Starting phenix.real_space_refine on Fri May 23 11:16:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bm0_44683/05_2025/9bm0_44683.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bm0_44683/05_2025/9bm0_44683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bm0_44683/05_2025/9bm0_44683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bm0_44683/05_2025/9bm0_44683.map" model { file = "/net/cci-nas-00/data/ceres_data/9bm0_44683/05_2025/9bm0_44683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bm0_44683/05_2025/9bm0_44683.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.038 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 4424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23710 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: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 117 Unusual residues: {' MG': 2, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 6, 'water': 3} Link IDs: {None: 8} Time building chain proxies: 12.61, per 1000 atoms: 0.53 Number of scatterers: 23710 At special positions: 0 Unit cell: (115.648, 192.192, 163.072, 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 4424 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.49 Conformation dependent library (CDL) restraints added in 3.0 seconds 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5588 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 20 sheets defined 64.2% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.64 Creating SS restraints... Processing helix chain 'A' and resid 1457 through 1473 removed outlier: 3.938A pdb=" N GLU A1461 " --> pdb=" O MET A1457 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1510 removed outlier: 3.681A pdb=" N LYS A1508 " --> pdb=" O VAL A1504 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A1510 " --> pdb=" O ALA A1506 " (cutoff:3.500A) Processing helix chain 'A' and resid 1511 through 1515 removed outlier: 3.724A pdb=" N LYS A1514 " --> pdb=" O PRO A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1554 removed outlier: 3.529A pdb=" N LYS A1526 " --> pdb=" O SER A1522 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A1536 " --> pdb=" O ALA A1532 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A1538 " --> pdb=" O PHE A1534 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A1546 " --> pdb=" O ARG A1542 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A1554 " --> pdb=" O ILE A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1561 removed outlier: 4.316A pdb=" N HIS A1559 " --> pdb=" O ALA A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1585 Processing helix chain 'A' and resid 1587 through 1593 Processing helix chain 'A' and resid 1596 through 1614 Processing helix chain 'A' and resid 1615 through 1626 removed outlier: 3.535A pdb=" N SER A1624 " --> pdb=" O GLU A1620 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1632 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1644 through 1645 No H-bonds generated for 'chain 'A' and resid 1644 through 1645' Processing helix chain 'A' and resid 1646 through 1651 removed outlier: 3.859A pdb=" N LYS A1649 " --> pdb=" O ASN A1646 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN A1651 " --> pdb=" O ALA A1648 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1658 removed outlier: 3.778A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1728 removed outlier: 3.526A pdb=" N THR A1703 " --> pdb=" O ASN A1699 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 4.191A 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 1769 removed outlier: 3.537A pdb=" N VAL A1751 " --> pdb=" O ALA A1747 " (cutoff:3.500A) Processing helix chain 'A' and resid 1770 through 1772 No H-bonds generated for 'chain 'A' and resid 1770 through 1772' Processing helix chain 'A' and resid 1777 through 1798 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 removed outlier: 3.512A pdb=" N LEU A1963 " --> pdb=" O PHE A1960 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1960 through 1963' Processing helix chain 'A' and resid 1964 through 1987 removed outlier: 4.085A pdb=" N GLN A1973 " --> pdb=" O SER A1969 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLN A1974 " --> pdb=" O ALA A1970 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN A1987 " --> pdb=" O ARG A1983 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2034 Processing helix chain 'A' and resid 2045 through 2058 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 2152 through 2165 removed outlier: 4.102A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2255 through 2259 removed outlier: 3.839A pdb=" N ILE A2259 " --> pdb=" O PRO A2256 " (cutoff:3.500A) Processing helix chain 'A' and resid 2260 through 2265 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2308 through 2313 Processing helix chain 'A' and resid 2315 through 2320 Processing helix chain 'A' and resid 2352 through 2358 removed outlier: 3.544A pdb=" N ARG A2358 " --> pdb=" O ALA A2354 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 2482 through 2504 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 removed outlier: 3.677A pdb=" N VAL A2562 " --> pdb=" O THR A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.573A 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: 4.074A 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 removed outlier: 3.756A pdb=" N PHE A2751 " --> pdb=" O ILE A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2757 through 2758 No H-bonds generated for 'chain 'A' and resid 2757 through 2758' Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 4.658A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2784 Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.708A 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 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 2954 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: 4.128A 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: 3.645A pdb=" N LYS A3076 " --> pdb=" O SER A3072 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A3080 " --> pdb=" O LYS A3076 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3086 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: 3.548A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A3220 " --> pdb=" O GLU A3216 " (cutoff:3.500A) Processing helix chain 'A' and resid 3450 through 3517 removed outlier: 4.381A pdb=" N ALA A3484 " --> pdb=" O LYS A3480 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLU A3485 " --> pdb=" O SER A3481 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LYS A3497 " --> pdb=" O SER A3493 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN A3498 " --> pdb=" O GLU A3494 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.188A 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 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 3651 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: 3.553A pdb=" N ILE A3767 " --> pdb=" O ASP A3763 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A3785 " --> pdb=" O THR A3781 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A3786 " --> pdb=" O ARG A3782 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN A3800 " --> pdb=" O THR A3796 " (cutoff:3.500A) removed outlier: 3.958A 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: 3.584A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3847 removed outlier: 3.661A pdb=" N LYS A3847 " --> pdb=" O PRO A3844 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3873 removed outlier: 3.529A pdb=" N PHE A3864 " --> pdb=" O THR A3860 " (cutoff:3.500A) Processing helix chain 'A' and resid 3874 through 3875 No H-bonds generated for 'chain 'A' and resid 3874 through 3875' Processing helix chain 'A' and resid 3876 through 3878 No H-bonds generated for 'chain 'A' and resid 3876 through 3878' Processing helix chain 'A' and resid 3879 through 3894 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 3917 through 3921 removed outlier: 3.936A pdb=" N THR A3921 " --> pdb=" O ALA A3918 " (cutoff:3.500A) Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3940 through 3945 removed outlier: 6.228A pdb=" N ALA A3943 " --> pdb=" O CYS A3940 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A3945 " --> pdb=" O PRO A3942 " (cutoff:3.500A) Processing helix chain 'A' and resid 3946 through 3953 Processing helix chain 'A' and resid 3956 through 3962 Processing helix chain 'A' and resid 3965 through 3970 removed outlier: 4.182A 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 Processing helix chain 'A' and resid 4026 through 4034 removed outlier: 3.773A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4062 Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 3.924A pdb=" N LYS A4089 " --> pdb=" O ASN A4085 " (cutoff:3.500A) Processing helix chain 'A' and resid 4098 through 4101 Processing helix chain 'A' and resid 4102 through 4115 removed outlier: 3.514A pdb=" N GLN A4108 " --> pdb=" O GLY A4104 " (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: 3.522A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4175 through 4195 removed outlier: 3.730A pdb=" N ARG A4195 " --> pdb=" O GLN A4191 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4227 Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4301 through 4311 Processing helix chain 'A' and resid 4317 through 4322 Processing helix chain 'A' and resid 4324 through 4327 Processing helix chain 'A' and