Starting phenix.real_space_refine on Mon Aug 25 00:27:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bms_44709/08_2025/9bms_44709.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bms_44709/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bms_44709/08_2025/9bms_44709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bms_44709/08_2025/9bms_44709.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bms_44709/08_2025/9bms_44709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bms_44709/08_2025/9bms_44709.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.28, per 1000 atoms: 0.22 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: 2.17 Conformation dependent library (CDL) restraints added in 931.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.55 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: 7.27 Time building geometry restraints manager: 2.85 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: 2.410 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.860 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.390 ------------------------------------------------------------------------------- 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 : 7.02 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (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 ARG 0.016 0.000 ARG A4633 TYR 0.019 0.001 TYR A1546 PHE 0.013 0.001 PHE A3109 TRP 0.020 0.001 TRP A1701 HIS 0.008 0.001 HIS A3188 Details of bonding type rmsd covalent geometry : bond 0.00371 (24213) covalent geometry : angle 0.60280 (32838) hydrogen bonds : bond 0.12034 ( 1430) hydrogen bonds : angle 5.44614 ( 4167) *********************** 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 : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2901 TYR cc_start: 0.8182 (m-10) cc_final: 0.7700 (m-10) REVERT: A 3627 LEU cc_start: 0.8398 (mt) cc_final: 0.8120 (mt) REVERT: A 4325 ASN cc_start: 0.8166 (m-40) cc_final: 0.7880 (m-40) outliers start: 3 outliers final: 0 residues processed: 583 average time/residue: 0.2156 time to fit residues: 184.7781 Evaluate side-chains 279 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 A1810 HIS 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 ** A4062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4079 GLN A4100 HIS A4249 GLN A4381 HIS A4566 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.138980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.106291 restraints weight = 35282.244| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.32 r_work: 0.3152 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 24213 Z= 0.210 Angle : 0.586 9.030 32838 Z= 0.295 Chirality : 0.043 0.185 3692 Planarity : 0.005 0.048 4206 Dihedral : 6.712 133.476 3261 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.31 % Allowed : 8.21 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.16), residues: 2929 helix: 2.06 (0.12), residues: 1727 sheet: -0.56 (0.33), residues: 237 loop : 0.51 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A4591 TYR 0.023 0.002 TYR A2748 PHE 0.018 0.002 PHE A3996 TRP 0.020 0.002 TRP A1701 HIS 0.005 0.001 HIS A1985 Details of bonding type rmsd covalent geometry : bond 0.00488 (24213) covalent geometry : angle 0.58576 (32838) hydrogen bonds : bond 0.04654 ( 1430) hydrogen bonds : angle 4.23901 ( 4167) *********************** 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 312 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 278 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1646 ASN cc_start: 0.8150 (t0) cc_final: 0.7836 (t0) REVERT: A 2012 MET cc_start: 0.8694 (ppp) cc_final: 0.8363 (ppp) REVERT: A 2117 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: A 2542 SER cc_start: 0.8667 (p) cc_final: 0.8317 (p) REVERT: A 2901 TYR cc_start: 0.8466 (m-10) cc_final: 0.7743 (m-10) REVERT: A 3024 ASP cc_start: 0.7788 (p0) cc_final: 0.7195 (t0) REVERT: A 3503 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8206 (tt) REVERT: A 3791 MET cc_start: 0.6651 (tpp) cc_final: 0.6395 (mmm) REVERT: A 3956 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8156 (mt0) REVERT: A 4213 ARG cc_start: 0.8039 (mtt90) cc_final: 0.7815 (mtm110) REVERT: A 4287 LYS cc_start: 0.8176 (ptmt) cc_final: 0.7696 (mptt) REVERT: A 4325 