Starting phenix.real_space_refine on Sat Jun 21 18:44:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bmb_44694/06_2025/9bmb_44694.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bmb_44694/06_2025/9bmb_44694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bmb_44694/06_2025/9bmb_44694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bmb_44694/06_2025/9bmb_44694.map" model { file = "/net/cci-nas-00/data/ceres_data/9bmb_44694/06_2025/9bmb_44694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bmb_44694/06_2025/9bmb_44694.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 2 5.21 5 S 122 5.16 5 C 15646 2.51 5 N 4254 2.21 5 O 4584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24617 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 24503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3043, 24503 Classifications: {'peptide': 3043} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 130, 'TRANS': 2909} Chain breaks: 3 Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 114 Unusual residues: {' MG': 2, 'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 14.81, per 1000 atoms: 0.60 Number of scatterers: 24617 At special positions: 0 Unit cell: (126.146, 170.123, 177.067, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 122 16.00 P 9 15.00 Mg 2 11.99 O 4584 8.00 N 4254 7.00 C 15646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.17 Conformation dependent library (CDL) restraints added in 3.4 seconds 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5788 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 19 sheets defined 63.6% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.14 Creating SS restraints... Processing helix chain 'A' and resid 1327 through 1348 Processing helix chain 'A' and resid 1350 through 1354 Processing helix chain 'A' and resid 1355 through 1372 Processing helix chain 'A' and resid 1374 through 1379 Processing helix chain 'A' and resid 1380 through 1396 Processing helix chain 'A' and resid 1396 through 1404 Processing helix chain 'A' and resid 1410 through 1421 Processing helix chain 'A' and resid 1430 through 1437 removed outlier: 4.163A pdb=" N ILE A1434 " --> pdb=" O THR A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1473 Processing helix chain 'A' and resid 1489 through 1507 Processing helix chain 'A' and resid 1508 through 1509 No H-bonds generated for 'chain 'A' and resid 1508 through 1509' Processing helix chain 'A' and resid 1510 through 1515 Processing helix chain 'A' and resid 1517 through 1554 removed outlier: 3.644A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER A1554 " --> pdb=" O ILE A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1561 removed outlier: 4.056A pdb=" N HIS A1559 " --> pdb=" O ALA A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1563 through 1585 removed outlier: 3.778A pdb=" N SER A1585 " --> pdb=" O LYS A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1593 Processing helix chain 'A' and resid 1596 through 1626 Processing helix chain 'A' and resid 1627 through 1632 Processing helix chain 'A' and resid 1634 through 1643 Processing helix chain 'A' and resid 1646 through 1652 removed outlier: 3.820A pdb=" N LYS A1649 " --> pdb=" O ASN A1646 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN A1651 " --> pdb=" O ALA A1648 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1658 Processing helix chain 'A' and resid 1697 through 1729 removed outlier: 3.645A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A1729 " --> pdb=" O GLU A1725 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 removed outlier: 3.528A pdb=" N TYR A1745 " --> pdb=" O TRP A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1772 removed outlier: 3.583A pdb=" N GLY A1771 " --> pdb=" O SER A1767 " (cutoff:3.500A) Processing helix chain 'A' and resid 1775 through 1798 removed outlier: 3.575A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1829 removed outlier: 3.865A pdb=" N HIS A1817 " --> pdb=" O THR A1813 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 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 removed outlier: 4.107A pdb=" N GLY A1942 " --> pdb=" O PHE A1938 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ARG A1943 " --> pdb=" O GLN A1939 " (cutoff:3.500A) Processing helix chain 'A' and resid 1959 through 1963 removed outlier: 3.537A pdb=" N LEU A1963 " --> pdb=" O PHE A1960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1964 through 1984 Processing helix chain 'A' and resid 2045 through 2057 Processing helix chain 'A' and resid 2061 through 2080 Proline residue: A2071 - end of helix removed outlier: 3.583A pdb=" N LEU A2080 " --> pdb=" O CYS A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2118 removed outlier: 3.805A pdb=" N VAL A2098 " --> pdb=" O LYS A2094 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2130 Processing helix chain 'A' and resid 2132 through 2146 removed outlier: 3.545A pdb=" N ILE A2136 " --> pdb=" O PRO A2132 " (cutoff:3.500A) Processing helix chain 'A' and resid 2147 through 2149 No H-bonds generated for 'chain 'A' and resid 2147 through 2149' Processing helix chain 'A' and resid 2152 through 2165 removed outlier: 4.382A pdb=" N LEU A2156 " --> pdb=" O GLU A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2200 through 2217 Processing helix chain 'A' and resid 2229 through 2246 Processing helix chain 'A' and resid 2260 through 2266 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2293 through 2297 Processing helix chain 'A' and resid 2314 through 2320 removed outlier: 4.241A pdb=" N VAL A2318 " --> pdb=" O ASN A2314 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2359 Processing helix chain 'A' and resid 2365 through 2369 removed outlier: 3.522A pdb=" N LEU A2369 " --> pdb=" O GLU A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2385 removed outlier: 3.622A pdb=" N ILE A2374 " --> pdb=" O SER A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2394 through 2400 removed outlier: 3.979A pdb=" N