resid 4328 through 4346 removed outlier: 3.511A pdb=" N MET A4343 " --> pdb=" O MET A4339 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A4346 " --> pdb=" O LYS A4342 " (cutoff:3.500A) Processing helix chain 'A' and resid 4375 through 4391 Processing helix chain 'A' and resid 4407 through 4439 removed outlier: 4.029A pdb=" N ARG A4415 " --> pdb=" O ARG A4411 " (cutoff:3.500A) Processing helix chain 'A' and resid 4445 through 4457 Processing helix chain 'A' and resid 4474 through 4498 Processing helix chain 'A' and resid 4500 through 4507 removed outlier: 3.683A pdb=" N LEU A4504 " --> pdb=" O GLY A4500 " (cutoff:3.500A) Processing helix chain 'A' and resid 4516 through 4533 removed outlier: 3.674A pdb=" N TYR A4520 " --> pdb=" O VAL A4516 " (cutoff:3.500A) 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 removed outlier: 3.634A pdb=" N PHE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1476 through 1480 removed outlier: 3.937A pdb=" N ASP A1476 " --> pdb=" O ARG A1488 " (cutoff:3.500A) removed outlier: 3.910A 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: 7.287A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.692A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.468A 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: 6.542A pdb=" N GLY A1901 " --> pdb=" O ARG A2037 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU A2039 " --> pdb=" O GLY A1901 " (cutoff:3.500A) removed outlier: 6.284A 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 2254 removed outlier: 6.775A pdb=" N GLY A2219 " --> pdb=" O GLY A2360 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL A2362 " --> pdb=" O GLY A2219 " (cutoff:3.500A) removed outlier: 6.330A 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: 6.444A pdb=" N GLU A2616 " --> pdb=" O VAL A2660 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N PHE A2662 " --> pdb=" O GLU A2616 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL A2618 " --> pdb=" O PHE A2662 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2643 removed outlier: 6.973A 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: 6.089A pdb=" N SER A2957 " --> pdb=" O ALA A2991 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE A2993 " --> pdb=" O SER A2957 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR A2959 " --> pdb=" O ILE A2993 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ASP A2995 " --> pdb=" O TYR A2959 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE A2990 " --> pdb=" O HIS A3063 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU A2933 " --> pdb=" O PHE A3066 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N MET A3068 " --> pdb=" O LEU A2933 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU A2935 " --> pdb=" O MET A3068 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N HIS A2932 " --> pdb=" O VAL A3090 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN A3092 " --> pdb=" O HIS A2932 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU A2934 " --> pdb=" O ASN A3092 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE A3094 " --> pdb=" O LEU A2934 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE A2936 " --> pdb=" O PHE A3094 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.238A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (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: 6.473A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU A4042 " --> pdb=" O PHE A4145 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N PHE A4147 " --> pdb=" O LEU A4042 " (cutoff:3.500A) removed outlier: 6.799A 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: 6.721A 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: 6.096A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 4564 through 4571 removed outlier: 7.436A pdb=" N ILE A4581 " --> pdb=" O GLY A4567 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N THR A4569 " --> pdb=" O ASN A4579 " (cutoff:3.500A) removed outlier: 9.485A pdb=" N ASN A4579 " --> pdb=" O THR A4569 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N ASN A4571 " --> pdb=" O LEU A4577 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N LEU A4577 " --> pdb=" O ASN A4571 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL A4609 " --> pdb=" O ILE A4619 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N THR A4621 " --> pdb=" O LEU A4607 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU A4607 " --> pdb=" O THR A4621 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASP A4623 " --> pdb=" O VAL A4605 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A4605 " --> pdb=" O ASP A4623 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A4641 " --> pdb=" O GLN A4566 " (cutoff:3.500A) 1420 hydrogen bonds defined for protein. 4131 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: 16.37 Time building geometry restraints manager: 7.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7803 1.34 - 1.46: 5017 1.46 - 1.58: 11184 1.58 - 1.70: 13 1.70 - 1.81: 196 Bond restraints: 24213 Sorted by residual: bond pdb=" N GLY A2647 " pdb=" CA GLY A2647 " ideal model delta sigma weight residual 1.447 1.477 -0.030 9.20e-03 1.18e+04 1.09e+01 bond pdb=" N ASP A2697 " pdb=" CA ASP A2697 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.00e-02 1.00e+04 9.94e+00 bond pdb=" N VAL A2557 " pdb=" CA VAL A2557 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.82e+00 bond pdb=" N ILE A3609 " pdb=" CA ILE A3609 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.69e+00 bond pdb=" N ARG A2811 " pdb=" CA ARG A2811 " ideal model delta sigma weight residual 1.462 1.486 -0.024 7.70e-03 1.69e+04 9.51e+00 ... (remaining 24208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 31629 1.62 - 3.25: 1049 3.25 - 4.87: 130 4.87 - 6.50: 26 6.50 - 8.12: 4 Bond angle restraints: 32838 Sorted by residual: angle pdb=" N PRO A2553 " pdb=" CA PRO A2553 " pdb=" CB PRO A2553 " ideal model delta sigma weight residual 103.25 99.03 4.22 1.05e+00 9.07e-01 1.62e+01 angle pdb=" N GLY A2749 " pdb=" CA GLY A2749 " pdb=" C GLY A2749 " ideal model delta sigma weight residual 112.77 107.83 4.94 1.28e+00 6.10e-01 1.49e+01 angle pdb=" CA PRO A1801 " pdb=" C PRO A1801 " pdb=" O PRO A1801 " ideal model delta sigma weight residual 120.90 118.24 2.66 7.20e-01 1.93e+00 1.37e+01 angle pdb=" CA ILE A2555 " pdb=" C ILE A2555 " pdb=" O ILE A2555 " ideal model delta sigma weight residual 122.13 118.17 3.96 1.11e+00 8.12e-01 1.27e+01 angle pdb=" N PRO A2411 " pdb=" CA PRO A2411 " pdb=" C PRO A2411 " ideal model delta sigma weight residual 113.53 108.59 4.94 1.39e+00 5.18e-01 1.26e+01 ... (remaining 32833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.35: 13566 24.35 - 48.70: 914 48.70 - 73.05: 175 73.05 - 97.40: 36 97.40 - 121.76: 2 Dihedral angle restraints: 14693 sinusoidal: 6090 harmonic: 8603 Sorted by residual: dihedral pdb=" C5' ADP A4703 " pdb=" O5' ADP A4703 " pdb=" PA ADP A4703 " pdb=" O2A ADP A4703 " ideal model delta sinusoidal sigma weight residual 300.00 178.25 121.76 1 2.00e+01 2.50e-03 3.66e+01 dihedral pdb=" O1B ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PB ADP A4701 " pdb=" PA ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 42.50 -102.50 1 2.00e+01 2.50e-03 2.92e+01 dihedral pdb=" C4' ADP A4704 " pdb=" C5' ADP A4704 " pdb=" O5' ADP A4704 " pdb=" PA ADP A4704 " ideal model delta sinusoidal sigma weight residual -180.00 -118.58 -61.42 1 2.00e+01 2.50e-03 1.25e+01 ... (remaining 14690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2883 0.048 - 0.096: 547 0.096 - 0.144: 215 0.144 - 0.192: 37 0.192 - 0.239: 10 Chirality restraints: 3692 Sorted by residual: chirality pdb=" CA VAL A3129 " pdb=" N VAL A3129 " pdb=" C VAL A3129 " pdb=" CB VAL A3129 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ILE A2415 " pdb=" N ILE A2415 " pdb=" C ILE A2415 " pdb=" CB ILE A2415 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ILE A4459 " pdb=" N ILE A4459 " pdb=" C ILE A4459 " pdb=" CB ILE A4459 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 3689 not shown) Planarity restraints: 4206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A2753 " 0.447 9.50e-02 1.11e+02 2.00e-01 2.46e+01 pdb=" NE ARG A2753 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A2753 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A2753 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A2753 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A3164 " 0.371 9.50e-02 1.11e+02 1.66e-01 1.71e+01 pdb=" NE ARG A3164 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG A3164 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A3164 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A3164 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A2642 " -0.292 9.50e-02 1.11e+02 1.31e-01 1.06e+01 pdb=" NE ARG A2642 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A2642 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A2642 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A2642 " -0.010 2.00e-02 2.50e+03 ... (remaining 4203 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 155 2.55 - 3.14: 18288 3.14 - 3.72: 39028 3.72 - 4.31: 54825 4.31 - 4.90: 89963 Nonbonded interactions: 202259 Sorted by model distance: nonbonded pdb=" OG1 THR A1913 " pdb="MG MG A4705 " model vdw 1.958 2.170 nonbonded pdb="MG MG A4705 " pdb=" O HOH A4801 " model vdw 1.961 2.170 nonbonded pdb="MG MG A4705 " pdb=" O HOH A4803 " model vdw 1.978 2.170 nonbonded pdb="MG MG A4705 " pdb=" O HOH A4802 " model vdw 1.988 2.170 nonbonded pdb=" OE2 GLU A2344 " pdb="MG MG A4706 " model vdw 2.045 2.170 ... (remaining 202254 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: 4.220 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: 0.010 Extract box with map and model: 0.950 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 62.140 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.120 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:15.