Starting phenix.real_space_refine on Fri Sep 19 07:20:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bm0_44683/09_2025/9bm0_44683.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bm0_44683/09_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_44683/09_2025/9bm0_44683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bm0_44683/09_2025/9bm0_44683.map" model { file = "/net/cci-nas-00/data/ceres_data/9bm0_44683/09_2025/9bm0_44683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bm0_44683/09_2025/9bm0_44683.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.038 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.64, per 1000 atoms: 0.24 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: 2.07 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5588 Finding SS restraints... Secondary structure from input PDB file: 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: 1.59 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: 7.56 Time building geometry restraints manager: 2.76 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: 6.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.990 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.010 ------------------------------------------------------------------------------- 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 : 8.80 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (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 ARG 0.011 0.000 ARG A1621 TYR 0.013 0.001 TYR A3183 PHE 0.015 0.001 PHE A4624 TRP 0.029 0.001 TRP A1701 HIS 0.002 0.001 HIS A3188 Details of bonding type rmsd covalent geometry : bond 0.00444 (24213) covalent geometry : angle 0.63230 (32838) hydrogen bonds : bond 0.19972 ( 1420) hydrogen bonds : angle 6.37005 ( 4131) 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 : 0.741 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: 0.7504 (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: 0.8301 (mm) REVERT: A 2867 MET cc_start: 0.8323 (tpp) cc_final: 0.7977 (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: 0.7200 (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: 0.7781 time to fit residues: 362.4532 Evaluate side-chains 293 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 288 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.138501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.105175 restraints weight = 29458.199| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.86 r_work: 0.3194 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1593 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= 0.169 Angle : 0.552 7.041 32838 Z= 0.280 Chirality : 0.041 0.169 3692 Planarity : 0.004 0.050 4206 Dihedral : 6.640 120.443 3272 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.49 % Allowed : 14.09 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.16), residues: 2929 helix: 2.10 (0.12), residues: 1716 sheet: 0.05 (0.34), residues: 248 loop : 0.64 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A3164 TYR 0.018 0.001 TYR A3183 PHE 0.016 0.002 PHE A3813 TRP 0.024 0.001 TRP A1701 HIS 0.005 0.001 HIS A4187 Details of bonding type rmsd covalent geometry : bond 0.00391 (24213) covalent geometry : angle 0.55247 (32838) hydrogen bonds : bond 0.05223 ( 1420) hydrogen bonds : angle 4.44902 ( 4131) Misc. bond : bond 0.00445 ( 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 389 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 298 time to evaluate : 0.902 Fit side-chains REVERT: A 1457 MET cc_start: 0.4567 (mpt) cc_final: 0.4137 (mpp) REVERT: A 1679 ARG cc_start: 0.7726 (ptp90) cc_final: 0.6716 (ptp-170) REVERT: A 1798 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.6105 (ptp) REVERT: A 1829 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8402 (mmpt) REVERT: A 2012 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.7712 (tmt) REVERT: A 2222 MET cc_start: 0.9067 (mtm) cc_final: 0.8708 (mtm) REVERT: A 2306 ASP cc_start: 0.8323 (m-30) cc_final: 0.8020 (m-30) REVERT: A 2353 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7651 (tm) REVERT: A 2367 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7702 (m-30) REVERT: A 2438 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7501 (tt0) REVERT: A 2471 GLN cc_start: 0.7136 (tt0) cc_final: 0.6915 (tt0) REVERT: A 2492 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7095 (mpt90) REVERT: A 2508 LEU cc_start: 0.8087 (tp) cc_final: 0.7881 (tp) REVERT: A 2643 ARG cc_start: 0.8015 (ttm-80) cc_final: 0.7513 (mtm-85) REVERT: A 2666 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8283 (pt) REVERT: A 2763 ARG cc_start: 0.7289 (mtm110) cc_final: 0.6658 (mtt90) REVERT: A 2855 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7668 (mm) REVERT: A 2917 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6724 (m-30) REVERT: A 2975 ASP cc_start: 0.7448 (m-30) cc_final: 0.7170 (m-30) REVERT: A 3025 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6488 (mm-30) REVERT: A 3077 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7349 (t0) REVERT: A 3188 HIS cc_start: 0.7649 (t-170) cc_final: 0.6445 (m-70) REVERT: A 3616 ASP cc_start: 0.6817 (t70) cc_final: 0.6608 (m-30) REVERT: A 3791 MET cc_start: 0.6923 (tpt) cc_final: 0.6611 (tpt) REVERT: A 3792 GLN cc_start: 0.7072 (tt0) cc_final: 0.6766 (tt0) REVERT: A 3802 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7449 (mt) REVERT: A 3841 TYR cc_start: 0.8717 (m-80) cc_final: 0.8516 (m-80) REVERT: A 3950 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.7197 (mttp) REVERT: A 4209 GLU cc_start: 0.7789 (tp30) cc_final: 0.7362 (tp30) REVERT: A 4276 ARG cc_start: 0.7716 (mmm-85) cc_final: 0.7242 (mmp-170) REVERT: A 4314 ASP cc_start: 0.8082 (t70) cc_final: 0.7717 (t0) REVERT: A 4419 MET cc_start: 0.7385 (mtm) cc_final: 0.6781 (mtp) REVERT: A 4574 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6614 (ttmm) REVERT: A 4625 GLU cc_start: 0.7587 (tt0) cc_final: 0.7151 (mt-10) outliers