ASN cc_start: 0.9182 (m-40) cc_final: 0.8722 (m-40) REVERT: A 4331 LEU cc_start: 0.8262 (tp) cc_final: 0.8045 (mt) outliers start: 34 outliers final: 20 residues processed: 301 average time/residue: 0.1858 time to fit residues: 86.8160 Evaluate side-chains 259 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 2117 GLU Chi-restraints excluded: chain A residue 2176 THR 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 2968 THR 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 3550 THR 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 3983 ILE Chi-restraints excluded: chain A residue 4199 LEU Chi-restraints excluded: chain A residue 4494 LEU Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 44 optimal weight: 0.2980 chunk 154 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 238 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN A1784 ASN A1876 GLN A1985 HIS A2187 GLN A2439 HIS A3233 ASN A3540 ASN ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4062 GLN A4573 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.138474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105563 restraints weight = 35309.624| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.35 r_work: 0.3141 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24213 Z= 0.138 Angle : 0.496 7.000 32838 Z= 0.249 Chirality : 0.040 0.146 3692 Planarity : 0.004 0.047 4206 Dihedral : 6.353 128.750 3261 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.42 % Allowed : 10.17 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.16), residues: 2929 helix: 2.28 (0.12), residues: 1726 sheet: -0.54 (0.34), residues: 229 loop : 0.54 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2763 TYR 0.022 0.001 TYR A1546 PHE 0.021 0.001 PHE A3957 TRP 0.018 0.001 TRP A2234 HIS 0.011 0.001 HIS A1985 Details of bonding type rmsd covalent geometry : bond 0.00315 (24213) covalent geometry : angle 0.49584 (32838) hydrogen bonds : bond 0.04078 ( 1430) hydrogen bonds : angle 3.99188 ( 4167) *********************** 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 305 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 268 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1649 LYS cc_start: 0.8075 (mttt) cc_final: 0.7653 (mttp) REVERT: A 1805 ARG cc_start: 0.8385 (ttp-110) cc_final: 0.7624 (ttm110) REVERT: A 2542 SER cc_start: 0.8806 (p) cc_final: 0.8441 (p) REVERT: A 2544 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7859 (pm20) REVERT: A 2901 TYR cc_start: 0.8445 (m-10) cc_final: 0.7629 (m-10) REVERT: A 3016 GLU cc_start: 0.8658 (pp20) cc_final: 0.8134 (pp20) REVERT: A 3503 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8151 (tt) REVERT: A 3506 ASP cc_start: 0.8042 (m-30) cc_final: 0.7670 (m-30) REVERT: A 3956 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7946 (pt0) REVERT: A 4287 LYS cc_start: 0.8167 (ptmt) cc_final: 0.7768 (mptt) REVERT: A 4423 LEU cc_start: 0.9025 (tp) cc_final: 0.8811 (tp) REVERT: A 4436 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7732 (mm110) REVERT: A 4453 ASN cc_start: 0.8419 (t0) cc_final: 0.8004 (t0) REVERT: A 4509 VAL cc_start: 0.8552 (t) cc_final: 0.8285 (p) REVERT: A 4542 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7366 (pt0) outliers start: 37 outliers final: 20 residues processed: 289 average time/residue: 0.1983 time to fit residues: 88.7241 Evaluate side-chains 259 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 236 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1662 SER Chi-restraints excluded: chain A residue 1724 VAL 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 2372 ASP Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2544 GLU 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 3503 ILE 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 3912 ASN Chi-restraints excluded: chain A residue 3959 ILE Chi-restraints excluded: chain A residue 3962 ASP Chi-restraints excluded: chain A residue 3963 SER Chi-restraints excluded: chain A residue 4081 ASP 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 252 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 158 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 159 optimal weight: 0.0370 chunk 283 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 