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 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 : 0.007 0.896 24214 Z= 0.657 Angle : 0.632 8.125 32838 Z= 0.421 Chirality : 0.047 0.239 3692 Planarity : 0.007 0.200 4206 Dihedral : 16.578 121.755 9105 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.84 % Allowed : 13.63 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.15), residues: 2929 helix: 1.52 (0.12), residues: 1706 sheet: -0.12 (0.34), residues: 231 loop : 0.62 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1701 HIS 0.002 0.001 HIS A3188 PHE 0.015 0.001 PHE A4624 TYR 0.013 0.001 TYR A3183 ARG 0.011 0.000 ARG A1621 Details of bonding type rmsd hydrogen bonds : bond 0.19972 ( 1420) hydrogen bonds : angle 6.37005 ( 4131) covalent geometry : bond 0.00444 (24213) covalent geometry : angle 0.63230 (32838) Misc. bond : bond 0.89626 ( 1) *********************** 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 422 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 400 time to evaluate : 2.899 Fit side-chains revert: symmetry clash REVERT: A 1457 MET cc_start: 0.4767 (mpt) cc_final: 0.4354 (mpp) REVERT: A 1507 MET cc_start: 0.6541 (ptp) cc_final: 0.5812 (mmt) REVERT: A 1589 MET cc_start: 0.7714 (mmm) cc_final: 0.7503 (mmt) REVERT: A 1679 ARG cc_start: 0.7993 (ptp90) cc_final: 0.7398 (ptp-170) REVERT: A 2222 MET cc_start: 0.8591 (mtm) cc_final: 0.8342 (mtm) REVERT: A 2306 ASP cc_start: 0.7891 (m-30) cc_final: 0.7673 (m-30) REVERT: A 2508 LEU cc_start: 0.8693 (tp) cc_final: 0.8453 (tp) REVERT: A 2510 MET cc_start: 0.8037 (mmt) cc_final: 0.7710 (mmt) REVERT: A 2855 LEU cc_start: 0.8541 (mm) cc_final: 0.8302 (mm) REVERT: A 2867 MET cc_start: 0.8323 (tpp) cc_final: 0.7978 (mtp) REVERT: A 3025 GLU cc_start: 0.7287 (mm-30) cc_final: 0.7007 (mt-10) REVERT: A 3188 HIS cc_start: 0.7766 (t-170) cc_final: 0.7380 (m-70) REVERT: A 3616 ASP cc_start: 0.7477 (t70) cc_final: 0.7199 (m-30) REVERT: A 3791 MET cc_start: 0.7795 (tpt) cc_final: 0.7412 (tpt) REVERT: A 4301 ARG cc_start: 0.7886 (mtp85) cc_final: 0.7495 (ttp-110) REVERT: A 4314 ASP cc_start: 0.8118 (t70) cc_final: 0.7841 (t0) REVERT: A 4329 ARG cc_start: 0.7943 (ttm170) cc_final: 0.7693 (ttm110) REVERT: A 4377 MET cc_start: 0.7703 (mmm) cc_final: 0.6968 (tpt) REVERT: A 4419 MET cc_start: 0.7803 (mtm) cc_final: 0.7453 (mtp) REVERT: A 4625 GLU cc_start: 0.7873 (tt0) cc_final: 0.7529 (mt-10) outliers start: 22 outliers final: 5 residues processed: 416 average time/residue: 1.6403 time to fit residues: 769.0390 Evaluate side-chains 294 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 289 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3644 VAL Chi-restraints excluded: chain A residue 3912 ASN Chi-restraints excluded: chain A residue 4137 ASN Chi-restraints excluded: chain A residue 4574 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 247 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 229 optimal weight: 0.0970 chunk 88 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 266 optimal weight: 3.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1855 GLN A1876 GLN A2212 GLN A2442 GLN A2475 ASN ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2752 ASN A2860 ASN A3014 ASN A3181 ASN ** A3233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3584 ASN A3650 ASN A3744 GLN A3968 GLN A4062 GLN A4079 GLN A4191 GLN A4526 GLN A4571 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.139118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.104407 restraints weight = 29449.191| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.89 r_work: 0.3183 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24214 Z= 0.158 Angle : 0.542 6.923 32838 Z= 0.275 Chirality : 0.041 0.176 3692 Planarity : 0.004 0.050 4206 Dihedral : 6.599 120.430 3272 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.34 % Allowed : 14.20 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.16), residues: 2929 helix: 2.13 (0.12), residues: 1716 sheet: 0.02 (0.34), residues: 238 loop : 0.65 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1701 HIS 0.004 0.001 HIS A4187 PHE 0.017 0.002 PHE A2912 TYR 0.018 0.001 TYR A3183 ARG 0.010 0.000 ARG A2763 Details of bonding type rmsd hydrogen bonds : bond 0.05239 ( 1420) hydrogen bonds : angle 4.44799 ( 4131) covalent geometry : bond 0.00363 (24213) covalent geometry : angle 0.54200 (32838) Misc. bond : bond 0.00797 ( 1) *********************** 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 385 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 298 time to evaluate : 2.755 Fit side-chains REVERT: A 1457 MET cc_start: 0.4616 (mpt) cc_final: 0.4172 (mpp) REVERT: A 1679 ARG cc_start: 0.7696 (ptp90) cc_final: 0.6683 (ptp-170) REVERT: A 1798 MET cc_start: 0.6357 (OUTLIER) cc_final: 0.6027 (ptp) REVERT: A 1829 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8361 (mmpt) REVERT: A 2222 MET cc_start: 0.9043 (mtm) cc_final: 0.8681 (mtm) REVERT: A 2306 ASP cc_start: 0.8327 (m-30) cc_final: 0.8038 (m-30) REVERT: A 2353 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7573 (tm) REVERT: A 2367 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7670 (m-30) REVERT: A 2438 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: A 2492 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7113 (mpt90) REVERT: A 2643 ARG cc_start: 0.8004 (ttm-80) cc_final: 0.7469 (mtm-85) REVERT: A 2666 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8245 (pt) REVERT: A 2763 ARG cc_start: 0.7270 (mtm110) cc_final: 0.6597 (mtt90) REVERT: A 2855 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7546 (mm) REVERT: A 2917 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6680 (m-30) REVERT: A 2975 ASP cc_start: 0.7402 (m-30) cc_final: 0.7141 (m-30) REVERT: A 3025 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6432 (mm-30) REVERT: A 3077 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7319 (t0) REVERT: A 3188 HIS cc_start: 0.7605 (t-170) cc_final: 0.6398 (m-70) REVERT: A 3616 ASP cc_start: 0.6766 (t70) cc_final: 0.6565 (m-30) REVERT: A 3639 GLU cc_start: 0.8140 (pm20) cc_final: 0.7938 (pm20) REVERT: A 3791 MET cc_start: 0.6847 (tpt) cc_final: 0.6546 (tpt) REVERT: A 3792 GLN cc_start: 0.7037 (tt0) cc_final: 0.6734 (tt0) REVERT: A 3802 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7384 (mt) REVERT: A 3841 TYR cc_start: 0.8671 (m-80) cc_final: 0.8422 (m-80) REVERT: A 3950 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.7146 (mttp) REVERT: A 4209 GLU cc_start: 0.7729 (tp30) cc_final: 0.7324 (tp30) REVERT: A 4276 ARG cc_start: 0.7646 (mmm-85) cc_final: 0.7162 (mmp-170) REVERT: A 4314 ASP cc_start: 0.8068 (t70) cc_final: 0.7699 (t0) REVERT: A 4419 MET cc_start: 0.7343 (mtm) cc_final: 0.6724 (mtp) REVERT: A 4625 GLU cc_start: 0.7558 (tt0) cc_final: 0.7128 (mt-10) outliers start: 87 outliers final: 26 residues processed: 360 average time/residue: 1.5146 time to fit residues: 621.5720 Evaluate side-chains 299 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 261 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1556 ASP Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1829 LYS Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1977 CYS Chi-restraints excluded: chain A residue 2162 SER Chi-restraints excluded: chain A residue 2260 SER Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2367 ASP Chi-restraints excluded: chain A residue 2438 GLU Chi-restraints excluded: chain A residue 2492 ARG Chi-restraints excluded: chain A residue 2551 LYS Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2696 SER Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2867 MET Chi-restraints excluded: chain A residue 2917 ASP Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 3077 ASP Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3545 THR Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3644 VAL Chi-restraints excluded: chain A residue 3702 THR Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3797 VAL Chi-restraints excluded: chain A residue 3802 LEU Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3912 ASN Chi-restraints excluded: chain A residue 3950 LYS Chi-restraints excluded: chain A residue 4045 SER Chi-restraints excluded: chain A residue 4280 SER Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4409 LEU Chi-restraints excluded: chain A residue 4475 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 26 optimal weight: 1.9990 chunk 257 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 237 optimal weight: 0.6980 chunk 222 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1855 GLN A2707 GLN A2752 ASN A3038 GLN A3198 GLN ** A3233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3537 GLN A3968 GLN A4012 ASN A4079 GLN A4393 GLN A4488 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.135135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.099892 