ARG A2398 " --> pdb=" O ALA A2394 " (cutoff:3.500A) Processing helix chain 'A' and resid 2410 through 2424 Processing helix chain 'A' and resid 2425 through 2428 removed outlier: 3.908A pdb=" N THR A2428 " --> pdb=" O PRO A2425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2425 through 2428' Processing helix chain 'A' and resid 2431 through 2443 removed outlier: 3.643A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A2443 " --> pdb=" O HIS A2439 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 removed outlier: 3.560A pdb=" N CYS A2454 " --> pdb=" O THR A2450 " (cutoff:3.500A) Processing helix chain 'A' and resid 2482 through 2503 removed outlier: 3.527A pdb=" N SER A2503 " --> pdb=" O LEU A2499 " (cutoff:3.500A) Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2549 through 2552 Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.577A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2611 Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 3.778A 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: 4.049A pdb=" N PHE A2751 " --> pdb=" O ILE A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2762 through 2764 No H-bonds generated for 'chain 'A' and resid 2762 through 2764' Processing helix chain 'A' and resid 2765 through 2784 Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 4.051A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2833 Processing helix chain 'A' and resid 2834 through 2837 removed outlier: 3.592A pdb=" N LEU A2837 " --> pdb=" O GLN A2834 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2834 through 2837' Processing helix chain 'A' and resid 2839 through 2858 removed outlier: 3.663A pdb=" N ASP A2851 " --> pdb=" O ASP A2847 " (cutoff:3.500A) Processing helix chain 'A' and resid 2862 through 2867 Processing helix chain 'A' and resid 2885 through 2904 Processing helix chain 'A' and resid 2912 through 2927 Processing helix chain 'A' and resid 2942 through 2954 removed outlier: 3.554A pdb=" N LEU A2946 " --> pdb=" O GLY A2942 " (cutoff:3.500A) Processing helix chain 'A' and resid 2968 through 2985 removed outlier: 3.559A pdb=" N PHE A2972 " --> pdb=" O THR A2968 " (cutoff:3.500A) Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 4.021A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A3006 " --> pdb=" O SER A3002 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG A3007 " --> pdb=" O GLY A3003 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 removed outlier: 3.559A pdb=" N GLU A3035 " --> pdb=" O THR A3031 " (cutoff:3.500A) Processing helix chain 'A' and resid 3046 through 3061 Processing helix chain 'A' and resid 3071 through 3082 Processing helix chain 'A' and resid 3083 through 3088 Processing helix chain 'A' and resid 3098 through 3110 Processing helix chain 'A' and resid 3138 through 3165 Processing helix chain 'A' and resid 3172 through 3221 removed outlier: 3.832A pdb=" N ASP A3221 " --> pdb=" O GLU A3217 " (cutoff:3.500A) Processing helix chain 'A' and resid 3471 through 3516 removed outlier: 5.013A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.299A 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 removed outlier: 3.538A pdb=" N ARG A3559 " --> pdb=" O ASN A3555 " (cutoff:3.500A) Processing helix chain 'A' and resid 3570 through 3582 Processing helix chain 'A' and resid 3594 through 3604 removed outlier: 3.694A pdb=" N GLU A3598 " --> pdb=" O GLY A3594 " (cutoff:3.500A) Processing helix chain 'A' and resid 3605 through 3608 Processing helix chain 'A' and resid 3618 through 3629 Processing helix chain 'A' and resid 3637 through 3641 removed outlier: 3.778A pdb=" N SER A3640 " --> pdb=" O ASP A3637 " (cutoff:3.500A) Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3651 Processing helix chain 'A' and resid 3689 through 3694 Processing helix chain 'A' and resid 3706 through 3721 Processing helix chain 'A' and resid 3721 through 3734 Processing helix chain 'A' and resid 3736 through 3755 removed outlier: 3.790A pdb=" N GLU A3755 " --> pdb=" O GLN A3751 " (cutoff:3.500A) Processing helix chain 'A' and resid 3758 through 3762 Processing helix chain 'A' and resid 3766 through 3786 removed outlier: 4.203A pdb=" N LEU A3770 " --> pdb=" O ILE A3766 " (cutoff:3.500A) Processing helix chain 'A' and resid 3786 through 3818 Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3819 through 3821 No H-bonds generated for 'chain 'A' and resid 3819 through 3821' Processing helix chain 'A' and resid 3828 through 3841 Processing helix chain 'A' and resid 3851 through 3874 removed outlier: 3.562A pdb=" N ARG A3873 " --> pdb=" O ASN A3869 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A3874 " --> pdb=" O ARG A3870 " (cutoff:3.500A) Processing helix chain 'A' and resid 3879 through 3895 Processing helix chain 'A' and resid 3901 through 3910 Processing helix chain 'A' and resid 3911 through 3913 No H-bonds generated for 'chain 'A' and resid 3911 through 3913' Processing helix chain 'A' and resid 3928 through 3940 removed outlier: 3.539A pdb=" N CYS A3940 " --> pdb=" O VAL A3936 " (cutoff:3.500A) Processing helix chain 'A' and resid 3941 through 3945 removed outlier: 3.568A pdb=" N LYS A3945 " --> pdb=" O PRO A3942 " (cutoff:3.500A) Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3963 removed outlier: 4.255A pdb=" N TRP A3960 " --> pdb=" O GLN A3956 " (cutoff:3.500A) Processing helix chain 'A' and resid 3965 through 3969 Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4013 Processing helix chain 'A' and resid 4014 through 4017 removed outlier: 3.539A pdb=" N PHE A4017 " --> pdb=" O GLY A4014 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4014 through 4017' Processing helix chain 'A' and resid 4018 through 4023 removed outlier: 3.563A pdb=" N GLU A4022 " --> pdb=" O MET A4018 " (cutoff:3.500A) Processing helix chain 'A' and resid 4026 through 4033 removed outlier: 3.613A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4062 removed outlier: 4.012A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4091 