overall best weight: 1.4862 ------------------------------------------------------------------------------- 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** A4573 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.134276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.102261 restraints weight = 35173.541| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.40 r_work: 0.3106 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24213 Z= 0.162 Angle : 0.515 6.544 32838 Z= 0.258 Chirality : 0.040 0.146 3692 Planarity : 0.004 0.048 4206 Dihedral : 6.184 127.733 3261 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.88 % Allowed : 11.09 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.16), residues: 2929 helix: 2.31 (0.12), residues: 1726 sheet: -0.69 (0.32), residues: 238 loop : 0.52 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2060 TYR 0.023 0.001 TYR A1546 PHE 0.015 0.001 PHE A4260 TRP 0.017 0.001 TRP A2234 HIS 0.014 0.001 HIS A1985 Details of bonding type rmsd covalent geometry : bond 0.00377 (24213) covalent geometry : angle 0.51525 (32838) hydrogen bonds : bond 0.04057 ( 1430) hydrogen bonds : angle 3.96228 ( 4167) *********************** 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 320 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 271 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1589 MET cc_start: 0.6634 (ttp) cc_final: 0.6212 (tmm) REVERT: A 1805 ARG cc_start: 0.8423 (ttp-110) cc_final: 0.7763 (ttm110) REVERT: A 2074 LYS cc_start: 0.8371 (mmmm) cc_final: 0.8090 (mptt) REVERT: A 2331 GLU cc_start: 0.8407 (tt0) cc_final: 0.8163 (tt0) REVERT: A 2901 TYR cc_start: 0.8536 (m-10) cc_final: 0.7731 (m-10) REVERT: A 3016 GLU cc_start: 0.8703 (pp20) cc_final: 0.8259 (pp20) REVERT: A 3024 ASP cc_start: 0.7915 (p0) cc_final: 0.7326 (t0) REVERT: A 3503 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8305 (tt) REVERT: A 3506 ASP cc_start: 0.8114 (m-30) cc_final: 0.7791 (m-30) REVERT: A 3540 ASN cc_start: 0.8802 (OUTLIER) cc_final: 0.8308 (m110) REVERT: A 4063 ASN cc_start: 0.8312 (t0) cc_final: 0.8108 (t0) REVERT: A 4287 LYS cc_start: 0.8136 (ptmt) cc_final: 0.7817 (mptt) REVERT: A 4423 LEU cc_start: 0.9137 (tp) cc_final: 0.8937 (tp) REVERT: A 4453 ASN cc_start: 0.8459 (t0) cc_final: 0.8057 (t0) REVERT: A 4509 VAL cc_start: 0.8719 (t) cc_final: 0.8498 (p) REVERT: A 4542 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7460 (pt0) outliers start: 49 outliers final: 24 residues processed: 308 average time/residue: 0.1791 time to fit residues: 86.1234 Evaluate side-chains 270 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 243 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1662 SER Chi-restraints excluded: chain A residue 1693 THR 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 2176 THR Chi-restraints excluded: chain A residue 2214 THR Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2557 VAL 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 3734 LEU Chi-restraints excluded: chain A residue 3785 GLU Chi-restraints excluded: chain A residue 3912 ASN Chi-restraints excluded: chain A residue 3963 SER Chi-restraints excluded: chain A residue 4038 ASN Chi-restraints excluded: chain A residue 4199 LEU Chi-restraints excluded: chain A residue 4542 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 133 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 234 optimal weight: 0.0980 chunk 148 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 104 optimal weight: 0.0980 chunk 43 optimal weight: 0.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- 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** A2187 GLN A2827 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.136415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104582 restraints weight = 34788.312| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.27 r_work: 0.3146 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24213 Z= 0.105 Angle : 0.477 10.711 32838 Z= 0.235 Chirality : 0.038 0.138 3692 Planarity : 0.003 0.047 4206 Dihedral : 6.033 128.243 3261 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.54 % Allowed : 11.86 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.16), residues: 2929 helix: 2.48 (0.12), residues: 