restraints weight = 29628.952| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.91 r_work: 0.3073 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 24214 Z= 0.204 Angle : 0.543 6.976 32838 Z= 0.273 Chirality : 0.042 0.154 3692 Planarity : 0.004 0.049 4206 Dihedral : 6.600 117.603 3264 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.26 % Allowed : 15.12 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.15), residues: 2929 helix: 2.10 (0.12), residues: 1718 sheet: -0.14 (0.33), residues: 249 loop : 0.55 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1701 HIS 0.005 0.001 HIS A3047 PHE 0.014 0.002 PHE A2912 TYR 0.023 0.002 TYR A2472 ARG 0.011 0.000 ARG A3164 Details of bonding type rmsd hydrogen bonds : bond 0.04959 ( 1420) hydrogen bonds : angle 4.28682 ( 4131) covalent geometry : bond 0.00489 (24213) covalent geometry : angle 0.54304 (32838) Misc. bond : bond 0.00365 ( 1) *********************** 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 368 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 283 time to evaluate : 2.820 Fit side-chains REVERT: A 1457 MET cc_start: 0.4812 (mpt) cc_final: 0.4397 (mpp) REVERT: A 1535 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7769 (m-30) REVERT: A 1679 ARG cc_start: 0.7740 (ptp90) cc_final: 0.6695 (ptp-170) REVERT: A 1798 MET cc_start: 0.6539 (OUTLIER) cc_final: 0.6181 (ptp) REVERT: A 2163 ASP cc_start: 0.7563 (m-30) cc_final: 0.7294 (m-30) REVERT: A 2222 MET cc_start: 0.9078 (mtm) cc_final: 0.8756 (mtm) REVERT: A 2306 ASP cc_start: 0.8173 (m-30) cc_final: 0.7711 (m-30) REVERT: A 2353 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7643 (tm) REVERT: A 2367 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7780 (m-30) REVERT: A 2492 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7222 (mpt90) REVERT: A 2643 ARG cc_start: 0.8093 (ttm-80) cc_final: 0.7504 (mtm-85) REVERT: A 2666 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8368 (pt) REVERT: A 2855 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7620 (mm) REVERT: A 2917 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6794 (m-30) REVERT: A 3025 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6446 (mm-30) REVERT: A 3077 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7335 (t0) REVERT: A 3188 HIS cc_start: 0.7621 (t-170) cc_final: 0.6331 (m-70) REVERT: A 3616 ASP cc_start: 0.6813 (t70) cc_final: 0.6608 (m-30) REVERT: A 3639 GLU cc_start: 0.8145 (pm20) cc_final: 0.7790 (pm20) REVERT: A 3791 MET cc_start: 0.6879 (tpt) cc_final: 0.6563 (tpt) REVERT: A 3792 GLN cc_start: 0.7100 (tt0) cc_final: 0.6750 (tt0) REVERT: A 3802 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7390 (mt) REVERT: A 4209 GLU cc_start: 0.7804 (tp30) cc_final: 0.7411 (tp30) REVERT: A 4276 ARG cc_start: 0.7685 (mmm-85) cc_final: 0.7424 (mmp-170) REVERT: A 4307 GLN cc_start: 0.7297 (mt0) cc_final: 0.6908 (tt0) REVERT: A 4314 ASP cc_start: 0.8048 (t70) cc_final: 0.7698 (t0) REVERT: A 4419 MET cc_start: 0.7386 (mtm) cc_final: 0.6711 (mtp) REVERT: A 4574 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6638 (ttmm) outliers start: 85 outliers final: 34 residues processed: 345 average time/residue: 1.5440 time to fit residues: 608.2112 Evaluate side-chains 312 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 267 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1556 ASP Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1798 MET Chi-restraints excluded: chain A residue 1977 CYS Chi-restraints excluded: chain A residue 2156 LEU Chi-restraints excluded: chain A residue 2162 SER Chi-restraints excluded: chain A residue 2260 SER Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2367 ASP Chi-restraints excluded: chain A residue 2388 ASP Chi-restraints excluded: chain A residue 2492 ARG Chi-restraints excluded: chain A residue 2551 LYS Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2559 THR Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2696 SER Chi-restraints excluded: chain A residue 2788 THR Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2867 MET Chi-restraints excluded: chain A residue 2917 ASP Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 3077 ASP Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3545 THR Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3644 VAL Chi-restraints excluded: chain A residue 3702 THR Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3802 LEU Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3975 SER Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4137 ASN Chi-restraints excluded: chain A residue 4163 SER Chi-restraints excluded: chain A residue 4280 SER Chi-restraints excluded: chain A residue 4456 VAL Chi-restraints excluded: chain A residue 4475 VAL Chi-restraints excluded: chain A residue 4574 LYS Chi-restraints excluded: chain A residue 4593 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 16 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 197 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 252 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1855 GLN A2928 GLN A3233 ASN A3537 GLN A4079 GLN A4571 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.136883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.101902 restraints weight = 29807.362| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.92 r_work: 0.3104 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24214 Z= 0.126 Angle : 0.483 6.515 32838 Z= 0.243 Chirality : 0.039 0.145 3692 Planarity : 0.004 0.050 4206 Dihedral : 6.330 119.942 3262 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.61 % Allowed : 15.82 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.16), residues: 2929 helix: 2.28 (0.12), residues: 1715 sheet: -0.17 (0.32), residues: 259 loop : 0.62 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.003 0.001 HIS A3907 PHE 0.014 0.001 PHE A2912 TYR 0.017 0.001 TYR A2496 ARG 0.010 0.000 ARG A2763 Details of bonding type rmsd hydrogen bonds : bond 0.04131 ( 1420) hydrogen bonds : angle 4.05448 ( 4131) covalent geometry : bond 0.00286 (24213) covalent geometry : angle 0.48282 (32838) Misc. bond : bond 0.00081 ( 1) *********************** 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 352 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 284 time to evaluate : 2.912 Fit side-chains REVERT: A 1457 MET cc_start: 0.4764 (mpt) cc_final: 0.4289 (mpp) REVERT: A 1679 ARG cc_start: 0.7728 (ptp90) cc_final: 0.6711 (ptp-170) REVERT: A 2163 ASP cc_start: 0.7459 (m-30) cc_final: 0.7125 (m-30) REVERT: A 2222 MET cc_start: 0.9016 (mtm) cc_final: 0.8661 (mtm) REVERT: A 2306 ASP cc_start: 0.8108 (m-30) cc_final: 0.7771 (m-30) REVERT: A 2353 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7631 (tm) REVERT: A 2367 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7778 (m-30) REVERT: A 2444 GLU cc_start: 0.8191 (tt0) cc_final: 0.7762 (tm-30) REVERT: A 2492 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7152 (mpt90) REVERT: A 2666 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8300 (pt) REVERT: A 2763 ARG cc_start: 0.7273 (mtm110) cc_final: 0.6597 (mtt90) REVERT: A 2855 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7593 (mm) REVERT: A 2917 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6673 (m-30) REVERT: A 3025 GLU cc_start: 0.6743 (mm-30) cc_final: 0.6354 (mm-30) REVERT: A 3181 ASN cc_start: 0.7842 (m-40) cc_final: 0.7601 (m110) REVERT: A 3188 HIS cc_start: 0.7610 (t-170) cc_final: 0.6310 (m-70) REVERT: A 3616 ASP cc_start: 0.6765 (t70) cc_final: 0.6546 (m-30) REVERT: A 3639 GLU cc_start: 0.8187 (pm20) cc_final: 0.7783 (pm20) REVERT: A 3782 ARG cc_start: 0.7045 (ttp-170) cc_final: 0.6739 (ttp-170) REVERT: A 3791 MET cc_start: 0.6849 (tpt) cc_final: 0.6510 (tpt) REVERT: A 3792 GLN cc_start: 0.7079 (tt0) cc_final: 0.6771 (tt0) REVERT: A 4209 GLU cc_start: 0.7790 (tp30) cc_final: 0.7364 (tp30) REVERT: A 4276 ARG cc_start: 0.7661 (mmm-85) cc_final: 0.7402 (mmp-170) REVERT: A 4307 GLN cc_start: 0.7261 (mt0) cc_final: 0.6885 (tt0) REVERT: A 4314 ASP cc_start: 0.8056 (t70) cc_final: 0.7705 (t0) REVERT: A 4419 MET cc_start: 0.7349 (mtm) cc_final: 0.6747 (mtp) REVERT: A 4429 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.6201 (tm-30) REVERT: A 4574 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6630 (ttmm) outliers start: 68 outliers final: 21 residues processed: 337 average time/residue: 1.5060 time to fit residues: 579.3850 Evaluate side-chains 295 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 266 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1655 LYS Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1977 CYS Chi-restraints excluded: chain A residue 2260 SER Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2367 ASP Chi-restraints excluded: chain A residue 2492 ARG Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2867 MET Chi-restraints excluded: chain A residue 2917 ASP Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3545 THR Chi-restraints excluded: chain A residue 3644 VAL Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3796 THR Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4137 ASN Chi-restraints excluded: chain A residue 4163 SER Chi-restraints excluded: chain A residue 4280 SER Chi-restraints excluded: chain A residue 4429 GLN Chi-restraints excluded: chain A residue 4574 LYS Chi-restraints excluded: chain A residue 