Processing helix chain 'A' and resid 4099 through 4101 No H-bonds generated for 'chain 'A' and resid 4099 through 4101' Processing helix chain 'A' and resid 4102 through 4115 Processing helix chain 'A' and resid 4135 through 4141 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 removed outlier: 3.576A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4174 through 4194 removed outlier: 3.961A pdb=" N ARG A4178 " --> pdb=" O ASN A4174 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4228 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 4321 Processing helix chain 'A' and resid 4326 through 4348 Processing helix chain 'A' and resid 4376 through 4391 Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4474 through 4500 Processing helix chain 'A' and resid 4501 through 4506 removed outlier: 4.092A pdb=" N LYS A4505 " --> pdb=" O ALA A4501 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN A4506 " --> pdb=" O LYS A4502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4501 through 4506' Processing helix chain 'A' and resid 4516 through 4532 removed outlier: 3.505A pdb=" N TYR A4520 " --> pdb=" O VAL A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4631 through 4638 removed outlier: 3.509A pdb=" N PHE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1477 through 1480 Processing sheet with id=AA2, first strand: chain 'A' and resid 1663 through 1666 removed outlier: 3.538A pdb=" N VAL A1690 " --> pdb=" O VAL A1673 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 11.029A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.593A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N PHE A1686 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 removed outlier: 3.705A pdb=" N LEU A2039 " --> pdb=" O SER A1903 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1930 removed outlier: 6.198A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA7, first strand: chain 'A' and resid 2249 through 2251 removed outlier: 6.586A pdb=" N VAL A2250 " --> pdb=" O TRP A2300 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL A2302 " --> pdb=" O VAL A2250 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AA9, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB1, first strand: chain 'A' and resid 2710 through 2712 Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2617 removed outlier: 5.969A pdb=" N GLU A2616 " --> pdb=" O VAL A2660 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2643 removed outlier: 4.212A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 5.972A pdb=" N ILE A2990 " --> pdb=" O HIS A3063 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL A3065 " --> pdb=" O ILE A2990 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE A2992 " --> pdb=" O VAL A3065 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR A3067 " --> pdb=" O PHE A2992 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N MET A2994 " --> pdb=" O THR A3067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.146A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE A3678 " --> pdb=" O LEU A3633 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3654 through 3656 Processing sheet with id=AB7, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.727A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A4128 " --> pdb=" O MET A4043 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU A4042 " --> pdb=" O PHE A4145 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N PHE A4147 " --> pdb=" O LEU A4042 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N CYS A4044 " --> pdb=" O PHE A4147 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4283 through 4285 removed outlier: 7.193A pdb=" N ILE A4294 " --> pdb=" O LEU A4284 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 6.217A pdb=" N VAL A4509 " --> pdb=" O THR A4561 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4564 through 4570 removed outlier: 3.639A pdb=" N GLY A4567 " --> pdb=" O ILE A4581 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE A4581 " --> pdb=" O GLY A4567 " (cutoff:3.500A) removed outlier: 9.865A pdb=" N THR A4569 " --> pdb=" O ASN A4579 " (cutoff:3.500A) removed outlier: 9.812A pdb=" N ASN A4579 " --> pdb=" O THR A4569 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) 1434 hydrogen bonds defined for protein. 4182 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: 14.67 Time building geometry restraints manager: 7.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8121 1.34 - 1.46: 5219 1.46 - 1.58: 11584 1.58 - 1.70: 12 1.70 - 1.81: 206 Bond restraints: 25142 Sorted by residual: bond pdb=" N ILE A1611 " pdb=" CA ILE A1611 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.21e+00 bond pdb=" N ASP A1606 " pdb=" CA ASP A1606 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.17e-02 7.31e+03 6.18e+00 bond pdb=" N PHE A1568 " pdb=" CA PHE A1568 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.16e+00 bond pdb=" N LEU A1607 " pdb=" CA LEU A1607 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.19e-02 7.06e+03 5.71e+00 bond pdb=" N LEU A1608 " pdb=" CA LEU A1608 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.53e+00 ... (remaining 25137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 33176 1.56 - 3.12: 742 3.12 - 4.68: 122 4.68 - 6.24: 43 6.24 - 7.81: 6 Bond angle restraints: 34089 Sorted by residual: angle pdb=" N ASP A1410 " pdb=" CA ASP A1410 " pdb=" C ASP A1410 " ideal model delta sigma weight residual 114.56 108.19 6.37 1.27e+00 6.20e-01 2.51e+01 angle pdb=" N GLU A1406 " pdb=" CA GLU A1406 " pdb=" C GLU A1406 " ideal model delta sigma weight residual 113.30 109.02 4.28 1.34e+00 5.57e-01 1.02e+01 angle pdb=" CA THR A1565 " pdb=" CB THR A1565 " pdb=" OG1 THR A1565 " ideal model delta sigma weight residual 109.60 104.89 4.71 1.50e+00 4.44e-01 9.86e+00 angle pdb=" CA THR A1565 " pdb=" C THR A1565 " pdb=" O THR A1565 " ideal model delta sigma weight residual 120.82 117.91 2.91 1.05e+00 9.07e-01 7.67e+00 angle pdb=" CA ASP A1606 " pdb=" C ASP A1606 " pdb=" O ASP A1606 " ideal model delta sigma weight residual 121.00 118.11 2.89 1.05e+00 9.07e-01 7.56e+00 ... (remaining 34084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 13581 17.51 - 35.02: 1374 35.02 - 52.52: 209 52.52 - 70.03: 66 70.03 - 87.54: 28 Dihedral angle restraints: 15258 sinusoidal: 6348 harmonic: 8910 Sorted by residual: dihedral pdb=" CA SER A1510 " pdb=" C SER A1510 " pdb=" N PRO A1511 " pdb=" CA PRO A1511 " ideal model delta harmonic sigma weight residual -180.00 -159.16 -20.84 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" O2A ADP A4701 " pdb=" O3A ADP A4701 " pdb=" PA ADP A4701 " pdb=" PB ADP A4701 " ideal model delta sinusoidal sigma weight residual -60.00 13.45 -73.44 1 2.00e+01 2.50e-03 1.72e+01 dihedral pdb=" C5' ADP A4703 " pdb=" O5' ADP A4703 " pdb=" PA ADP A4703 " pdb=" O2A ADP A4703 " ideal model delta sinusoidal sigma weight residual -60.00 -131.09 71.10 1 2.00e+01 2.50e-03 1.62e+01 ... (remaining 15255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3034 0.047 - 0.095: 640 0.095 - 0.142: 139 0.142 - 0.190: 7 0.190 - 0.237: 1 Chirality restraints: 3821 Sorted by residual: chirality pdb=" CB ILE A3171 " pdb=" CA ILE A3171 " pdb=" CG1 ILE A3171 " pdb=" CG2 ILE A3171 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB ILE A3662 " pdb=" CA ILE A3662 " pdb=" CG1 ILE A3662 " pdb=" CG2 ILE A3662 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CA ILE A1611 " pdb=" N ILE A1611 " pdb=" C ILE A1611 " pdb=" CB ILE A1611 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.32e-01 ... (remaining 3818 not shown) Planarity restraints: 4367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A4482 " 0.024 2.00e-02 2.50e+03 2.19e-02 8.37e+00 pdb=" CG PHE A4482 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE A4482 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A4482 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A4482 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A4482 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A4482 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A2529 " 0.038 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO A2530 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A2530 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A2530 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A3552 " 0.010 2.00e-02 2.50e+03 1.49e-02 4.41e+00 pdb=" CG TYR A3552 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A3552 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A3552 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A3552 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A3552 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A3552 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR A3552 " -0.008 2.00e-02 2.50e+03 ... (remaining 4364 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 149 2.53 - 3.12: 19234 3.12 - 3.71: 39608 3.71 - 4.31: 51739 4.31 - 4.90: 87358 Nonbonded interactions: 198088 Sorted by model distance: nonbonded pdb=" O3B ATP A4702 " pdb="MG MG A4706 " model vdw 1.937 2.170 nonbonded pdb=" O2G ATP A4702 " pdb="MG MG A4706 " model vdw 2.018 2.170 nonbonded pdb=" O1A ADP A4701 " pdb="MG MG A4705 " model vdw 2.026 2.170 nonbonded pdb=" O1B ATP A4702 " pdb="MG MG A4706 " model vdw 2.047 2.170 nonbonded pdb=" OH TYR A3103 " pdb=" OE1 GLU A3141 " model vdw 2.065 3.040 ... (remaining 198083 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.960 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 62.490 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25142 Z= 0.154 Angle : 0.588 7.806 34089 Z= 0.314 Chirality : 0.041 0.237 3821 Planarity : 0.004 0.057 4367 Dihedral : 14.556 87.538 9470 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.16), residues: 3035 helix: 1.74 (0.13), residues: 1751 sheet: -0.90 (0.32), residues: 268 loop : 0.24 (0.21), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1435 HIS 0.008 0.001 HIS A2463 PHE 0.049 0.002 PHE A4482 TYR 0.035 0.001 TYR A3552 ARG 0.008 0.000 ARG A2642 Details of bonding type rmsd hydrogen bonds : bond 0.12560 ( 1434) hydrogen bonds : angle 5.27208 ( 4182) covalent geometry : bond 0.00315 (25142) covalent geometry : angle 0.58818 (34089) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 3.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1417 MET cc_start: 0.7918 (tmm) cc_final: 0.7663 (tmm) REVERT: A 1531 MET cc_start: 0.7813 (tpt) cc_final: 0.7581 (tpp) REVERT: A 1798 MET cc_start: 0.8017 (mtp) cc_final: 0.7674 (mtp) REVERT: A 2324 LEU cc_start: 0.8037 (tt) cc_final: 0.7138 (tt) REVERT: A 2461 MET cc_start: 0.7695 (ttm) cc_final: 0.7450 (ttm) REVERT: A 3043 MET cc_start: 0.6571 (mmp) cc_final: 0.5668 (mmp) REVERT: A 3962 ASP cc_start: 0.8205 (t70) cc_final: 0.7795 (t0) REVERT: A 4339 MET cc_start: 0.8016 (tmm) cc_final: 0.7668 (tmm) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.3676 time to fit residues: 188.0992 Evaluate side-chains 235 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.9990 chunk 230 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 177 optimal weight: 0.6980 chunk 276 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1495 ASN A1653 HIS ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2752 ASN A3069 ASN A3709 GLN ** A3865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4156 ASN A4466 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.132289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.097931 restraints weight = 43569.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.101598 restraints weight = 22311.