1723 sheet: -0.66 (0.32), residues: 239 loop : 0.52 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2060 TYR 0.024 0.001 TYR A1546 PHE 0.016 0.001 PHE A2088 TRP 0.018 0.001 TRP A2234 HIS 0.010 0.001 HIS A1985 Details of bonding type rmsd covalent geometry : bond 0.00226 (24213) covalent geometry : angle 0.47723 (32838) hydrogen bonds : bond 0.03644 ( 1430) hydrogen bonds : angle 3.83254 ( 4167) *********************** 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 313 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 273 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1547 LEU cc_start: 0.8092 (mt) cc_final: 0.7773 (mt) REVERT: A 1589 MET cc_start: 0.6641 (ttp) cc_final: 0.6201 (tmm) REVERT: A 1649 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7241 (tptp) REVERT: A 1805 ARG cc_start: 0.8371 (ttp-110) cc_final: 0.7723 (ttm110) REVERT: A 2074 LYS cc_start: 0.8255 (mmmm) cc_final: 0.7891 (mptt) REVERT: A 2078 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7575 (mm-30) REVERT: A 2901 TYR cc_start: 0.8439 (m-10) cc_final: 0.7649 (m-10) REVERT: A 3503 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8281 (tt) REVERT: A 3506 ASP cc_start: 0.8179 (m-30) cc_final: 0.7907 (m-30) REVERT: A 3785 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: A 3944 PHE cc_start: 0.7414 (m-10) cc_final: 0.7157 (m-10) REVERT: A 4063 ASN cc_start: 0.8232 (t0) cc_final: 0.8021 (t0) REVERT: A 4287 LYS cc_start: 0.8101 (ptmt) cc_final: 0.7761 (mptt) REVERT: A 4453 ASN cc_start: 0.8439 (t0) cc_final: 0.8228 (t0) REVERT: A 4542 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7385 (pt0) outliers start: 40 outliers final: 26 residues processed: 299 average time/residue: 0.1861 time to fit residues: 86.2660 Evaluate side-chains 275 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 246 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 1662 SER Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2175 MET 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 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 3963 SER 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 4321 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4542 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 100 optimal weight: 0.2980 chunk 258 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 234 optimal weight: 0.0570 chunk 110 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 291 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.0704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN A1985 HIS A2827 HIS ** A3158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.134979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.102925 restraints weight = 35126.360| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.25 r_work: 0.3127 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24213 Z= 0.131 Angle : 0.490 8.166 32838 Z= 0.241 Chirality : 0.039 0.221 3692 Planarity : 0.004 0.049 4206 Dihedral : 5.950 127.221 3261 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.61 % Allowed : 12.40 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.16), residues: 2929 helix: 2.51 (0.12), residues: 1722 sheet: -0.71 (0.31), residues: 246 loop : 0.56 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2060 TYR 0.024 0.001 TYR A1546 PHE 0.016 0.001 PHE A3813 TRP 0.016 0.001 TRP A2234 HIS 0.009 0.001 HIS A1985 Details of bonding type rmsd covalent geometry : bond 0.00301 (24213) covalent geometry : angle 0.49042 (32838) hydrogen bonds : bond 0.03717 ( 1430) hydrogen bonds : angle 3.81377 ( 4167) *********************** 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 304 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 262 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 1547 LEU cc_start: 0.8022 (mt) cc_final: 0.7682 (mt) REVERT: A 1589 MET cc_start: 0.6633 (ttp) cc_final: 0.5937 (tmm) REVERT: A 1649 LYS cc_start: 0.8109 (mtpt) cc_final: 0.7684 (mttp) REVERT: A 1805 ARG cc_start: 0.8398 (ttp-110) cc_final: 0.7740 (ttm110) REVERT: A 2074 LYS cc_start: 0.8314 (mmmm) cc_final: 0.7988 (mptt) REVERT: A 2901 TYR cc_start: 0.8487 (m-10) cc_final: 0.7668 (m-10) REVERT: A 3503 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8319 (tt) REVERT: A 3506 ASP