4593 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 155 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 175 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 268 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 221 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1855 GLN A1974 GLN A2475 ASN ** A3233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3537 GLN A4079 GLN A4397 HIS A4488 GLN A4571 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.132813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.100062 restraints weight = 30011.848| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.67 r_work: 0.3064 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 24214 Z= 0.257 Angle : 0.589 7.348 32838 Z= 0.295 Chirality : 0.044 0.188 3692 Planarity : 0.005 0.050 4206 Dihedral : 6.584 115.135 3262 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.34 % Allowed : 15.82 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.15), residues: 2929 helix: 2.00 (0.12), residues: 1720 sheet: -0.41 (0.33), residues: 236 loop : 0.38 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A4222 HIS 0.009 0.001 HIS A3047 PHE 0.017 0.002 PHE A2165 TYR 0.024 0.002 TYR A1546 ARG 0.010 0.001 ARG A3164 Details of bonding type rmsd hydrogen bonds : bond 0.05048 ( 1420) hydrogen bonds : angle 4.26428 ( 4131) covalent geometry : bond 0.00630 (24213) covalent geometry : angle 0.58857 (32838) Misc. bond : bond 0.00202 ( 1) *********************** 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 362 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 275 time to evaluate : 2.600 Fit side-chains REVERT: A 1457 MET cc_start: 0.4815 (mpt) cc_final: 0.4316 (mpp) REVERT: A 1679 ARG cc_start: 0.7732 (ptp90) cc_final: 0.6723 (ptp-170) REVERT: A 2163 ASP cc_start: 0.7457 (m-30) cc_final: 0.7111 (m-30) REVERT: A 2222 MET cc_start: 0.9048 (mtm) cc_final: 0.8709 (mtm) REVERT: A 2306 ASP cc_start: 0.8250 (m-30) cc_final: 0.8034 (m-30) REVERT: A 2353 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7607 (tm) REVERT: A 2367 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7832 (m-30) REVERT: A 2438 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: A 2444 GLU cc_start: 0.8305 (tt0) cc_final: 0.7832 (tm-30) REVERT: A 2492 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7216 (mpt90) REVERT: A 2666 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8410 (pt) REVERT: A 2688 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7702 (tp30) REVERT: A 2841 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6591 (mm-30) REVERT: A 2855 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7659 (mm) REVERT: A 2917 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.6797 (m-30) REVERT: A 3025 GLU cc_start: 0.6824 (mm-30) cc_final: 0.6441 (mm-30) REVERT: A 3049 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: A 3077 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7297 (t0) REVERT: A 3163 LYS cc_start: 0.6844 (OUTLIER) cc_final: 0.6376 (tmmt) REVERT: A 3181 ASN cc_start: 0.7877 (m-40) cc_final: 0.7621 (m110) REVERT: A 3188 HIS cc_start: 0.7663 (t-170) cc_final: 0.6361 (m-70) REVERT: A 3481 SER cc_start: 0.6201 (OUTLIER) cc_final: 0.5828 (p) REVERT: A 3639 GLU cc_start: 0.8239 (pm20) cc_final: 0.7797 (pm20) REVERT: A 3782 ARG cc_start: 0.7109 (ttp-170) cc_final: 0.6806 (ttp-170) REVERT: A 3791 MET cc_start: 0.7002 (tpt) cc_final: 0.6656 (tpt) REVERT: A 3792 GLN cc_start: 0.7169 (tt0) cc_final: 0.6828 (tt0) REVERT: A 3802 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7396 (mt) REVERT: A 4143 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7820 (tpt90) REVERT: A 4209 GLU cc_start: 0.7810 (tp30) cc_final: 0.7389 (tp30) REVERT: A 4276 ARG cc_start: 0.7671 (mmm-85) cc_final: 0.7418 (mmp-170) REVERT: A 4307 GLN cc_start: 0.7294 (mt0) cc_final: 0.6908 (tt0) REVERT: A 4314 ASP cc_start: 0.8048 (t70) cc_final: 0.7708 (t0) REVERT: A 4329 ARG cc_start: 0.7087 (ttm170) cc_final: 0.6727 (mtp-110) REVERT: A 4419 MET cc_start: 0.7338 (mtm) cc_final: 0.6678 (mtp) REVERT: A 4429 GLN cc_start: 0.6940 (OUTLIER) cc_final: 0.5984 (tm-30) REVERT: A 4633 ARG cc_start: 0.7214 (mtm180) cc_final: 0.6628 (mtm110) outliers start: 87 outliers final: 40 residues processed: 341 average time/residue: 1.5000 time to fit residues: 584.0847 Evaluate side-chains 322 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 266 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1571 ILE Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1611 ILE Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1977 CYS Chi-restraints excluded: chain A residue 2156 LEU Chi-restraints excluded: chain A residue 2162 SER Chi-restraints excluded: chain A residue 2260 SER Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2367 ASP Chi-restraints excluded: chain A residue 2388 ASP Chi-restraints excluded: chain A residue 2438 GLU Chi-restraints excluded: chain A residue 2492 ARG Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2688 GLU Chi-restraints excluded: chain A residue 2696 SER Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2788 THR Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2867 MET Chi-restraints excluded: chain A residue 2917 ASP Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 3049 GLU Chi-restraints excluded: chain A residue 3077 ASP Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3163 LYS Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3545 THR Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3644 VAL Chi-restraints excluded: chain A residue 3691 ASP Chi-restraints excluded: chain A residue 3702 THR Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3797 VAL Chi-restraints excluded: chain A residue 3802 LEU Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3847 LYS Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4052 SER Chi-restraints excluded: chain A residue 4061 GLU Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4137 ASN Chi-restraints excluded: chain A residue 4143 ARG Chi-restraints excluded: chain A residue 4163 SER Chi-restraints excluded: chain A residue 4280 SER Chi-restraints excluded: chain A residue 4429 GLN Chi-restraints excluded: chain A residue 4456 VAL Chi-restraints excluded: chain A residue 4574 LYS Chi-restraints excluded: chain A residue 4593 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 150 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 187 optimal weight: 0.9980 chunk 199 optimal weight: 1.9990 chunk 289 optimal weight: 0.0070 chunk 258 optimal weight: 0.5980 chunk 190 optimal weight: 4.9990 chunk 147 optimal weight: 0.5980 chunk 66 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1855 GLN ** A3233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3537 GLN A4079 GLN A4571 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.136327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.101243 restraints weight = 29633.148| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.93 r_work: 0.3096 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24214 Z= 0.110 Angle : 0.480 6.238 32838 Z= 0.242 Chirality : 0.039 0.145 3692 Planarity : 0.004 0.050 4206 Dihedral : 6.245 123.540 3262 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.42 % Allowed : 17.24 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.16), residues: 2929 helix: 2.29 (0.12), residues: 1723 sheet: -0.23 (0.32), residues: 252 loop : 0.56 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2234 HIS 0.005 0.001 HIS A4006 PHE 0.013 0.001 PHE A3813 TYR 0.018 0.001 TYR A2496 ARG 0.009 0.000 ARG A2763 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 1420) hydrogen bonds : angle 3.98711 ( 4131) covalent geometry : bond 0.00239 (24213) covalent geometry : angle 0.47986 (32838) Misc. bond : bond 0.00054 ( 1) *********************** 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 344 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 281 time to evaluate : 3.163 Fit side-chains REVERT: A 1457 MET cc_start: 0.4789 (mpt) cc_final: 0.4285 (mpp) REVERT: A 1679 ARG cc_start: 0.7724 (ptp90) cc_final: 0.6735 (ptp-170) REVERT: A 1998 THR cc_start: 0.8291 (p) cc_final: 0.8083 (p) REVERT: A 2047 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8416 (tp40) REVERT: A 2113 ARG cc_start: 0.7410 (ttm170) cc_final: 0.7030 (tpp-160) REVERT: A 2163 ASP cc_start: 0.7469 (m-30) cc_final: 0.7109 (m-30) REVERT: A 2222 MET cc_start: 0.8966 (mtm) cc_final: 0.8582 (mtm) REVERT: A 2306 ASP cc_start: 0.8108 (m-30) cc_final: 0.7830 (m-30) REVERT: A 2353 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7593 (tm) REVERT: A 2367 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7841 (m-30) REVERT: A 2444 GLU cc_start: 0.8246 (tt0) cc_final: 0.7797 (tm-30) REVERT: A 2471 GLN cc_start: 0.7153 (tt0) cc_final: 0.6720 (tt0) REVERT: A 2492 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7235 (mpt90) REVERT: A 2643 ARG cc_start: 0.8087 (ttm-80) cc_final: 0.7527 (mtm-85) REVERT: A 2666 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8299 (pt) REVERT: A 2763 ARG cc_start: 0.7273 (mtm110) cc_final: 0.6594 (mtt90) REVERT: A 2917 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6702 (m-30) REVERT: A 3025 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6385 (mm-30) REVERT: A 3181 ASN cc_start: 0.7860 (m-40) cc_final: 0.7629 (m110) REVERT: A 3188 HIS cc_start: 0.7673 (t-170) cc_final: 0.6351 (m-70) REVERT: A 3481 SER cc_start: 0.6188 (OUTLIER) cc_final: 0.5796 (p) REVERT: A 3639 GLU cc_start: 0.8252 (pm20) cc_final: 0.7776 (pm20) REVERT: A 3782 ARG cc_start: 0.7110 (ttp-170) cc_final: 0.6824 (ttp-170) REVERT: A 3791 MET cc_start: 0.6903 (tpt) cc_final: 0.6563 (tpt) REVERT: A 3792 GLN cc_start: 0.7128 (tt0) cc_final: 0.6811 (tt0) REVERT: A 4143 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7785 (tpt90) REVERT: A 4209 GLU cc_start: 0.7800 (tp30) cc_final: 0.7439 (tp30) REVERT: A 4276 ARG cc_start: 0.7653 (mmm-85) cc_final: 0.7372 (mmp-170) REVERT: A 4307 GLN cc_start: 0.7253 (mt0) cc_final: 0.6881 (tt0) REVERT: A 4314 ASP cc_start: 0.8091 (t70) cc_final: 0.7759 (t0) REVERT: A 4321 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8041 (mt) REVERT: A 4419 MET cc_start: 0.7338 (mtm) cc_final: 0.6742 (mtp) REVERT: A 4429 GLN cc_start: 0.6899 (OUTLIER) cc_final: 0.6014 (tm-30) REVERT: A 4574 LYS cc_start: 0.7066 (OUTLIER) cc_final: 0.6729 (ttmm) outliers start: 63 outliers final: 28 residues processed: 332 average time/residue: 1.4765 time to fit residues: 562.6503 Evaluate side-chains 309 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 270 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1655 LYS Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 1977 CYS Chi-restraints excluded: chain A residue 2047 GLN Chi-restraints excluded: chain A residue 2156 LEU Chi-restraints excluded: chain A residue 2260 SER Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2367 ASP Chi-restraints excluded: chain A residue 2450 THR Chi-restraints excluded: chain A residue 2492 ARG Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2867 MET Chi-restraints excluded: chain A residue 2917 ASP Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3545 THR Chi-restraints excluded: chain A residue 3702 THR Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3796 THR Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4121 CYS Chi-restraints excluded: chain A residue 4137 ASN Chi-restraints excluded: chain A residue 4143 ARG Chi-restraints excluded: chain A residue 4280 SER Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4429 GLN Chi-restraints excluded: chain A residue 4574 LYS Chi-restraints excluded: chain A residue 4593 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 168 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1855 GLN ** A3233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3537 GLN A4079 GLN A4386 ASN A4526 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.135237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.101501 restraints weight = 29888.865| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.85 r_work: 0.3110 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24214 Z= 0.154 Angle : 0.505 6.792 32838 Z= 0.252 Chirality : 0.040 0.213 3692 Planarity : 0.004 0.051 4206 Dihedral : 6.194 117.807 3261 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.69 % Allowed : 17.01 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.16), residues: 2929 helix: 2.29 (0.12), residues: 1722 sheet: -0.39 (0.32), residues: 251 loop : 0.56 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.005 0.001 HIS A4006 PHE 0.014 0.001 PHE A2912 TYR 0.019 0.001 TYR A1546 ARG 0.013 0.000 ARG A3164 Details of bonding type rmsd hydrogen bonds : bond 0.04159 ( 1420) hydrogen bonds : angle 3.99354 ( 4131) covalent geometry : bond 0.00367 (24213) covalent geometry : angle 0.50541 (32838) Misc. bond : bond 0.00090 ( 1) *********************** 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 347 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 277 time to evaluate : 2.986 Fit side-chains REVERT: A 1457 MET cc_start: 0.4812 (mpt) cc_final: 0.3965 (mpp) REVERT: A 1679 ARG cc_start: 0.7762 (ptp90) cc_final: 0.6780 (ptp-170) REVERT: A 2047 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8448 (tp40) REVERT: A 2163 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7130 (m-30) REVERT: A 2222 MET cc_start: 0.9016 (mtm) cc_final: 0.8629 (mtm) REVERT: A 2353 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7694 (tm) REVERT: A 2367 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7866 (m-30) REVERT: A 2444 GLU cc_start: 0.8261 (tt0) cc_final: 0.7814 (tm-30) REVERT: A 2471 GLN cc_start: 0.7184 (tt0) cc_final: 0.6733 (tt0) REVERT: A 2492 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7322 (mpt90) REVERT: A 2643 ARG cc_start: 0.8077 (ttm-80) cc_final: 0.7527 (mtm-85) REVERT: A 2666 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8356 (pt) REVERT: A 2763 ARG cc_start: 0.7337 (mtm110) cc_final: 0.6662 (mtt90) REVERT: A 2841 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6616 (mm-30) REVERT: A 2917 ASP cc_start: 0.7145 (OUTLIER) cc_final: 0.6733 (m-30) REVERT: A 3025 GLU cc_start: 0.6787 (mm-30) cc_final: 0.6425 (mm-30) REVERT: A 3077 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7278 (t0) REVERT: A 3181 ASN cc_start: 0.7946 (m-40) cc_final: 0.7725 (m110) REVERT: A 3188 HIS cc_start: 0.7708 (t-170) cc_final: 0.6411 (m-70) REVERT: A 3481 SER cc_start: 0.6285 (OUTLIER) cc_final: 0.5895 (p) REVERT: A 3639 GLU cc_start: 0.8287 (pm20) cc_final: 0.7804 (pm20) REVERT: A 3782 ARG cc_start: 0.7129 (ttp-170) cc_final: 0.6842 (ttp-170) REVERT: A 3791 MET cc_start: 0.6952 (tpt) cc_final: 0.6635 (tpt) REVERT: A 3792 GLN cc_start: 0.7139 (tt0) cc_final: 0.6833 (tt0) REVERT: A 4143 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7856 (tpt90) REVERT: A 4209 GLU cc_start: 0.7824 (tp30) cc_final: 0.7493 (tp30) REVERT: A 4276 ARG cc_start: 0.7693 (mmm-85) cc_final: 0.7424 (mmp-170) REVERT: A 4307 GLN cc_start: 0.7309 (mt0) cc_final: 0.6953 (tt0) REVERT: A 4314 ASP cc_start: 0.8131 (t70) cc_final: 0.7804 (t0) REVERT: A 4321 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8128 (mt) REVERT: A 4419 MET cc_start: 0.7363 (mtm) cc_final: 0.6786 (mtp) REVERT: A 4429 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.5990 (tm-30) REVERT: A 4488 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7233 (tt0) REVERT: A 4574 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6865 (ttmm) outliers start: 70 outliers final: 36 residues processed: 332 average time/residue: 1.4252 time to fit residues: 541.8586 Evaluate side-chains 323 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 272 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1655 LYS Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1977 CYS Chi-restraints excluded: chain A residue 2047 GLN Chi-restraints excluded: chain A residue 2156 LEU Chi-restraints excluded: chain A residue 2163 ASP Chi-restraints excluded: chain A residue 2260 SER Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2367 ASP Chi-restraints excluded: chain A residue 2388 ASP Chi-restraints excluded: chain A residue 2450 THR Chi-restraints excluded: chain A residue 2492 ARG Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2788 THR Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2867 MET Chi-restraints excluded: chain A residue 2917 ASP Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 3077 ASP Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3545 THR Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3702 THR Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3796 THR Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3847 LYS Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4137 ASN Chi-restraints excluded: chain A residue 4143 ARG Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4280 SER Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4429 GLN Chi-restraints excluded: chain A residue 4488 GLN Chi-restraints excluded: chain A residue 4574 LYS Chi-restraints excluded: chain A residue 4593 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 26 optimal weight: 0.8980 chunk 200 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 261 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 267 optimal weight: 0.9980 chunk 188 optimal weight: 8.9990 chunk 240 optimal weight: 0.7980 chunk 277 optimal weight: 0.8980 chunk 178 optimal weight: 8.9990 chunk 239 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1855 GLN A3009 ASN A3038 GLN ** A3233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3537 GLN A4079 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.136206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.101230 restraints weight = 29712.981| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.91 r_work: 0.3113 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24214 Z= 0.123 Angle : 0.486 6.421 32838 Z= 0.242 Chirality : 0.039 0.185 3692 Planarity : 0.004 0.051 4206 Dihedral : 6.090 118.797 3261 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.69 % Allowed : 17.16 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.16), residues: 2929 helix: 2.37 (0.12), residues: 1723 sheet: -0.31 (0.33), residues: 245 loop : 0.59 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.005 0.001 HIS A4006 PHE 0.013 0.001 PHE A3813 TYR 0.017 0.001 TYR A2496 ARG 0.014 0.000 ARG A3164 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 1420) hydrogen bonds : angle 3.90661 ( 4131) covalent geometry : bond 0.00281 (24213) covalent geometry : angle 0.48556 (32838) Misc. bond : bond 0.00047 ( 1) *********************** 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 358 