start: 91 outliers final: 28 residues processed: 361 average time/residue: 0.7499 time to fit residues: 306.2705 Evaluate side-chains 304 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 262 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 2012 MET 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 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 4137 ASN 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 139 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 238 optimal weight: 0.9980 chunk 188 optimal weight: 0.7980 chunk 202 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 143 optimal weight: 0.0270 chunk 70 optimal weight: 0.6980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1855 GLN ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2752 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.138502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.103419 restraints weight = 29592.909| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.93 r_work: 0.3131 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1858 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= 0.117 Angle : 0.482 6.380 32838 Z= 0.243 Chirality : 0.039 0.148 3692 Planarity : 0.004 0.050 4206 Dihedral : 6.489 118.833 3270 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.69 % Allowed : 15.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.16), residues: 2929 helix: 2.33 (0.12), residues: 1711 sheet: -0.13 (0.33), residues: 249 loop : 0.70 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3164 TYR 0.021 0.001 TYR A2472 PHE 0.014 0.001 PHE A2912 TRP 0.018 0.001 TRP A1701 HIS 0.003 0.001 HIS A3047 Details of bonding type rmsd covalent geometry : bond 0.00252 (24213) covalent geometry : angle 0.48194 (32838) hydrogen bonds : bond 0.04323 ( 1420) hydrogen bonds : angle 4.13185 ( 4131) Misc. bond : bond 0.00013 ( 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 357 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 287 time to evaluate : 0.882 Fit side-chains REVERT: A 1457 MET cc_start: 0.4734 (mpt) cc_final: 0.4274 (mpp) REVERT: A 1679 ARG cc_start: 0.7678 (ptp90) cc_final: 0.6670 (ptp-170) REVERT: A 2222 MET cc_start: 0.9004 (mtm) cc_final: 0.8669 (mtm) REVERT: A 2231 SER cc_start: 0.8882 (t) cc_final: 0.8458 (m) REVERT: A 2306 ASP cc_start: 0.8094 (m-30) cc_final: 0.7769 (m-30) REVERT: A 2353 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7551 (tm) REVERT: A 2367 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7711 (m-30) REVERT: A 2471 GLN cc_start: 0.6997 (tt0) cc_final: 0.6786 (tt0) REVERT: A 2492 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7119 (mpt90) REVERT: A 2643 ARG cc_start: 0.8083 (ttm-80) cc_final: 0.7514 (mtm-85) REVERT: A 2666 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8210 (pt) REVERT: A 2855 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7622 (mm) REVERT: A 2917 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6680 (m-30) REVERT: A 3025 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6375 (mm-30) REVERT: A 3043 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7353 (mpt) REVERT: A 3181 ASN cc_start: 0.7839 (m-40) cc_final: 0.7638 (m110) REVERT: A 3188 HIS cc_start: 0.7583 (t-170) cc_final: 0.6341 (m-70) REVERT: A 3782 ARG cc_start: 0.6938 (ttp-170) cc_final: 0.6609 (ttp-170) REVERT: A 3791 MET cc_start: 0.6811 (tpt) cc_final: 0.6507 (tpt) REVERT: A 3792 GLN cc_start: 0.7058 (tt0) cc_final: 0.6763 (tt0) REVERT: A 3802 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7236 (mt) REVERT: A 3975 SER cc_start: 0.8306 (p) cc_final: 0.8098 (t) REVERT: A 4209 GLU cc_start: 0.7702 (tp30) cc_final: 0.7283 (tp30) REVERT: A 4276 ARG cc_start: 0.7597 (mmm-85) cc_final: 0.7214 (mmp-170) REVERT: A 4314 ASP cc_start: 0.8024 (t70) cc_final: 0.7672 (t0) REVERT: A 4419 MET cc_start: 0.7349 (mtm) cc_final: 0.6661 (mtp) outliers start: 70 outliers final: 29 residues processed: 340 average time/residue: 0.7197 time to fit residues: 278.1705 Evaluate side-chains 302 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 265 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1977 CYS 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 2388 ASP Chi-restraints excluded: chain A residue 2492 ARG 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 2785 THR 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 3043 MET Chi-restraints excluded: chain A residue 3048 GLU 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 3644 VAL 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 3981 THR Chi-restraints excluded: chain A residue 4045 SER Chi-restraints excluded: chain A residue 4163 SER Chi-restraints excluded: chain A residue 4280 SER Chi-restraints excluded: chain A residue 4475 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 183 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 159 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3537 GLN A3952 GLN A3968 GLN A4079 GLN A4397 HIS A4571 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.132481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.098733 restraints weight = 30002.975| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.80 r_work: 0.3048 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 24214 Z= 0.291 Angle : 0.615 7.331 32838 Z= 0.308 Chirality : 0.045 0.184 3692 Planarity : 0.005 0.050 4206 Dihedral : 6.699 115.226 3262 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.34 % Allowed : 15.39 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.15), residues: 2929 helix: 1.93 (0.12), residues: 1720 sheet: -0.40 (0.33), residues: 242 loop : 0.37 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A3164 TYR 0.025 0.002 TYR A1546 PHE 0.018 0.002 PHE A2165 TRP 0.017 0.002 TRP A2234 HIS 0.010 0.001 HIS A3047 Details of bonding type rmsd covalent geometry : bond 0.00720 (24213) covalent geometry : angle 0.61482 (32838) hydrogen bonds : bond 0.05323 ( 1420) hydrogen bonds : angle 