cc_start: 0.8148 (m-30) cc_final: 0.7873 (m-30) REVERT: A 3540 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8297 (m110) REVERT: A 3785 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: A 3944 PHE cc_start: 0.7577 (m-10) cc_final: 0.7334 (m-10) REVERT: A 4063 ASN cc_start: 0.8212 (t0) cc_final: 0.8006 (t0) REVERT: A 4287 LYS cc_start: 0.8093 (ptmt) cc_final: 0.7775 (mptt) REVERT: A 4377 MET cc_start: 0.7365 (tpp) cc_final: 0.6869 (tpp) REVERT: A 4453 ASN cc_start: 0.8464 (t0) cc_final: 0.8249 (t0) REVERT: A 4462 ARG cc_start: 0.8879 (mmm-85) cc_final: 0.8573 (ttm170) REVERT: A 4542 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7298 (pt0) outliers start: 42 outliers final: 30 residues processed: 292 average time/residue: 0.1877 time to fit residues: 85.3515 Evaluate side-chains 277 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 243 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 1662 SER Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1780 SER Chi-restraints excluded: chain A residue 1877 ASP Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2321 ASP Chi-restraints excluded: chain A residue 2372 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 2574 THR 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 3963 SER 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 4516 VAL Chi-restraints excluded: chain A residue 4542 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 163 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 291 optimal weight: 0.9980 chunk 292 optimal weight: 0.3980 chunk 119 optimal weight: 0.2980 chunk 183 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 212 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN A1985 HIS A2827 HIS ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.135557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.103833 restraints weight = 34797.589| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.32 r_work: 0.3138 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24213 Z= 0.110 Angle : 0.477 7.281 32838 Z= 0.235 Chirality : 0.038 0.149 3692 Planarity : 0.003 0.049 4206 Dihedral : 5.858 127.640 3261 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.57 % Allowed : 12.78 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.43 (0.16), residues: 2929 helix: 2.56 (0.12), residues: 1723 sheet: -0.69 (0.32), residues: 244 loop : 0.58 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2060 TYR 0.024 0.001 TYR A1546 PHE 0.015 0.001 PHE A3813 TRP 0.017 0.001 TRP A2234 HIS 0.008 0.001 HIS A1985 Details of bonding type rmsd covalent geometry : bond 0.00247 (24213) covalent geometry : angle 0.47730 (32838) hydrogen bonds : bond 0.03570 ( 1430) hydrogen bonds : angle 3.77225 ( 4167) *********************** 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 298 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 257 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1547 LEU cc_start: 0.7983 (mt) cc_final: 0.7651 (mt) REVERT: A 1589 MET cc_start: 0.6627 (ttp) cc_final: 0.5936 (tmm) REVERT: A 1805 ARG cc_start: 0.8407 (ttp-110) cc_final: 0.7741 (ttm110) REVERT: A 2074 LYS cc_start: 0.8352 (mmmm) cc_final: 0.7968 (mptt) REVERT: A 2198 GLU cc_start: 0.8602 (mp0) cc_final: 0.8267 (mp0) REVERT: A 2901 TYR cc_start: 0.8425 (m-10) cc_final: 0.7574 (m-10) REVERT: A 3503 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8293 (tt) REVERT: A 3506 ASP cc_start: 0.8153 (m-30) cc_final: 0.7867 (m-30) REVERT: A 4287 LYS cc_start: 0.8134 (ptmt) cc_final: 0.7861 (mmtp) REVERT: A 4377 MET cc_start: 0.7340 (tpp) cc_final: 0.7079 (tpp) REVERT: A 4453 ASN cc_start: 0.8525 (t0) cc_final: 0.8324 (t0) REVERT: A 4462 ARG cc_start: 0.8843 (mmm-85) cc_final: 0.8529 (ttm170) REVERT: A 4526 GLN cc_start: 0.7330 (tp40) cc_final: 0.7064 (mm-40) REVERT: A 4542 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7367 (pt0) outliers start: 41 outliers final: 32 residues processed: 285 average time/residue: 0.1793 time to fit residues: 80.3116 Evaluate side-chains 277 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 243 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 1662 SER Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1780 SER Chi-restraints excluded: chain A residue 1877 