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 288 time to evaluate : 2.666 Fit side-chains REVERT: A 1457 MET cc_start: 0.4772 (mpt) cc_final: 0.3900 (mpp) REVERT: A 1668 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7895 (pm20) REVERT: A 1679 ARG cc_start: 0.7721 (ptp90) cc_final: 0.6733 (ptp-170) REVERT: A 1799 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7229 (tt0) REVERT: A 1998 THR cc_start: 0.8293 (p) cc_final: 0.8074 (p) REVERT: A 2047 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8408 (tp40) REVERT: A 2113 ARG cc_start: 0.7447 (ttm170) cc_final: 0.7069 (tpp-160) REVERT: A 2163 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.7045 (m-30) REVERT: A 2222 MET cc_start: 0.8978 (mtm) cc_final: 0.8589 (mtm) REVERT: A 2353 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7597 (tm) REVERT: A 2367 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7874 (m-30) REVERT: A 2438 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7416 (tt0) REVERT: A 2444 GLU cc_start: 0.8219 (tt0) cc_final: 0.7759 (tm-30) REVERT: A 2471 GLN cc_start: 0.7092 (tt0) cc_final: 0.6666 (tt0) REVERT: A 2643 ARG cc_start: 0.8072 (ttm-80) cc_final: 0.7490 (mtm-85) REVERT: A 2666 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8296 (pt) REVERT: A 2763 ARG cc_start: 0.7262 (mtm110) cc_final: 0.6597 (mtt90) REVERT: A 2855 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7566 (mm) REVERT: A 2917 ASP cc_start: 0.7055 (OUTLIER) cc_final: 0.6653 (m-30) REVERT: A 3025 GLU cc_start: 0.6680 (mm-30) cc_final: 0.6338 (mm-30) REVERT: A 3077 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7180 (t0) REVERT: A 3160 ARG cc_start: 0.6049 (ttp-170) cc_final: 0.5828 (ttm-80) REVERT: A 3181 ASN cc_start: 0.7878 (m-40) cc_final: 0.7661 (m110) REVERT: A 3188 HIS cc_start: 0.7631 (t-170) cc_final: 0.6318 (m-70) REVERT: A 3481 SER cc_start: 0.6290 (OUTLIER) cc_final: 0.5923 (p) REVERT: A 3639 GLU cc_start: 0.8255 (pm20) cc_final: 0.7748 (pm20) REVERT: A 3782 ARG cc_start: 0.7101 (ttp-170) cc_final: 0.6827 (ttp-170) REVERT: A 3792 GLN cc_start: 0.7102 (tt0) cc_final: 0.6817 (tt0) REVERT: A 4143 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7774 (tpt90) REVERT: A 4209 GLU cc_start: 0.7764 (tp30) cc_final: 0.7390 (tp30) REVERT: A 4276 ARG cc_start: 0.7610 (mmm-85) cc_final: 0.7326 (mmp-170) REVERT: A 4307 GLN cc_start: 0.7245 (mt0) cc_final: 0.6865 (tt0) REVERT: A 4314 ASP cc_start: 0.8148 (t70) cc_final: 0.7839 (t0) REVERT: A 4321 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8094 (mt) REVERT: A 4419 MET cc_start: 0.7331 (mtm) cc_final: 0.6746 (mtp) REVERT: A 4429 GLN cc_start: 0.6897 (OUTLIER) cc_final: 0.6007 (tm-30) REVERT: A 4488 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7151 (tt0) REVERT: A 4574 LYS cc_start: 0.7072 (OUTLIER) cc_final: 0.6757 (ttmm) REVERT: A 4633 ARG cc_start: 0.7122 (mtm180) cc_final: 0.6506 (mtm110) outliers start: 70 outliers final: 40 residues processed: 342 average time/residue: 1.4512 time to fit residues: 570.1894 Evaluate side-chains 331 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 275 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1655 LYS Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1799 GLU Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1977 CYS Chi-restraints excluded: chain A residue 2047 GLN Chi-restraints excluded: chain A residue 2156 LEU Chi-restraints excluded: chain A residue 2162 SER Chi-restraints excluded: chain A residue 2163 ASP Chi-restraints excluded: chain A residue 2260 SER Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2367 ASP Chi-restraints excluded: chain A residue 2388 ASP Chi-restraints excluded: chain A residue 2438 GLU Chi-restraints excluded: chain A residue 2450 THR Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2696 SER Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2788 THR Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2867 MET Chi-restraints excluded: chain A residue 2917 ASP Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 3077 ASP Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3545 THR Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3691 ASP Chi-restraints excluded: chain A residue 3702 THR Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3796 THR Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3847 LYS Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4137 ASN Chi-restraints excluded: chain A residue 4143 ARG Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4280 SER Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4429 GLN Chi-restraints excluded: chain A residue 4488 GLN Chi-restraints excluded: chain A residue 4574 LYS Chi-restraints excluded: chain A residue 4593 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 61 optimal weight: 4.9990 chunk 264 optimal weight: 2.9990 chunk 256 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 232 optimal weight: 0.7980 chunk 190 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 250 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3038 GLN A3233 ASN A3537 GLN A4079 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.136117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.102614 restraints weight = 29752.138| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.87 r_work: 0.3112 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24214 Z= 0.127 Angle : 0.490 6.442 32838 Z= 0.244 Chirality : 0.039 0.161 3692 Planarity : 0.004 0.052 4206 Dihedral : 6.026 116.534 3261 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.76 % Allowed : 17.20 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.16), residues: 2929 helix: 2.42 (0.12), residues: 1717 sheet: -0.33 (0.32), residues: 246 loop : 0.62 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.004 0.001 HIS A4006 PHE 0.013 0.001 PHE A3813 TYR 0.018 0.001 TYR A1546 ARG 0.014 0.000 ARG A3164 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 1420) hydrogen bonds : angle 3.89705 ( 4131) covalent geometry : bond 0.00294 (24213) covalent geometry : angle 0.48992 (32838) Misc. bond : bond 0.00053 ( 1) *********************** 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 351 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 279 time to evaluate : 2.758 Fit side-chains REVERT: A 1457 MET cc_start: 0.4789 (mpt) cc_final: 0.3908 (mpp) REVERT: A 1492 ASP cc_start: 0.8198 (m-30) cc_final: 0.7891 (m-30) REVERT: A 1535 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7840 (m-30) REVERT: A 1679 ARG cc_start: 0.7724 (ptp90) cc_final: 0.6755 (ptp-170) REVERT: A 1855 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8232 (tp40) REVERT: A 1998 THR cc_start: 0.8329 (p) cc_final: 0.8106 (p) REVERT: A 2113 ARG cc_start: 0.7443 (ttm170) cc_final: 0.7084 (tpp-160) REVERT: A 2163 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.7035 (m-30) REVERT: A 2222 MET cc_start: 0.8993 (mtm) cc_final: 0.8542 (mtm) REVERT: A 2353 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7626 (tm) REVERT: A 2367 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7890 (m-30) REVERT: A 2438 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7444 (tt0) REVERT: A 2444 GLU cc_start: 0.8251 (tt0) cc_final: 0.7805 (tm-30) REVERT: A 2471 GLN cc_start: 0.7128 (tt0) cc_final: 0.6715 (tt0) REVERT: A 2643 ARG cc_start: 0.8067 (ttm-80) cc_final: 0.7520 (mtm-85) REVERT: A 2666 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8327 (pt) REVERT: A 2688 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7487 (tp30) REVERT: A 2763 ARG cc_start: 0.7305 (mtm110) cc_final: 0.6661 (mtt90) REVERT: A 2811 ARG cc_start: 0.8249 (ttm-80) cc_final: 0.7976 (ttm-80) REVERT: A 2855 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7602 (mm) REVERT: A 2917 ASP cc_start: 0.7068 (OUTLIER) cc_final: 0.6679 (m-30) REVERT: A 3025 GLU cc_start: 0.6696 (mm-30) cc_final: 0.6352 (mm-30) REVERT: A 3077 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7216 (t0) REVERT: A 3160 ARG cc_start: 0.6120 (ttp-170) cc_final: 0.5904 (ttm-80) REVERT: A 3181 ASN cc_start: 0.7917 (m-40) cc_final: 0.7705 (m110) REVERT: A 3188 HIS cc_start: 0.7667 (t-170) cc_final: 0.6366 (m-70) REVERT: A 3481 SER cc_start: 0.6311 (OUTLIER) cc_final: 0.5945 (p) REVERT: A 3639 GLU cc_start: 0.8256 (pm20) cc_final: 0.7762 (pm20) REVERT: A 3751 GLN cc_start: 0.7097 (tt0) cc_final: 0.6172 (mm110) REVERT: A 3782 ARG cc_start: 0.7122 (ttp-170) cc_final: 0.6846 (ttp-170) REVERT: A 3791 MET cc_start: 0.6810 (tpt) cc_final: 0.6469 (tpt) REVERT: A 3792 GLN cc_start: 0.7087 (tt0) cc_final: 0.6829 (tt0) REVERT: A 3910 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.7005 (mtm110) REVERT: A 4143 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7833 (tpt90) REVERT: A 4209 GLU cc_start: 0.7778 (tp30) cc_final: 0.7429 (tp30) REVERT: A 4276 ARG cc_start: 0.7646 (mmm-85) cc_final: 0.7370 (mmp-170) REVERT: A 4307 GLN cc_start: 0.7270 (mt0) cc_final: 0.6950 (tt0) REVERT: A 4314 ASP cc_start: 0.8161 (t70) cc_final: 0.7869 (t0) REVERT: A 4321 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8141 (mt) REVERT: A 4419 MET cc_start: 0.7360 (mtm) cc_final: 0.6747 (mtp) REVERT: A 4429 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6023 (tm-30) REVERT: A 4574 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6837 (ttmm) REVERT: A 4633 ARG cc_start: 0.7171 (mtm180) cc_final: 0.6566 (mtm110) outliers start: 72 outliers final: 41 residues processed: 333 average time/residue: 1.4329 time to fit residues: 548.3018 Evaluate side-chains 332 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 275 time to evaluate : 2.