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.104034 restraints weight = 14642.953| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25142 Z= 0.145 Angle : 0.566 9.345 34089 Z= 0.284 Chirality : 0.040 0.182 3821 Planarity : 0.004 0.050 4367 Dihedral : 5.914 86.182 3377 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.89 % Allowed : 6.91 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.16), residues: 3035 helix: 2.02 (0.12), residues: 1775 sheet: -0.98 (0.32), residues: 264 loop : 0.33 (0.22), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2234 HIS 0.007 0.001 HIS A2463 PHE 0.019 0.002 PHE A1960 TYR 0.020 0.001 TYR A2748 ARG 0.005 0.000 ARG A2642 Details of bonding type rmsd hydrogen bonds : bond 0.04397 ( 1434) hydrogen bonds : angle 4.23581 ( 4182) covalent geometry : bond 0.00327 (25142) covalent geometry : angle 0.56590 (34089) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 266 time to evaluate : 2.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1417 MET cc_start: 0.7860 (tmm) cc_final: 0.7555 (tmm) REVERT: A 1512 TYR cc_start: 0.7248 (OUTLIER) cc_final: 0.6856 (m-80) REVERT: A 1589 MET cc_start: 0.8529 (mmm) cc_final: 0.8311 (mmm) REVERT: A 1892 MET cc_start: 0.8281 (mmp) cc_final: 0.8018 (mmp) REVERT: A 2192 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8307 (p) REVERT: A 2464 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8530 (tm-30) REVERT: A 2481 MET cc_start: 0.6668 (pmm) cc_final: 0.6377 (pmm) REVERT: A 3043 MET cc_start: 0.6796 (mmp) cc_final: 0.5809 (mmp) REVERT: A 3962 ASP cc_start: 0.8186 (t70) cc_final: 0.7740 (t0) REVERT: A 4339 MET cc_start: 0.8098 (tmm) cc_final: 0.7675 (tmm) outliers start: 24 outliers final: 15 residues processed: 277 average time/residue: 0.4176 time to fit residues: 190.3160 Evaluate side-chains 251 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 234 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1512 TYR Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 2192 THR Chi-restraints excluded: chain A residue 2226 SER Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2327 LEU Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3489 TRP Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4390 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 163 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 224 optimal weight: 0.0770 chunk 198 optimal weight: 1.9990 chunk 273 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 111 optimal weight: 0.0170 chunk 116 optimal weight: 0.6980 chunk 262 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1755 GLN A1922 GLN ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3087 ASN ** A3175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3197 GLN ** A3534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3602 ASN A3865 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.136573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.101637 restraints weight = 43615.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.105642 restraints weight = 22169.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.108315 restraints weight = 14440.544| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25142 Z= 0.114 Angle : 0.526 7.780 34089 Z= 0.261 Chirality : 0.039 0.171 3821 Planarity : 0.004 0.045 4367 Dihedral : 5.746 76.880 3377 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.15 % Allowed : 9.20 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.16), residues: 3035 helix: 2.15 (0.12), residues: 1777 sheet: -0.92 (0.32), residues: 264 loop : 0.35 (0.21), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2234 HIS 0.007 0.001 HIS A3155 PHE 0.019 0.001 PHE A2635 TYR 0.028 0.001 TYR A1513 ARG 0.005 0.000 ARG A2642 Details of bonding type rmsd hydrogen bonds : bond 0.03841 ( 1434) hydrogen bonds : angle 4.02131 ( 4182) covalent geometry : bond 0.00252 (25142) covalent geometry : angle 0.52566 (34089) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 263 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1417 MET cc_start: 0.7550 (tmm) cc_final: 0.7232 (tmm) REVERT: A 1512 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.6999 (m-80) REVERT: A 1589 MET cc_start: 0.8518 (mmm) cc_final: 0.8303 (mmm) REVERT: A 2296 GLN cc_start: 0.8770 (mp10) cc_final: 0.8523 (mp10) REVERT: A 2324 LEU cc_start: 0.8048 (tt) cc_final: 0.7152 (tt) REVERT: A 2327 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7578 (mm) REVERT: A 2412 MET cc_start: 0.7100 (mmm) cc_final: 0.6759 (tpt) REVERT: A 2461 MET cc_start: 0.7611 (ttm) cc_final: 0.7071 (ttm) REVERT: A 2464 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8386 (tm-30) REVERT: A 2671 MET cc_start: 0.7164 (pmm) cc_final: 0.6801 (pmm) REVERT: A 2752 ASN cc_start: 0.6933 (m-40) cc_final: 0.6476 (m-40) REVERT: A 2792 TYR cc_start: 0.8165 (m-80) cc_final: 0.7861 (m-80) REVERT: A 3043 MET cc_start: 0.6871 (mmp) cc_final: 0.6166 (mmp) REVERT: A 4339 MET cc_start: 0.7858 (tmm) cc_final: 0.7385 (tmm) REVERT: A 4484 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8376 (mp0) outliers start: 31 outliers final: 19 residues processed: 283 average time/residue: 0.4011 time to fit residues: 186.0556 Evaluate side-chains 252 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain A residue 1512 TYR Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 2226 SER Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2327 LEU Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3087 ASN Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3489 TRP Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4447 TYR Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4516 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 195 optimal weight: 0.6980 chunk 219 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 199 optimal weight: 0.0270 chunk 215 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 289 optimal weight: 8.9990 chunk 178 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 chunk 292 optimal weight: 4.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2322 ASN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3197 GLN ** A3534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3880 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.134530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.099424 restraints weight = 44092.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.103270 restraints weight = 23024.