4.36439 ( 4131) Misc. bond : bond 0.00238 ( 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 365 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 278 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 1457 MET cc_start: 0.4900 (mpt) cc_final: 0.4415 (mpp) REVERT: A 1535 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7795 (m-30) REVERT: A 1567 ARG cc_start: 0.6426 (OUTLIER) cc_final: 0.6189 (mtt90) REVERT: A 1679 ARG cc_start: 0.7744 (ptp90) cc_final: 0.6749 (ptp-170) REVERT: A 2012 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.7644 (tmt) REVERT: A 2163 ASP cc_start: 0.7490 (m-30) cc_final: 0.7150 (m-30) REVERT: A 2222 MET cc_start: 0.9053 (mtm) cc_final: 0.8640 (mtm) REVERT: A 2353 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7650 (tm) REVERT: A 2367 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7837 (m-30) REVERT: A 2492 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7339 (mpt90) REVERT: A 2643 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7575 (mtm-85) REVERT: A 2666 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8473 (pt) REVERT: A 2688 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7831 (tp30) REVERT: A 2763 ARG cc_start: 0.7359 (mtm110) cc_final: 0.6679 (mtt90) REVERT: A 2841 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6651 (mm-30) REVERT: A 2917 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6831 (m-30) REVERT: A 3025 GLU cc_start: 0.6896 (mm-30) cc_final: 0.6503 (mm-30) REVERT: A 3077 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.7340 (t0) REVERT: A 3100 GLU cc_start: 0.7833 (tt0) cc_final: 0.7081 (mp0) REVERT: A 3181 ASN cc_start: 0.7926 (m-40) cc_final: 0.7667 (m110) REVERT: A 3188 HIS cc_start: 0.7704 (t-170) cc_final: 0.6393 (m-70) REVERT: A 3782 ARG cc_start: 0.7122 (ttp-170) cc_final: 0.6803 (ttp-170) REVERT: A 3791 MET cc_start: 0.7074 (tpt) cc_final: 0.6737 (tpt) REVERT: A 3792 GLN cc_start: 0.7251 (tt0) cc_final: 0.6938 (tt0) REVERT: A 3802 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7525 (mt) REVERT: A 3950 LYS cc_start: 0.7560 (OUTLIER) cc_final: 0.7220 (ttmt) REVERT: A 4209 GLU cc_start: 0.7829 (tp30) cc_final: 0.7453 (tp30) REVERT: A 4307 GLN cc_start: 0.7361 (mt0) cc_final: 0.7004 (tt0) REVERT: A 4314 ASP cc_start: 0.8024 (t70) cc_final: 0.7688 (t0) REVERT: A 4329 ARG cc_start: 0.7172 (ttm170) cc_final: 0.6780 (mtp-110) REVERT: A 4419 MET cc_start: 0.7396 (mtm) cc_final: 0.6716 (mtp) REVERT: A 4459 ILE cc_start: 0.7283 (mm) cc_final: 0.6998 (mt) REVERT: A 4488 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7273 (tt0) REVERT: A 4589 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8237 (mt0) REVERT: A 4633 ARG cc_start: 0.7285 (mtm180) cc_final: 0.6708 (mtm110) outliers start: 87 outliers final: 43 residues processed: 342 average time/residue: 0.7654 time to fit residues: 295.9740 Evaluate side-chains 321 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 263 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 1564 GLU Chi-restraints excluded: chain A residue 1567 ARG 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 2012 MET Chi-restraints excluded: chain A residue 2156 LEU Chi-restraints excluded: chain A residue 2162 SER Chi-restraints excluded: chain A residue 2188 GLU 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 2552 VAL Chi-restraints excluded: chain A residue 2559 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 2788 THR Chi-restraints excluded: chain A residue 2841 GLU Chi-restraints excluded: chain A residue 2848 GLU Chi-restraints excluded: chain A residue 2867 MET Chi-restraints excluded: chain A residue 2917 ASP Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 2968 THR Chi-restraints excluded: chain A residue 3048 GLU 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 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 3950 LYS Chi-restraints excluded: chain A residue 3975 SER Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4127 THR Chi-restraints excluded: chain A residue 4131 ASN 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 4488 GLN Chi-restraints excluded: chain A residue 4574 LYS Chi-restraints excluded: chain A residue 4589 GLN 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 8 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 181 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 0.0570 chunk 243 optimal weight: 3.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A2928 GLN A3038 GLN ** A3233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3537 GLN A3952 GLN A4079 GLN A4571 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.135809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.100958 restraints weight = 29587.871| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.91 r_work: 0.3083 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24214 Z= 0.125 Angle : 0.492 6.526 32838 Z= 0.248 Chirality : 0.039 0.146 3692 Planarity : 0.004 0.049 4206 Dihedral : 6.381 123.403 3262 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.11 % Allowed : 16.12 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.16), residues: 2929 helix: 2.23 (0.12), residues: 1714 sheet: -0.36 (0.32), residues: 259 loop : 0.52 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3164 TYR 0.019 0.001 TYR A2496 PHE 0.014 0.001 PHE A2912 TRP 0.018 0.001 TRP A2234 HIS 0.004 0.001 HIS A4006 Details of bonding type rmsd covalent geometry : bond 0.00277 (24213) covalent geometry : angle 0.49227 (32838) hydrogen bonds : bond 0.04152 ( 1420) hydrogen bonds : angle 4.08046 ( 4131) Misc. bond : bond 0.00080 ( 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 358 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 277 time to evaluate : 0.993 Fit side-chains REVERT: A 1457 MET cc_start: 0.4801 (mpt) cc_final: 0.4261 (mpp) REVERT: A 1679 ARG cc_start: 0.7703 (ptp90) cc_final: 0.6701 (ptp-170) REVERT: A 2012 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.7762 (tmt) REVERT: A 2113 ARG cc_start: 0.7425 (ttm170) cc_final: 0.7044 (tpp-160) REVERT: A 2163 ASP cc_start: 0.7436 (m-30) cc_final: 0.7079 (m-30) REVERT: A 2222 MET cc_start: 0.8985 (mtm) cc_final: 0.8541 (mtm) REVERT: A 2353 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7581 (tm) REVERT: A 2367 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7804 (m-30) REVERT: A 2444 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: A 2492 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7120 (mpt90) REVERT: A 2643 ARG cc_start: 0.8190 (ttm-80) cc_final: 0.7582 (mtm-85) REVERT: A 2666 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8262 (pt) REVERT: A 2763 ARG cc_start: 0.7296 (mtm110) cc_final: 0.6613 (mtt90) REVERT: A 2841 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6528 (mm-30) REVERT: A 2917 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6674 (m-30) REVERT: A 3025 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6380 (mm-30) REVERT: A 3077 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7197 (t0) REVERT: A 3181 ASN cc_start: 0.7838 (m-40) cc_final: 0.7618 (m110) REVERT: A 3188 HIS cc_start: 0.7619 (t-170) cc_final: 0.6325 (m-70) REVERT: A 3481 SER cc_start: 0.6141 (OUTLIER) cc_final: 0.5727 (p) REVERT: A 3500 MET cc_start: 0.8181 (tpp) cc_final: 0.7876 (tpp) REVERT: A 3782 ARG cc_start: 0.7103 (ttp-170) cc_final: 0.6802 (ttp-170) REVERT: A 3791 MET cc_start: 0.6886 (tpt) cc_final: 0.6553 (tpt) REVERT: A 3792 GLN cc_start: 0.7116 (tt0) cc_final: 0.6825 (tt0) REVERT: A 3950 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7117 (ttmt) REVERT: A 4143 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7762 (tpt90) REVERT: A 4209 GLU cc_start: 0.7793 (tp30) cc_final: 0.7411 (tp30) REVERT: A 4276 ARG cc_start: 0.7644 (mmm-85) cc_final: 0.7348 (mmp-170) REVERT: A 4307 GLN cc_start: 0.7226 (mt0) cc_final: 0.6855 (tt0) REVERT: A 4314 ASP cc_start: 0.8068 (t70) cc_final: 0.7726 (t0) REVERT: A 4321 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8047 (mt) REVERT: A 4419 MET cc_start: 0.7298 (mtm) cc_final: 0.6721 (mtp) REVERT: A 4429 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6022 (tm-30) REVERT: A 4459 ILE cc_start: 0.7239 (mm) cc_final: 0.6951 (mt) REVERT: A 4488 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7158 (tt0) REVERT: A 4574 LYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6663 (ttmm) REVERT: A 4633 ARG cc_start: 0.7069 (mtm180) cc_final: 0.6466 (mtm110) outliers start: 81 outliers final: 25 residues processed: 339 average time/residue: 0.7351 time to fit residues: 282.5712 Evaluate side-chains 308 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 267 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 1691 SER Chi-restraints excluded: chain A residue 1977 CYS Chi-restraints excluded: chain A residue 2012 MET 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 2444 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 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 3077 ASP 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 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 3796 THR Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3950 LYS Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4121 CYS Chi-restraints excluded: chain A residue 4131 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 4488 GLN 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 225 optimal weight: 6.9990 chunk 259 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 260 optimal weight: 0.8980 chunk 241 optimal weight: 1.9990 chunk 176 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 A2475 ASN ** A3233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3537 GLN A3952 GLN A4079 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.134351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.099193 restraints weight = 29897.237| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.92 r_work: 0.3061 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2297 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= 0.177 Angle : 0.525 6.987 32838 Z= 0.262 Chirality : 0.041 0.156 3692 Planarity : 0.004 0.050 4206 Dihedral : 6.359 118.011 3262 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.96 % Allowed : 16.62 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.16), residues: 2929 helix: 2.18 (0.12), residues: 1720 sheet: -0.40 (0.32), residues: 245 loop : 0.49 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1467 TYR 0.020 0.001 TYR A1546 PHE 0.014 0.002 PHE A2912 TRP 0.017 0.001 TRP A2234 HIS 0.005 0.001 HIS A3047 Details of bonding type rmsd covalent geometry : bond 0.00426 (24213) covalent geometry : angle 0.52503 (32838) hydrogen bonds : bond 0.04397 ( 1420) hydrogen bonds : angle 4.09970 ( 4131) Misc. bond : bond 0.00106 ( 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 350 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 273 time to evaluate : 0.796 Fit side-chains REVERT: A 1457 MET cc_start: 0.4867 (mpt) cc_final: 0.4369 (mpp) REVERT: A 1679 ARG cc_start: 0.7720 (ptp90) cc_final: 0.6747 (ptp-170) REVERT: A 2012 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.7795 (tmt) REVERT: A 2145 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7948 (mmp) REVERT: A 2163 ASP cc_start: 0.7474 (m-30) cc_final: 0.7131 (m-30) REVERT: A 2222 MET cc_start: 0.9036 (mtm) cc_final: 0.8673 (mtm) REVERT: A 2306 ASP cc_start: 0.8251 (m-30) cc_final: 0.7967 (m-30) REVERT: A 2353 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7623 (tm) REVERT: A 2367 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7855 (m-30) REVERT: A 2444 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: A 2492 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7289 (mpt90) REVERT: A 2643 ARG cc_start: 0.8232 (ttm-80) cc_final: 0.7620 (mtm-85) REVERT: A 2666 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8349 (pt) REVERT: A 2841 