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1535 ASP Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1655 LYS Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1977 CYS Chi-restraints excluded: chain A residue 2156 LEU Chi-restraints excluded: chain A residue 2162 SER Chi-restraints excluded: chain A residue 2163 ASP Chi-restraints excluded: chain A residue 2260 SER Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2312 VAL Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2367 ASP Chi-restraints excluded: chain A residue 2388 ASP Chi-restraints excluded: chain A residue 2438 GLU Chi-restraints excluded: chain A residue 2450 THR Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2688 GLU Chi-restraints excluded: chain A residue 2696 SER Chi-restraints excluded: chain A residue 2755 MET Chi-restraints excluded: chain A residue 2788 THR Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2867 MET Chi-restraints excluded: chain A residue 2917 ASP Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 3077 ASP Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3545 THR Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3691 ASP Chi-restraints excluded: chain A residue 3702 THR Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3731 LEU Chi-restraints excluded: chain A residue 3796 THR Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3847 LYS Chi-restraints excluded: chain A residue 3910 ARG Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4137 ASN Chi-restraints excluded: chain A residue 4143 ARG Chi-restraints excluded: chain A residue 4163 SER Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4280 SER Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4429 GLN Chi-restraints excluded: chain A residue 4574 LYS Chi-restraints excluded: chain A residue 4593 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 72 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 117 optimal weight: 0.0070 chunk 2 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 241 optimal weight: 0.5980 chunk 237 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 31 optimal weight: 0.0770 chunk 40 optimal weight: 2.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2067 ASN A3038 GLN A3537 GLN A4079 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.104973 restraints weight = 29770.992| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.91 r_work: 0.3158 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24214 Z= 0.100 Angle : 0.470 7.976 32838 Z= 0.234 Chirality : 0.038 0.147 3692 Planarity : 0.004 0.058 4206 Dihedral : 5.832 116.811 3261 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.77 % Allowed : 18.31 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.16), residues: 2929 helix: 2.55 (0.12), residues: 1717 sheet: -0.20 (0.33), residues: 253 loop : 0.68 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2234 HIS 0.003 0.000 HIS A3907 PHE 0.018 0.001 PHE A3496 TYR 0.016 0.001 TYR A2496 ARG 0.015 0.000 ARG A3164 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 1420) hydrogen bonds : angle 3.79119 ( 4131) covalent geometry : bond 0.00214 (24213) covalent geometry : angle 0.47003 (32838) Misc. bond : bond 0.00004 ( 1) ********************** 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 331 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 285 time to evaluate : 2.955 Fit side-chains REVERT: A 1457 MET cc_start: 0.4586 (mpt) cc_final: 0.3753 (mpp) REVERT: A 1492 ASP cc_start: 0.8137 (m-30) cc_final: 0.7843 (m-30) REVERT: A 1668 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7905 (pm20) REVERT: A 1679 ARG cc_start: 0.7725 (ptp90) cc_final: 0.6754 (ptp-170) REVERT: A 1799 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7143 (tt0) REVERT: A 1855 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8215 (tp40) REVERT: A 1998 THR cc_start: 0.8305 (p) cc_final: 0.8077 (p) REVERT: A 2113 ARG cc_start: 0.7438 (ttm170) cc_final: 0.7072 (tpp-160) REVERT: A 2163 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.7023 (m-30) REVERT: A 2222 MET cc_start: 0.8951 (mtm) cc_final: 0.8511 (mtm) REVERT: A 2353 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7609 (tm) REVERT: A 2367 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7929 (m-30) REVERT: A 2444 GLU cc_start: 0.8202 (tt0) cc_final: 0.7749 (tm-30) REVERT: A 2471 GLN cc_start: 0.7171 (tt0) cc_final: 0.6783 (tt0) REVERT: A 2643 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7582 (mtm-85) REVERT: A 2666 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8310 (pt) REVERT: A 2763 ARG cc_start: 0.7302 (mtm110) cc_final: 0.6677 (mtt90) REVERT: A 2811 ARG cc_start: 0.8227 (ttm-80) cc_final: 0.7915 (ttm-80) REVERT: A 2855 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7580 (mm) REVERT: A 2917 ASP cc_start: 0.7023 (OUTLIER) cc_final: 0.6634 (m-30) REVERT: A 3025 GLU cc_start: 0.6655 (mm-30) cc_final: 0.6338 (mm-30) REVERT: A 3160 ARG cc_start: 0.6014 (ttp-170) cc_final: 0.5682 (ttt180) REVERT: A 3181 ASN cc_start: 0.7926 (m-40) cc_final: 0.7696 (m110) REVERT: A 3188 HIS cc_start: 0.7667 (t-170) cc_final: 0.6386 (m-70) REVERT: A 3481 SER cc_start: 0.6300 (OUTLIER) cc_final: 0.5932 (p) REVERT: A 3639 GLU cc_start: 0.8258 (pm20) cc_final: 0.7732 (mp0) REVERT: A 3706 SER cc_start: 0.8226 (OUTLIER) cc_final: 0.7971 (p) REVERT: A 3751 GLN cc_start: 0.7005 (tt0) cc_final: 0.6081 (mm110) REVERT: A 3782 ARG cc_start: 0.7134 (ttp-170) cc_final: 0.6871 (ttp-170) REVERT: A 3792 GLN cc_start: 0.7026 (tt0) cc_final: 0.6806 (tt0) REVERT: A 4209 GLU cc_start: 0.7752 (tp30) cc_final: 0.7398 (tp30) REVERT: A 4276 ARG cc_start: 0.7618 (mmm-85) cc_final: 0.7339 (mmp-170) REVERT: A 4314 ASP cc_start: 0.8145 (t70) cc_final: 0.7878 (t0) REVERT: A 4321 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8189 (mt) REVERT: A 4419 MET cc_start: 0.7377 (mtm) cc_final: 0.6792 (mtp) REVERT: A 4574 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6883 (ttmm) outliers start: 46 outliers final: 25 residues processed: 321 average time/residue: 1.5544 time to fit residues: 578.8342 Evaluate side-chains 312 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 276 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1573 THR Chi-restraints excluded: chain A residue 1666 LEU Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1698 ILE Chi-restraints excluded: chain A residue 1799 GLU Chi-restraints excluded: chain A residue 1851 THR Chi-restraints excluded: chain A residue 1977 CYS Chi-restraints excluded: chain A residue 2156 LEU Chi-restraints excluded: chain A residue 2163 ASP Chi-restraints excluded: chain A residue 2276 THR Chi-restraints excluded: chain A residue 2353 LEU Chi-restraints excluded: chain A residue 2367 ASP Chi-restraints excluded: chain A residue 2450 THR Chi-restraints excluded: chain A residue 2508 LEU Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2574 THR Chi-restraints excluded: chain A residue 2617 VAL Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2855 LEU Chi-restraints excluded: chain A residue 2867 MET Chi-restraints excluded: chain A residue 2917 ASP Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3481 SER Chi-restraints excluded: chain A residue 3503 ILE Chi-restraints excluded: chain A residue 3545 THR Chi-restraints excluded: chain A residue 3610 THR Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3796 THR Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 4137 ASN Chi-restraints excluded: chain A residue 4233 ILE Chi-restraints excluded: chain A residue 4321 LEU Chi-restraints excluded: chain A residue 4574 LYS Chi-restraints excluded: chain A residue 4593 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 290 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 89 optimal weight: 0.0470 chunk 124 optimal weight: 0.0370 chunk 43 optimal weight: 0.9980 chunk 172 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 179 optimal weight: 20.0000 chunk 176 optimal weight: 5.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2217 ASN A3038 GLN A3537 GLN A4079 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.138085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.103298 restraints weight = 29753.958| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.92 r_work: 0.3131 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24214 Z= 0.105 Angle : 0.474 7.515 32838 Z= 0.235 Chirality : 0.039 0.146 3692 Planarity : 0.004 0.057 4206 Dihedral : 5.726 112.712 3261 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.80 % Allowed : 18.46 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.16), residues: 2929 helix: 2.56 (0.12), residues: 1723 sheet: -0.23 (0.33), residues: 245 loop : 0.71 (0.21), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.005 0.001 HIS A4006 PHE 0.013 0.001 PHE A3813 TYR 0.017 0.001 TYR A1546 ARG 0.014 0.000 ARG A3164 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 1420) hydrogen bonds : angle 3.77475 ( 4131) covalent geometry : bond 0.00231 (24213) covalent geometry : angle 0.47373 (32838) Misc. bond : bond 0.00021 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20068.10 seconds wall clock time: 346 minutes 17.40 seconds (20777.40 seconds total)