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.105829 restraints weight = 15248.609| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25142 Z= 0.151 Angle : 0.551 10.590 34089 Z= 0.272 Chirality : 0.039 0.178 3821 Planarity : 0.004 0.045 4367 Dihedral : 5.688 79.303 3377 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.33 % Allowed : 10.68 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.16), residues: 3035 helix: 2.16 (0.12), residues: 1772 sheet: -0.96 (0.32), residues: 264 loop : 0.33 (0.22), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2234 HIS 0.005 0.001 HIS A2827 PHE 0.016 0.002 PHE A2635 TYR 0.031 0.001 TYR A1513 ARG 0.007 0.000 ARG A3088 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 1434) hydrogen bonds : angle 4.00598 ( 4182) covalent geometry : bond 0.00354 (25142) covalent geometry : angle 0.55065 (34089) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 241 time to evaluate : 2.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1417 MET cc_start: 0.7425 (tmm) cc_final: 0.7065 (tmm) REVERT: A 1589 MET cc_start: 0.8535 (mmm) cc_final: 0.8328 (mmm) REVERT: A 2192 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8185 (p) REVERT: A 2296 GLN cc_start: 0.8815 (mp10) cc_final: 0.8589 (mp10) REVERT: A 2412 MET cc_start: 0.7445 (mmm) cc_final: 0.6964 (tpt) REVERT: A 2464 GLN cc_start: 0.8846 (tm-30) cc_final: 0.8398 (tm-30) REVERT: A 2642 ARG cc_start: 0.6985 (ttp-110) cc_final: 0.6597 (ptp-110) REVERT: A 2752 ASN cc_start: 0.7034 (m-40) cc_final: 0.6683 (m110) REVERT: A 2901 TYR cc_start: 0.7260 (m-10) cc_final: 0.6896 (m-10) REVERT: A 3043 MET cc_start: 0.6928 (mmp) cc_final: 0.6492 (mmp) REVERT: A 3552 TYR cc_start: 0.8151 (t80) cc_final: 0.7647 (t80) REVERT: A 3799 GLN cc_start: 0.7707 (tm-30) cc_final: 0.7390 (tm-30) REVERT: A 4484 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8350 (mp0) outliers start: 36 outliers final: 23 residues processed: 264 average time/residue: 0.3791 time to fit residues: 166.2456 Evaluate side-chains 250 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 225 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2192 THR Chi-restraints excluded: chain A residue 2226 SER Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2733 VAL Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3489 TRP Chi-restraints excluded: chain A residue 3600 ILE Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4009 VAL Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4043 MET Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4250 SER Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4484 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 99 optimal weight: 0.2980 chunk 287 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 260 optimal weight: 2.9990 chunk 272 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 285 optimal weight: 0.8980 chunk 223 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2577 HIS A3057 GLN ** A3175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4386 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.135477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.100322 restraints weight = 43960.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.104274 restraints weight = 22483.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.106899 restraints weight = 14723.853| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25142 Z= 0.119 Angle : 0.528 10.272 34089 Z= 0.259 Chirality : 0.038 0.178 3821 Planarity : 0.004 0.044 4367 Dihedral : 5.585 80.690 3377 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.29 % Allowed : 11.57 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.16), residues: 3035 helix: 2.23 (0.12), residues: 1779 sheet: -0.93 (0.32), residues: 265 loop : 0.37 (0.22), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2234 HIS 0.004 0.001 HIS A3155 PHE 0.017 0.001 PHE A2635 TYR 0.022 0.001 TYR A1513 ARG 0.004 0.000 ARG A3655 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 1434) hydrogen bonds : angle 3.90680 ( 4182) covalent geometry : bond 0.00270 (25142) covalent geometry : angle 0.52830 (34089) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 249 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1417 MET cc_start: 0.7573 (tmm) cc_final: 0.7197 (tmm) REVERT: A 2192 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8206 (p) REVERT: A 2296 GLN cc_start: 0.8842 (mp10) cc_final: 0.8611 (mp10) REVERT: A 2412 MET cc_start: 0.7161 (mmm) cc_final: 0.6772 (tpt) REVERT: A 2464 GLN cc_start: 0.8852 (tm-30) cc_final: 0.8373 (tm-30) REVERT: A 2752 ASN cc_start: 0.6922 (m-40) cc_final: 0.6478 (m110) REVERT: A 2792 TYR cc_start: 0.8206 (m-80) cc_final: 0.7954 (m-80) REVERT: A 3043 MET cc_start: 0.6852 (mmp) cc_final: 0.6595 (mmp) REVERT: A 3552 TYR cc_start: 0.8218 (t80) cc_final: 0.7766 (t80) REVERT: A 3786 GLU cc_start: 0.7904 (pt0) cc_final: 0.7648 (pt0) REVERT: A 3799 GLN cc_start: 0.7576 (tm-30) cc_final: 0.7272 (tm-30) REVERT: A 4484 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8089 (mp0) outliers start: 35 outliers final: 25 residues processed: 271 average time/residue: 0.3572 time to fit residues: 158.4840 Evaluate side-chains 249 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 222 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2192 THR Chi-restraints excluded: chain A residue 2226 SER Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2623 SER Chi-restraints excluded: chain A residue 2799 MET Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3489 TRP Chi-restraints excluded: chain A residue 3600 ILE Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3716 VAL Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4043 MET Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4250 SER Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4516 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 168 optimal weight: 1.9990 chunk 245 optimal weight: 0.4980 chunk 115 optimal weight: 0.2980 chunk 165 optimal weight: 0.8980 chunk 251 optimal weight: 7.9990 chunk 85 optimal weight: 0.4980 chunk 180 optimal weight: 0.6980 chunk 178 optimal weight: 0.0050 chunk 195 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3057 GLN ** A3175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.135140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.100098 restraints weight = 43690.