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6602 (mm-30) REVERT: A 2917 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6744 (m-30) REVERT: A 3025 GLU cc_start: 0.6781 (mm-30) cc_final: 0.6409 (mm-30) REVERT: A 3077 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7288 (t0) REVERT: A 3181 ASN cc_start: 0.7917 (m-40) cc_final: 0.7703 (m110) REVERT: A 3188 HIS cc_start: 0.7690 (t-170) cc_final: 0.6364 (m-70) REVERT: A 3481 SER cc_start: 0.6106 (OUTLIER) cc_final: 0.5721 (p) REVERT: A 3782 ARG cc_start: 0.7124 (ttp-170) cc_final: 0.6833 (ttp-170) REVERT: A 3791 MET cc_start: 0.6950 (tpt) cc_final: 0.6600 (tpt) REVERT: A 3792 GLN cc_start: 0.7165 (tt0) cc_final: 0.6841 (tt0) REVERT: A 3802 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7341 (mt) REVERT: A 4143 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7879 (tpt90) REVERT: A 4209 GLU cc_start: 0.7836 (tp30) cc_final: 0.7432 (tp30) REVERT: A 4276 ARG cc_start: 0.7728 (mmm-85) cc_final: 0.7408 (mmp-170) REVERT: A 4307 GLN cc_start: 0.7287 (mt0) cc_final: 0.6905 (tt0) REVERT: A 4314 ASP cc_start: 0.8114 (t70) cc_final: 0.7800 (t0) REVERT: A 4321 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8093 (mt) REVERT: A 4419 MET cc_start: 0.7332 (mtm) cc_final: 0.6754 (mtp) REVERT: A 4429 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6022 (tm-30) REVERT: A 4459 ILE cc_start: 0.7308 (mm) cc_final: 0.7056 (mt) REVERT: A 4488 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7230 (tt0) REVERT: A 4574 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6772 (ttmm) REVERT: A 4633 ARG cc_start: 0.7164 (mtm180) cc_final: 0.6568 (mtm110) outliers start: 77 outliers final: 34 residues processed: 334 average time/residue: 0.6912 time to fit residues: 262.8056 Evaluate side-chains 318 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 267 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 1691 SER Chi-restraints excluded: chain A residue 1977 CYS Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2145 MET 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 2444 GLU Chi-restraints excluded: chain A residue 2450 THR 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 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 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 3796 THR 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 3975 SER Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4052 SER Chi-restraints excluded: chain A residue 4131 ASN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 3 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 278 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 168 optimal weight: 0.8980 chunk 225 optimal weight: 2.9990 chunk 149 optimal weight: 0.4980 chunk 184 optimal weight: 3.9990 chunk 198 optimal weight: 0.9980 chunk 266 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 A3537 GLN A3952 GLN A4079 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.135286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.100158 restraints weight = 29673.252| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.92 r_work: 0.3080 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24214 Z= 0.136 Angle : 0.495 6.588 32838 Z= 0.248 Chirality : 0.040 0.145 3692 Planarity : 0.004 0.050 4206 Dihedral : 6.249 120.316 3261 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.03 % Allowed : 16.89 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.16), residues: 2929 helix: 2.27 (0.12), residues: 1724 sheet: -0.33 (0.33), residues: 239 loop : 0.52 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A2763 TYR 0.017 0.001 TYR A2496 PHE 0.013 0.001 PHE A2912 TRP 0.018 0.001 TRP A2234 HIS 0.004 0.001 HIS A4006 Details of bonding type rmsd covalent geometry : bond 0.00315 (24213) covalent geometry : angle 0.49520 (32838) hydrogen bonds : bond 0.04068 ( 1420) hydrogen bonds : angle 3.99485 ( 4131) Misc. bond : bond 0.00067 ( 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 358 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 279 time to evaluate : 1.012 Fit side-chains REVERT: A 1457 MET cc_start: 0.4821 (mpt) cc_final: 0.4346 (mpp) REVERT: A 1679 ARG cc_start: 0.7721 (ptp90) cc_final: 0.6742 (ptp-170) REVERT: A 1998 THR cc_start: 0.8297 (p) cc_final: 0.8088 (p) REVERT: A 2012 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.7859 (tmt) REVERT: A 2113 ARG cc_start: 0.7443 (ttm170) cc_final: 0.7065 (tpp-160) REVERT: A 2145 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7930 (mmp) REVERT: A 2163 ASP cc_start: 0.7463 (m-30) cc_final: 0.7091 (m-30) REVERT: A 2222 MET cc_start: 0.8999 (mtm) cc_final: 0.8527 (mtm) REVERT: A 2353 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7589 (tm) REVERT: A 2367 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7849 (m-30) REVERT: A 2444 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7728 (tm-30) REVERT: A 2492 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7258 (mpt90) REVERT: A 2643 ARG cc_start: 0.8191 (ttm-80) cc_final: 0.7567 (mtm-85) REVERT: A 2666 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8323 (pt) REVERT: A 2763 ARG cc_start: 0.7292 (mtm110) cc_final: 0.6589 (mtt90) REVERT: A 2841 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6566 (mm-30) REVERT: A 2917 ASP cc_start: 0.7124 (OUTLIER) cc_final: 0.6704 (m-30) REVERT: A 3025 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6391 (mm-30) REVERT: A 3077 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7218 (t0) REVERT: A 3181 ASN cc_start: 0.7892 (m-40) cc_final: 0.7671 (m110) REVERT: A 3188 HIS cc_start: 0.7681 (t-170) cc_final: 0.6357 (m-70) REVERT: A 3481 SER cc_start: 0.6207 (OUTLIER) cc_final: 0.5835 (p) REVERT: A 3782 ARG cc_start: 0.7096 (ttp-170) cc_final: 0.6814 (ttp-170) REVERT: A 3791 MET cc_start: 0.6886 (tpt) cc_final: 0.6585 (tpt) REVERT: A 3792 GLN cc_start: 0.7100 (tt0) cc_final: 0.6795 (tt0) REVERT: A 4143 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7822 (tpt90) REVERT: A 4209 GLU cc_start: 0.7801 (tp30) cc_final: 0.7435 (tp30) REVERT: A 4225 ASP cc_start: 0.7822 (t0) cc_final: 0.7588 (t0) REVERT: A 4276 ARG cc_start: 0.7663 (mmm-85) cc_final: 0.7345 (mmp-170) REVERT: A 4307 GLN cc_start: 0.7272 (mt0) cc_final: 0.6897 (tt0) REVERT: A 4314 ASP cc_start: 0.8097 (t70) cc_final: 0.7762 (t0) REVERT: A 4321 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8120 (mt) REVERT: A 4419 MET cc_start: 0.7288 (mtm) cc_final: 0.6685 (mtp) REVERT: A 4429 GLN cc_start: 0.6910 (OUTLIER) cc_final: 0.5970 (tm-30) REVERT: A 4459 ILE cc_start: 0.7321 (mm) cc_final: 0.7075 (mt) REVERT: A 4488 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7180 (tt0) REVERT: A 4574 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6678 (ttmm) REVERT: A 4633 ARG cc_start: 0.7139 (mtm180) cc_final: 0.6536 (mtm110) outliers start: 79 outliers final: 39 residues processed: 338 average time/residue: 0.7333 time to fit residues: 283.0321 Evaluate side-chains 321 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 266 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 1691 SER Chi-restraints excluded: chain A residue 1977 CYS Chi-restraints excluded: chain A residue 2012 MET Chi-restraints excluded: chain A residue 2145 MET 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 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 2444 GLU Chi-restraints excluded: chain A residue 2450 THR 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 2617 VAL Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2668 LEU 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 2867 MET Chi-restraints excluded: chain A residue 2917 ASP Chi-restraints excluded: chain A residue 2953 MET 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 4131 ASN 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 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 95 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 85 optimal weight: 0.0870 chunk 227 optimal weight: 0.9980 chunk 230 optimal weight: 0.9990 chunk 104 optimal weight: 0.0870 chunk 274 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.5536 ------------------------------------------------------------------------------- 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 A3537 GLN A4079 GLN A4386 ASN A4526 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.102842 restraints weight = 29629.932| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.91 r_work: 0.3132 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 24214 Z= 0.106 Angle : 0.473 6.370 32838 Z= 0.237 Chirality : 0.039 0.155 3692 Planarity : 0.004 0.050 4206 Dihedral : 5.976 119.067 3261 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.46 % Allowed : 17.54 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.41 (0.16), residues: 2929 helix: 2.46 (0.12), residues: 1717 sheet: -0.24 (0.33), residues: 253 loop : 0.64 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3164 TYR 0.016 0.001 TYR A2496 PHE 0.013 0.001 PHE A3813 TRP 0.018 0.001 TRP A2234 HIS 0.003 0.000 HIS A3907 Details of bonding type rmsd covalent geometry : bond 0.00233 (24213) covalent geometry : angle 0.47345 (32838) hydrogen bonds : bond 0.03667 ( 1420) hydrogen bonds : angle 3.85838 ( 4131) Misc. bond : bond 0.00025 ( 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 347 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 283 time to evaluate : 0.929 Fit side-chains REVERT: A 1457 MET cc_start: 0.4739 (mpt) cc_final: 0.3844 (mpp) REVERT: A 1492 ASP cc_start: 0.8213 (m-30) cc_final: 0.7909 (m-30) REVERT: A 1668 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7887 (pm20) REVERT: A 1679 ARG cc_start: 0.7728 (ptp90) cc_final: 0.6760 (ptp-170) REVERT: A 1855 GLN cc_start: 0.8508 (mm-40) cc_final: 0.8221 (tp40) REVERT: A 1998 THR cc_start: 0.8314 (p) cc_final: 0.8092 (p) REVERT: A 2163 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7063 (m-30) REVERT: A 2222 MET cc_start: 0.8967 (mtm) cc_final: 0.8554 (mtm) REVERT: A 2353 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7600 (tm) REVERT: A 2367 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7889 (m-30) REVERT: A 2444 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7649 (tm-30) REVERT: A 2643 ARG cc_start: 0.8169 (ttm-80) cc_final: 0.7646 (mtm-85) REVERT: A 2666 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8330 (pt) REVERT: A 2763 ARG cc_start: 0.7342 (mtm110) cc_final: 0.6666 (mtt90) REVERT: A 2841 GLU cc_start: 0.6929 (pt0) cc_final: 0.6580 (mm-30) REVERT: A 2855 LEU cc_start: 0.7708 (mm) cc_final: 0.7424 (mm) REVERT: A 2917 ASP cc_start: 0.7064 (OUTLIER) cc_final: 0.6652 (m-30) REVERT: A 3025 GLU cc_start: 0.6716 (mm-30) cc_final: 0.6397 (mm-30) REVERT: A 3160 ARG cc_start: 0.6271 (ttp-170) cc_final: 0.6034 (ttm-80) REVERT: A 3181 ASN cc_start: 0.7940 (m-40) cc_final: 0.7712 (m110) REVERT: A 3188 HIS cc_start: 0.7671 (t-170) cc_final: 0.6387 (m-70) REVERT: A 3481 SER cc_start: 0.6349 (OUTLIER) cc_final: 0.5933 (p) REVERT: A 3706 SER cc_start: 0.8244 (OUTLIER) cc_final: 0.7972 (p) REVERT: A 3751 GLN cc_start: 0.7087 (tt0) cc_final: 0.6124 (mm110) REVERT: A 3792 GLN cc_start: 0.7150 (tt0) cc_final: 0.6858 (tt0) REVERT: A 4117 GLN cc_start: 0.8402 (mt0) cc_final: 0.8198 (tt0) REVERT: A 4143 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7820 (tpt90) REVERT: A 4209 GLU cc_start: 0.7790 (tp30) cc_final: 0.7443 (tp30) REVERT: A 4225 ASP cc_start: 0.7862 (t0) cc_final: 0.7605 (t0) REVERT: A 4276 ARG cc_start: 0.7673 (mmm-85) cc_final: 0.7345 (mmp-170) REVERT: A 4307 GLN cc_start: 0.7322 (mt0) cc_final: 0.6998 (tt0) REVERT: A 4314 ASP cc_start: 0.8131 (t70) cc_final: 0.7828 (t0) REVERT: A 4321 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8236 (mt) REVERT: A 4419 MET cc_start: 0.7354 (mtm) cc_final: 0.6745 (mtp) REVERT: A 4429 GLN cc_start: 0.7001 (OUTLIER) cc_final: 0.6055 (tm-30) REVERT: A 4459 ILE cc_start: 0.7416 (mm) cc_final: 0.7200 (mt) REVERT: A 4574 