ASP Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2175 MET Chi-restraints excluded: chain A residue 2321 ASP Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2449 LEU Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2734 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 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 3912 ASN Chi-restraints excluded: chain A residue 3963 SER 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 4516 VAL Chi-restraints excluded: chain A residue 4542 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 117 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 chunk 245 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 289 optimal weight: 4.9990 chunk 225 optimal weight: 0.8980 chunk 240 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN A1985 HIS ** A3158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3658 r_free = 0.3658 target = 0.132507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.100362 restraints weight = 35037.473| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.26 r_work: 0.3089 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24213 Z= 0.176 Angle : 0.525 7.664 32838 Z= 0.261 Chirality : 0.040 0.143 3692 Planarity : 0.004 0.050 4206 Dihedral : 5.881 126.080 3261 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.73 % Allowed : 12.82 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.16), residues: 2929 helix: 2.43 (0.12), residues: 1727 sheet: -0.73 (0.31), residues: 241 loop : 0.51 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2060 TYR 0.022 0.001 TYR A1546 PHE 0.016 0.001 PHE A2343 TRP 0.016 0.001 TRP A2234 HIS 0.008 0.001 HIS A1985 Details of bonding type rmsd covalent geometry : bond 0.00419 (24213) covalent geometry : angle 0.52532 (32838) hydrogen bonds : bond 0.03952 ( 1430) hydrogen bonds : angle 3.88509 ( 4167) *********************** 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 298 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 253 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 1589 MET cc_start: 0.6644 (ttp) cc_final: 0.5950 (tmm) REVERT: A 1649 LYS cc_start: 0.8172 (mtpt) cc_final: 0.7708 (mttp) REVERT: A 2074 LYS cc_start: 0.8351 (mmmm) cc_final: 0.7969 (mptt) REVERT: A 2157 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7885 (tp) REVERT: A 2901 TYR cc_start: 0.8568 (m-10) cc_final: 0.7723 (m-10) REVERT: A 3024 ASP cc_start: 0.7977 (p0) cc_final: 0.7324 (t0) REVERT: A 3503 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8353 (tt) REVERT: A 3506 ASP cc_start: 0.8144 (m-30) cc_final: 0.7871 (m-30) REVERT: A 3540 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8290 (m110) REVERT: A 3595 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8052 (mp10) REVERT: A 4287 LYS cc_start: 0.8147 (ptmt) cc_final: 0.7836 (mptt) REVERT: A 4453 ASN cc_start: 0.8512 (t0) cc_final: 0.8298 (t0) REVERT: A 4462 ARG cc_start: 0.8858 (mmm-85) cc_final: 0.8534 (ttm170) REVERT: A 4492 ILE cc_start: 0.8352 (mt) cc_final: 0.8087 (mt) REVERT: A 4526 GLN cc_start: 0.7328 (tp40) cc_final: 0.7126 (mm-40) REVERT: A 4542 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7396 (pt0) outliers start: 45 outliers final: 31 residues processed: 285 average time/residue: 0.1656 time to fit residues: 73.5592 Evaluate side-chains 277 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 241 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 1662 SER Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1780 SER Chi-restraints excluded: chain A residue 1877 ASP Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2154 ILE Chi-restraints excluded: chain A residue 2157 LEU Chi-restraints excluded: chain A residue 2321 ASP Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2449 LEU Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2524 VAL Chi-restraints excluded: chain A residue 2557 VAL Chi-restraints excluded: chain A residue 2574 THR 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 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 3912 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 4516 VAL Chi-restraints excluded: chain A residue 4542 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 156 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 279 optimal weight: 4.9990 chunk 42 optimal weight: 0.0040 chunk 290 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 284 optimal weight: 8.9990 chunk 259 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 285 optimal weight: 0.8980 chunk 240 optimal weight: 1.