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.104050 restraints weight = 22355.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.106670 restraints weight = 14640.265| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25142 Z= 0.107 Angle : 0.528 11.098 34089 Z= 0.259 Chirality : 0.038 0.178 3821 Planarity : 0.004 0.048 4367 Dihedral : 5.494 82.150 3377 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.29 % Allowed : 12.93 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.16), residues: 3035 helix: 2.31 (0.12), residues: 1777 sheet: -0.85 (0.33), residues: 260 loop : 0.36 (0.22), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2234 HIS 0.004 0.001 HIS A3155 PHE 0.016 0.001 PHE A2635 TYR 0.028 0.001 TYR A1513 ARG 0.006 0.000 ARG A2292 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 1434) hydrogen bonds : angle 3.85163 ( 4182) covalent geometry : bond 0.00234 (25142) covalent geometry : angle 0.52848 (34089) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 243 time to evaluate : 2.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1417 MET cc_start: 0.7511 (tmm) cc_final: 0.7137 (tmm) REVERT: A 2012 MET cc_start: 0.7576 (tpt) cc_final: 0.7329 (tpp) REVERT: A 2192 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8182 (p) REVERT: A 2310 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7971 (mp0) REVERT: A 2412 MET cc_start: 0.7058 (mmm) cc_final: 0.6712 (tpt) REVERT: A 2461 MET cc_start: 0.7662 (ttm) cc_final: 0.7222 (ttm) REVERT: A 2464 GLN cc_start: 0.8853 (tm-30) cc_final: 0.8570 (tm-30) REVERT: A 2642 ARG cc_start: 0.7079 (ttp-110) cc_final: 0.6745 (ptp-110) REVERT: A 2752 ASN cc_start: 0.6882 (m-40) cc_final: 0.6423 (m110) REVERT: A 2839 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7808 (tm-30) REVERT: A 3552 TYR cc_start: 0.8221 (t80) cc_final: 0.7760 (t80) REVERT: A 3786 GLU cc_start: 0.7871 (pt0) cc_final: 0.7609 (pt0) REVERT: A 3799 GLN cc_start: 0.7569 (tm-30) cc_final: 0.7261 (tm-30) REVERT: A 4484 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8109 (mp0) outliers start: 35 outliers final: 25 residues processed: 266 average time/residue: 0.3565 time to fit residues: 155.1733 Evaluate side-chains 253 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2192 THR Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2310 GLU Chi-restraints excluded: chain A residue 2623 SER Chi-restraints excluded: chain A residue 2799 MET Chi-restraints excluded: chain A residue 2871 ILE Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3047 HIS Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3489 TRP Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3716 VAL Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4250 SER Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4516 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 0.0670 chunk 18 optimal weight: 4.9990 chunk 115 optimal weight: 0.5980 chunk 127 optimal weight: 0.9980 chunk 171 optimal weight: 7.9990 chunk 147 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 203 optimal weight: 0.7980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1482 ASN ** A1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3057 GLN ** A3175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.135239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.100320 restraints weight = 43892.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.104252 restraints weight = 22440.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.106868 restraints weight = 14709.193| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25142 Z= 0.122 Angle : 0.540 11.235 34089 Z= 0.266 Chirality : 0.038 0.179 3821 Planarity : 0.004 0.050 4367 Dihedral : 5.367 85.251 3377 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.63 % Allowed : 13.01 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.16), residues: 3035 helix: 2.31 (0.12), residues: 1777 sheet: -0.86 (0.32), residues: 262 loop : 0.33 (0.22), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2234 HIS 0.004 0.001 HIS A3155 PHE 0.043 0.001 PHE A3149 TYR 0.023 0.001 TYR A4447 ARG 0.010 0.000 ARG A2332 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 1434) hydrogen bonds : angle 3.83505 ( 4182) covalent geometry : bond 0.00278 (25142) covalent geometry : angle 0.54025 (34089) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 234 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1417 MET cc_start: 0.7625 (tmm) cc_final: 0.7265 (tmm) REVERT: A 2192 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8198 (p) REVERT: A 2292 ARG cc_start: 0.7105 (mtm-85) cc_final: 0.6493 (mtm110) REVERT: A 2310 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8028 (mp0) REVERT: A 2412 MET cc_start: 0.7143 (mmm) cc_final: 0.6852 (tpt) REVERT: A 2461 MET cc_start: 0.7738 (ttm) cc_final: 0.7194 (ttm) REVERT: A 2464 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8588 (tm-30) REVERT: A 2481 MET cc_start: 0.6333 (pmm) cc_final: 0.5290 (mtm) REVERT: A 2642 ARG cc_start: 0.7093 (ttp-110) cc_final: 0.6762 (ptp-110) REVERT: A 2752 ASN cc_start: 0.6910 (m-40) cc_final: 0.6451 (m110) REVERT: A 2840 ASP cc_start: 0.8632 (t0) cc_final: 0.8098 (t0) REVERT: A 3552 TYR cc_start: 0.8280 (t80) cc_final: 0.7712 (t80) REVERT: A 3786 GLU cc_start: 0.7836 (pt0) cc_final: 0.7623 (pt0) REVERT: A 3799 GLN cc_start: 0.7588 (tm-30) cc_final: 0.7284 (tm-30) REVERT: A 4004 MET cc_start: 0.7635 (tpp) cc_final: 0.7370 (tpp) REVERT: A 4484 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8128 (mp0) outliers start: 44 outliers final: 31 residues processed: 267 average time/residue: 0.3525 time to fit residues: 155.1882 Evaluate side-chains 261 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 2.