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6849 (ttmm) outliers start: 64 outliers final: 30 residues processed: 335 average time/residue: 0.6807 time to fit residues: 260.2924 Evaluate side-chains 311 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 269 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 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 2444 GLU Chi-restraints excluded: chain A residue 2450 THR 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 2953 MET 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 3610 THR Chi-restraints excluded: chain A residue 3702 THR Chi-restraints excluded: chain A residue 3706 SER Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4131 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 116 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 277 optimal weight: 0.9980 chunk 278 optimal weight: 7.9990 chunk 31 optimal weight: 0.4980 chunk 96 optimal weight: 5.9990 chunk 140 optimal weight: 0.0870 chunk 17 optimal weight: 0.9980 chunk 239 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 228 optimal weight: 0.3980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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** ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3038 GLN A3537 GLN A4079 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.137613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.103648 restraints weight = 29740.368| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.95 r_work: 0.3138 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24214 Z= 0.109 Angle : 0.480 7.031 32838 Z= 0.238 Chirality : 0.039 0.149 3692 Planarity : 0.004 0.051 4206 Dihedral : 5.871 116.113 3261 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.00 % Allowed : 18.16 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.16), residues: 2929 helix: 2.51 (0.12), residues: 1717 sheet: -0.20 (0.33), residues: 253 loop : 0.67 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2763 TYR 0.017 0.001 TYR A1546 PHE 0.013 0.001 PHE A3813 TRP 0.017 0.001 TRP A2234 HIS 0.004 0.000 HIS A4006 Details of bonding type rmsd covalent geometry : bond 0.00242 (24213) covalent geometry : angle 0.47952 (32838) hydrogen bonds : bond 0.03648 ( 1420) hydrogen bonds : angle 3.83549 ( 4131) Misc. bond : bond 0.00028 ( 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 329 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 277 time to evaluate : 0.969 Fit side-chains REVERT: A 1457 MET cc_start: 0.4574 (mpt) cc_final: 0.3745 (mpp) REVERT: A 1492 ASP cc_start: 0.8160 (m-30) cc_final: 0.7859 (m-30) REVERT: A 1669 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.6987 (t0) REVERT: A 1679 ARG cc_start: 0.7708 (ptp90) cc_final: 0.6727 (ptp-170) REVERT: A 1855 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8178 (tp40) REVERT: A 1998 THR cc_start: 0.8273 (p) cc_final: 0.8046 (p) REVERT: A 2163 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.7009 (m-30) REVERT: A 2222 MET cc_start: 0.8967 (mtm) cc_final: 0.8534 (mtm) REVERT: A 2353 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7579 (tm) REVERT: A 2367 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7873 (m-30) REVERT: A 2444 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: A 2643 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7549 (mtm-85) REVERT: A 2666 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8317 (pt) REVERT: A 2763 ARG cc_start: 0.7297 (mtm110) cc_final: 0.6618 (mtt90) REVERT: A 2855 LEU cc_start: 0.7703 (mm) cc_final: 0.7423 (mm) REVERT: A 2917 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.6594 (m-30) REVERT: A 3025 GLU cc_start: 0.6660 (mm-30) cc_final: 0.6341 (mm-30) REVERT: A 3160 ARG cc_start: 0.6198 (ttp-170) cc_final: 0.5856 (ttt180) REVERT: A 3163 LYS cc_start: 0.7010 (tmmt) cc_final: 0.6469 (tmtt) REVERT: A 3181 ASN cc_start: 0.7934 (m-40) cc_final: 0.7713 (m110) REVERT: A 3188 HIS cc_start: 0.7632 (t-170) cc_final: 0.6340 (m-70) REVERT: A 3481 SER cc_start: 0.6282 (OUTLIER) cc_final: 0.5923 (p) REVERT: A 3706 SER cc_start: 0.8207 (OUTLIER) cc_final: 0.7935 (p) REVERT: A 3751 GLN cc_start: 0.7011 (tt0) cc_final: 0.6090 (mm110) REVERT: A 3791 MET cc_start: 0.6793 (tpt) cc_final: 0.6470 (tpt) REVERT: A 3792 GLN cc_start: 0.6993 (tt0) cc_final: 0.6740 (tt0) REVERT: A 4143 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7774 (tpt90) REVERT: A 4209 GLU cc_start: 0.7777 (tp30) cc_final: 0.7413 (tp30) REVERT: A 4225 ASP cc_start: 0.7853 (t0) cc_final: 0.7614 (t0) REVERT: A 4276 ARG cc_start: 0.7630 (mmm-85) cc_final: 0.7300 (mmp-170) REVERT: A 4314 ASP cc_start: 0.8159 (t70) cc_final: 0.7857 (t0) REVERT: A 4321 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8148 (mt) REVERT: A 4419 MET cc_start: 0.7355 (mtm) cc_final: 0.6739 (mtp) REVERT: A 4429 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.5981 (tm-30) REVERT: A 4459 ILE cc_start: 0.7323 (mm) cc_final: 0.7117 (mt) outliers start: 52 outliers final: 33 residues processed: 317 average time/residue: 0.6716 time to fit residues: 242.9603 Evaluate side-chains 316 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 271 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 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 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 2444 GLU Chi-restraints excluded: chain A residue 2450 THR 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 2953 MET 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 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 3796 THR Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3912 ASN Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4131 ASN 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 4593 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 292 optimal weight: 0.6980 chunk 227 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 286 optimal weight: 0.0470 chunk 184 optimal weight: 3.9990 chunk 206 optimal weight: 0.9980 chunk 240 optimal weight: 0.4980 chunk 70 optimal weight: 0.7980 chunk 273 optimal weight: 3.