 0.9130 (t60) cc_final: 0.8924 (t60) REVERT: A 4377 MET cc_start: 0.7572 (tpp) cc_final: 0.7129 (tpp) REVERT: A 4462 ARG cc_start: 0.8873 (mmm-85) cc_final: 0.8558 (ttm110) REVERT: A 4492 ILE cc_start: 0.8322 (mt) cc_final: 0.8086 (mt) outliers start: 31 outliers final: 22 residues processed: 278 average time/residue: 0.3679 time to fit residues: 161.6140 Evaluate side-chains 265 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 240 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1780 SER Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2321 ASP Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2449 LEU Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2780 SER Chi-restraints excluded: chain A residue 3038 GLN Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3595 GLN Chi-restraints excluded: chain A residue 3631 ASN Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 3734 LEU Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4556 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 163 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 251 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 266 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN A1985 HIS ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.133592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.101455 restraints weight = 35185.445| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.30 r_work: 0.3100 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24213 Z= 0.136 Angle : 0.500 8.106 32838 Z= 0.247 Chirality : 0.039 0.155 3692 Planarity : 0.004 0.049 4206 Dihedral : 5.746 126.373 3261 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.19 % Allowed : 14.32 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.16), residues: 2929 helix: 2.56 (0.12), residues: 1727 sheet: -0.81 (0.31), residues: 243 loop : 0.51 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.011 0.001 HIS A1985 PHE 0.015 0.001 PHE A2088 TYR 0.024 0.001 TYR A1546 ARG 0.008 0.000 ARG A2060 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 1430) hydrogen bonds : angle 3.80114 ( 4167) covalent geometry : bond 0.00319 (24213) covalent geometry : angle 0.49970 (32838) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 238 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1589 MET cc_start: 0.6666 (ttp) cc_final: 0.6234 (tmm) REVERT: A 1649 LYS cc_start: 0.8312 (mtpt) cc_final: 0.7342 (tptp) REVERT: A 1861 MET cc_start: 0.8842 (ttt) cc_final: 0.8624 (ttt) REVERT: A 2074 LYS cc_start: 0.8244 (mmmm) cc_final: 0.7831 (mptt) REVERT: A 2077 ASP cc_start: 0.8239 (t0) cc_final: 0.7991 (t0) REVERT: A 2113 ARG cc_start: 0.6912 (mmp80) cc_final: 0.6678 (mpt180) REVERT: A 2777 TYR cc_start: 0.9106 (t80) cc_final: 0.8681 (t80) REVERT: A 2901 TYR cc_start: 0.8515 (m-10) cc_final: 0.7768 (m-10) REVERT: A 3030 MET cc_start: 0.8086 (mmt) cc_final: 0.7651 (mmm) REVERT: A 3503 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8283 (tt) REVERT: A 3506 ASP cc_start: 0.8167 (m-30) cc_final: 0.7918 (m-30) REVERT: A 3595 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7926 (mp10) REVERT: A 3785 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: A 3791 MET cc_start: 0.7384 (tpt) cc_final: 0.7072 (mmm) REVERT: A 4287 LYS cc_start: 0.7978 (ptmt) cc_final: 0.7744 (mmtm) REVERT: A 4308 TRP cc_start: 0.9143 (t60) cc_final: 0.8933 (t60) REVERT: A 4377 MET cc_start: 0.7534 (tpp) cc_final: 0.7052 (tpp) REVERT: A 4462 ARG cc_start: 0.8911 (mmm-85) cc_final: 0.8587 (ttm110) REVERT: A 4492 ILE cc_start: 0.8345 (mt) cc_final: 0.8105 (mt) outliers start: 31 outliers final: 25 residues processed: 260 average time/residue: 0.3880 time to fit residues: 160.2156 Evaluate side-chains 263 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 235 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1579 MET Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1780 SER Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2321 ASP Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2446 ILE Chi-restraints excluded: chain A residue 2449 LEU Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2780 SER Chi-restraints excluded: chain A residue 3038 GLN Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3595 GLN Chi-restraints excluded: chain A residue 3631 ASN Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3726 GLU Chi-restraints excluded: chain A residue 3734 LEU Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 3799 GLN Chi-restraints excluded: chain A residue 4038 ASN Chi-restraints excluded: chain A residue 4137 ASN Chi-restraints excluded: chain A residue 4274 THR Chi-restraints excluded: chain A residue 4556 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 84 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 214 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 114 optimal weight: 0.4980 chunk 235 optimal weight: 0.9980 chunk 278 optimal weight: 4.9990 chunk 242 optimal weight: 0.5980 chunk 130 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN ** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.134847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.103109 restraints weight = 34958.371| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.44 r_work: 0.3121 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24213 Z= 0.110 Angle : 0.484 9.120 32838 Z= 0.239 Chirality : 0.039 0.145 3692 Planarity : 0.003 0.048 4206 Dihedral : 5.677 125.975 3261 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.07 % Allowed : 14.40 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.16), residues: 2929 helix: 2.62 (0.12), residues: 1727 sheet: -0.74 (0.30), residues: 252 loop : 0.53 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.003 0.000 HIS A1985 PHE 0.016 0.001 PHE A2088 TYR 0.024 0.001 TYR A1546 ARG 0.007 0.000 ARG A2060 Details of bonding type rmsd hydrogen bonds : bond 0.03467 ( 1430) hydrogen bonds : angle 3.75938 ( 4167) covalent geometry : bond 0.00249 (24213) covalent geometry : angle 0.48373 (32838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14533.04 seconds wall clock time: 251 minutes 11.46 seconds (15071.46 seconds total)