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.133525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.101713 restraints weight = 35155.082| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.33 r_work: 0.3105 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24213 Z= 0.135 Angle : 0.497 6.634 32838 Z= 0.247 Chirality : 0.039 0.138 3692 Planarity : 0.004 0.047 4206 Dihedral : 5.805 126.100 3261 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.42 % Allowed : 13.51 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.16), residues: 2929 helix: 2.49 (0.12), residues: 1728 sheet: -0.73 (0.31), residues: 241 loop : 0.46 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2060 TYR 0.024 0.001 TYR A1546 PHE 0.015 0.001 PHE A3813 TRP 0.018 0.001 TRP A2234 HIS 0.009 0.001 HIS A1985 Details of bonding type rmsd covalent geometry : bond 0.00313 (24213) covalent geometry : angle 0.49747 (32838) hydrogen bonds : bond 0.03718 ( 1430) hydrogen bonds : angle 3.83006 ( 4167) *********************** 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 283 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 246 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1589 MET cc_start: 0.6738 (ttp) cc_final: 0.6056 (tmm) REVERT: A 1649 LYS cc_start: 0.8187 (mtpt) cc_final: 0.7720 (mttp) REVERT: A 2074 LYS cc_start: 0.8359 (mmmm) cc_final: 0.7927 (mptt) REVERT: A 2157 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7817 (tp) REVERT: A 2901 TYR cc_start: 0.8467 (m-10) cc_final: 0.7655 (m-10) REVERT: A 3024 ASP cc_start: 0.7989 (p0) cc_final: 0.7324 (t0) REVERT: A 3206 ARG cc_start: 0.8196 (mtm110) cc_final: 0.7640 (ttp80) REVERT: A 3503 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8316 (tt) REVERT: A 3506 ASP cc_start: 0.8176 (m-30) cc_final: 0.7891 (m-30) REVERT: A 3595 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7902 (mp10) REVERT: A 4287 LYS cc_start: 0.8120 (ptmt) cc_final: 0.7873 (mmtp) REVERT: A 4377 MET cc_start: 0.7437 (tpp) cc_final: 0.7054 (tpp) REVERT: A 4453 ASN cc_start: 0.8489 (t0) cc_final: 0.8281 (t0) REVERT: A 4462 ARG cc_start: 0.8901 (mmm-85) cc_final: 0.8563 (ttm110) REVERT: A 4492 ILE cc_start: 0.8370 (mt) cc_final: 0.8114 (mt) REVERT: A 4542 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7388 (pt0) outliers start: 37 outliers final: 32 residues processed: 274 average time/residue: 0.1555 time to fit residues: 67.6599 Evaluate side-chains 276 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 1662 SER Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1780 SER Chi-restraints excluded: chain A residue 1877 ASP Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2154 ILE Chi-restraints excluded: chain A residue 2157 LEU Chi-restraints excluded: chain A residue 2321 ASP Chi-restraints excluded: chain A residue 2334 SER Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2449 LEU Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2524 VAL 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 3550 THR 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 3912 ASN Chi-restraints excluded: chain A residue 4038 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 4516 VAL Chi-restraints excluded: chain A residue 4542 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 184 optimal weight: 0.0980 chunk 216 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 278 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 269 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1985 HIS ** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4526 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.135002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.103446 restraints weight = 35064.337| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.31 r_work: 0.3130 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24213 Z= 0.108 Angle : 0.483 6.926 32838 Z= 0.239 Chirality : 0.038 0.144 3692 Planarity : 0.003 0.048 4206 Dihedral : 5.688 125.106 3261 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.31 % Allowed : 13.86 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.16), residues: 2929 helix: 2.59 (0.12), residues: 1729 sheet: -0.69 (0.32), residues: 239 loop : 0.51 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2060 TYR 0.025 0.001 TYR A1546 PHE 0.014 0.001 PHE A3813 TRP 0.017 0.001 TRP A2234 HIS 0.009 0.001 HIS A1985 Details of bonding type rmsd covalent geometry : bond 0.00242 (24213) covalent geometry : angle 0.48264 (32838) hydrogen bonds : bond 0.03501 ( 1430) hydrogen bonds : angle 3.76194 ( 4167) ********************** 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 286 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 252 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1589 MET cc_start: 0.6754 (ttp) cc_final: 0.6067 (tmm) REVERT: A 1649 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7273 (tptp) REVERT: A 2074 LYS cc_start: 0.8347 (mmmm) cc_final: 0.7916 (mptt) REVERT: A 2157 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7817 (tp) REVERT: A 2901 TYR cc_start: 0.8445 (m-10) cc_final: 0.7631 (m-10) REVERT: A 3024 ASP cc_start: 0.7989 (p0) cc_final: 0.7319 (t0) REVERT: A 3503 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8298 (tt) REVERT: A 3506 ASP cc_start: 0.8171 (m-30) cc_final: 0.7881 (m-30) REVERT: A 3595 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7855 (mp10) REVERT: A 4213 ARG cc_start: 0.8262 (mtt90) cc_final: 0.8049 (mtm110) REVERT: A 4287 LYS cc_start: 0.8085 (ptmt) cc_final: 0.7847 (mmtp) REVERT: A 4377 MET cc_start: 0.7339 (tpp) cc_final: 0.6962 (tpp) REVERT: A 4453 ASN cc_start: 0.8518 (t0) cc_final: 0.7968 (m-40) REVERT: A 4462 ARG cc_start: 0.8869 (mmm-85) cc_final: 0.8555 (ttm110) REVERT: A 4492 ILE cc_start: 0.8309 (mt) cc_final: 0.8052 (mt) REVERT: A 4542 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7428 (pt0) outliers start: 34 outliers final: 25 residues processed: 277 average time/residue: 0.1502 time to fit residues: 66.3675 Evaluate side-chains 261 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 232 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 1662 SER Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1780 SER Chi-restraints excluded: chain A residue 1877 ASP Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2117 GLU Chi-restraints excluded: chain A residue 2154 ILE Chi-restraints excluded: chain A residue 2157 LEU Chi-restraints excluded: chain A residue 2321 ASP Chi-restraints excluded: chain A residue 2372 ASP Chi-restraints excluded: chain A residue 2449 LEU Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2524 VAL 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 3550 THR 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 4274 THR Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4542 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 205 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 55 optimal weight: 0.0980 chunk 226 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 240 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 275 optimal weight: 0.6980 chunk 88 optimal weight: 0.0270 chunk 102 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.135954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.104340 restraints weight = 34803.633| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.33 r_work: 0.3143 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24213 Z= 0.101 Angle : 0.483 11.977 32838 Z= 0.237 Chirality : 0.038 0.146 3692 Planarity : 0.003 0.048 4206 Dihedral : 5.596 123.097 3261 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.11 % Allowed : 14.28 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.50 (0.16), residues: 2929 helix: 2.65 (0.12), residues: 1730 sheet: -0.67 (0.32), residues: 242 loop : 0.53 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2060 TYR 0.026 0.001 TYR A1546 PHE 0.013 0.001 PHE A3813 TRP 0.019 0.001 TRP A4592 HIS 0.014 0.001 HIS A1985 Details of bonding type rmsd covalent geometry : bond 0.00219 (24213) covalent geometry : angle 0.48267 (32838) hydrogen bonds : bond 0.03389 ( 1430) hydrogen bonds : angle 3.71141 ( 4167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7491.93 seconds wall clock time: 128 minutes 44.75 seconds (7724.75 seconds total)