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 A3537 GLN A4079 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.138084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.103380 restraints weight = 29655.791| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.92 r_work: 0.3127 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24214 Z= 0.105 Angle : 0.475 7.681 32838 Z= 0.236 Chirality : 0.039 0.146 3692 Planarity : 0.004 0.051 4206 Dihedral : 5.774 114.263 3261 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.92 % Allowed : 18.23 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.55 (0.16), residues: 2929 helix: 2.57 (0.12), residues: 1716 sheet: -0.17 (0.33), residues: 253 loop : 0.68 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1467 TYR 0.017 0.001 TYR A1546 PHE 0.013 0.001 PHE A3813 TRP 0.018 0.001 TRP A2234 HIS 0.005 0.000 HIS A4006 Details of bonding type rmsd covalent geometry : bond 0.00233 (24213) covalent geometry : angle 0.47482 (32838) hydrogen bonds : bond 0.03570 ( 1420) hydrogen bonds : angle 3.79462 ( 4131) Misc. bond : bond 0.00022 ( 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 330 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 280 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 1457 MET cc_start: 0.4555 (mpt) cc_final: 0.3718 (mpp) REVERT: A 1492 ASP cc_start: 0.8116 (m-30) cc_final: 0.7831 (m-30) REVERT: A 1679 ARG cc_start: 0.7672 (ptp90) cc_final: 0.6692 (ptp-170) REVERT: A 1855 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8174 (tp40) REVERT: A 1998 THR cc_start: 0.8227 (p) cc_final: 0.8004 (p) REVERT: A 2163 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.6998 (m-30) REVERT: A 2222 MET cc_start: 0.8957 (mtm) cc_final: 0.8508 (mtm) REVERT: A 2353 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7524 (tm) REVERT: A 2367 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7883 (m-30) REVERT: A 2444 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7589 (tm-30) REVERT: A 2643 ARG cc_start: 0.8099 (ttm-80) cc_final: 0.7505 (mtm-85) REVERT: A 2666 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8287 (pt) REVERT: A 2763 ARG cc_start: 0.7275 (mtm110) cc_final: 0.6584 (mtt90) REVERT: A 2855 LEU cc_start: 0.7669 (mm) cc_final: 0.7377 (mm) REVERT: A 2917 ASP cc_start: 0.6973 (OUTLIER) cc_final: 0.6532 (m-30) REVERT: A 3160 ARG cc_start: 0.6056 (ttp-170) cc_final: 0.5637 (ttt180) REVERT: A 3181 ASN cc_start: 0.7906 (m-40) cc_final: 0.7694 (m110) REVERT: A 3188 HIS cc_start: 0.7584 (t-170) cc_final: 0.6269 (m-70) REVERT: A 3481 SER cc_start: 0.6280 (OUTLIER) cc_final: 0.5910 (p) REVERT: A 3706 SER cc_start: 0.8163 (OUTLIER) cc_final: 0.7900 (p) REVERT: A 3751 GLN cc_start: 0.6979 (tt0) cc_final: 0.6064 (mm110) REVERT: A 3792 GLN cc_start: 0.6974 (tt0) cc_final: 0.6756 (tt0) REVERT: A 4143 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7711 (tpt90) REVERT: A 4209 GLU cc_start: 0.7704 (tp30) cc_final: 0.7337 (tp30) REVERT: A 4225 ASP cc_start: 0.7844 (t0) cc_final: 0.7597 (t0) REVERT: A 4276 ARG cc_start: 0.7585 (mmm-85) cc_final: 0.7256 (mmp-170) REVERT: A 4314 ASP cc_start: 0.8144 (t70) cc_final: 0.7871 (t0) REVERT: A 4321 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8170 (mt) REVERT: A 4419 MET cc_start: 0.7321 (mtm) cc_final: 0.6730 (mtp) REVERT: A 4429 GLN cc_start: 0.6875 (OUTLIER) cc_final: 0.5933 (tm-30) REVERT: A 4459 ILE cc_start: 0.7306 (mm) cc_final: 0.7104 (mt) REVERT: A 4574 LYS cc_start: 0.6933 (OUTLIER) cc_final: 0.6662 (ttmm) outliers start: 50 outliers final: 34 residues processed: 319 average time/residue: 0.7374 time to fit residues: 268.6198 Evaluate side-chains 320 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 274 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 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 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 2444 GLU Chi-restraints excluded: chain A residue 2450 THR 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 2755 MET Chi-restraints excluded: chain A residue 2867 MET Chi-restraints excluded: chain A residue 2917 ASP Chi-restraints excluded: chain A residue 2953 MET 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 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 3796 THR Chi-restraints excluded: chain A residue 3809 SER Chi-restraints excluded: chain A residue 3912 ASN Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4131 ASN 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 42 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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** ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3038 GLN A3537 GLN A4079 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.135407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.101731 restraints weight = 29588.522| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.85 r_work: 0.3118 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24214 Z= 0.157 Angle : 0.517 7.493 32838 Z= 0.257 Chirality : 0.040 0.158 3692 Planarity : 0.004 0.052 4206 Dihedral : 5.969 112.442 3261 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.26 % Allowed : 18.04 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.16), residues: 2929 helix: 2.44 (0.12), residues: 1718 sheet: -0.33 (0.32), residues: 252 loop : 0.64 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1467 TYR 0.020 0.001 TYR A1546 PHE 0.014 0.001 PHE A1568 TRP 0.015 0.001 TRP A2234 HIS 0.006 0.001 HIS A4006 Details of bonding type rmsd covalent geometry : bond 0.00374 (24213) covalent geometry : angle 0.51744 (32838) hydrogen bonds : bond 0.04060 ( 1420) hydrogen bonds : angle 3.93419 ( 4131) Misc. bond : bond 0.00087 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10016.41 seconds wall clock time: 170 minutes 45.96 seconds (10245.96 seconds total)