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2192 THR Chi-restraints excluded: chain A residue 2226 SER Chi-restraints excluded: chain A residue 2310 GLU Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2623 SER Chi-restraints excluded: chain A residue 2799 MET Chi-restraints excluded: chain A residue 2958 VAL Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3047 HIS Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3489 TRP Chi-restraints excluded: chain A residue 3600 ILE Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3716 VAL Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4043 MET Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4250 SER Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4445 THR Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4516 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 169 optimal weight: 0.8980 chunk 154 optimal weight: 0.5980 chunk 205 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 276 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 87 optimal weight: 0.2980 chunk 114 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 270 optimal weight: 0.0470 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1961 ASN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3057 GLN ** A3175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.135612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.100683 restraints weight = 43853.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.104682 restraints weight = 22378.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.107304 restraints weight = 14560.841| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25142 Z= 0.113 Angle : 0.539 12.226 34089 Z= 0.262 Chirality : 0.038 0.179 3821 Planarity : 0.004 0.052 4367 Dihedral : 5.228 88.838 3377 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.40 % Allowed : 13.64 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.16), residues: 3035 helix: 2.37 (0.12), residues: 1776 sheet: -0.84 (0.32), residues: 262 loop : 0.35 (0.22), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2234 HIS 0.004 0.001 HIS A3155 PHE 0.036 0.001 PHE A3149 TYR 0.028 0.001 TYR A1513 ARG 0.006 0.000 ARG A2292 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 1434) hydrogen bonds : angle 3.79632 ( 4182) covalent geometry : bond 0.00254 (25142) covalent geometry : angle 0.53895 (34089) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 239 time to evaluate : 2.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2292 ARG cc_start: 0.6962 (mtm-85) cc_final: 0.6361 (mtm110) REVERT: A 2310 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: A 2412 MET cc_start: 0.7156 (mmm) cc_final: 0.6890 (tpt) REVERT: A 2461 MET cc_start: 0.7712 (ttm) cc_final: 0.7084 (ttm) REVERT: A 2464 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8574 (tm-30) REVERT: A 2603 MET cc_start: 0.7974 (ttp) cc_final: 0.7694 (tpp) REVERT: A 2642 ARG cc_start: 0.7125 (ttp-110) cc_final: 0.6760 (ptp-110) REVERT: A 2752 ASN cc_start: 0.6871 (m-40) cc_final: 0.6378 (m110) REVERT: A 3552 TYR cc_start: 0.8230 (t80) cc_final: 0.7657 (t80) REVERT: A 3799 GLN cc_start: 0.7586 (tm-30) cc_final: 0.7280 (tm-30) REVERT: A 4004 MET cc_start: 0.7646 (tpp) cc_final: 0.7445 (tpp) REVERT: A 4484 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8129 (mp0) outliers start: 38 outliers final: 28 residues processed: 268 average time/residue: 0.3731 time to fit residues: 163.8381 Evaluate side-chains 261 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 231 time to evaluate : 2.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2310 GLU Chi-restraints excluded: chain A residue 2623 SER Chi-restraints excluded: chain A residue 2799 MET Chi-restraints excluded: chain A residue 2871 ILE Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3489 TRP Chi-restraints excluded: chain A residue 3600 ILE Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3716 VAL Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4043 MET Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4250 SER Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4516 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 63 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 176 optimal weight: 0.7980 chunk 256 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 47 optimal weight: 0.0030 chunk 110 optimal weight: 0.7980 chunk 270 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1481 GLN A1961 ASN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3057 GLN ** A3175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.135437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.100643 restraints weight = 44194.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.104537 restraints weight = 22882.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.107103 restraints weight = 15087.092| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25142 Z= 0.118 Angle : 0.557 14.283 34089 Z= 0.269 Chirality : 0.039 0.180 3821 Planarity : 0.004 0.052 4367 Dihedral : 5.090 82.028 3377 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.37 % Allowed : 13.78 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.16), residues: 3035 helix: 2.36 (0.12), residues: 1777 sheet: -0.86 (0.32), residues: 262 loop : 0.36 (0.22), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1544 HIS 0.020 0.001 HIS A3880 PHE 0.032 0.001 PHE A3149 TYR 0.030 0.001 TYR A1513 ARG 0.006 0.000 ARG A2292 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 1434) hydrogen bonds : angle 3.80914 ( 4182) covalent geometry : bond 0.00269 (25142) covalent geometry : angle 0.55701 (34089) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 2.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1417 MET cc_start: 0.7127 (tmm) cc_final: 0.6919 (tmm) REVERT: A 2292 ARG cc_start: 0.6966 (mtm-85) cc_final: 0.6381 (mtm110) REVERT: A 2310 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: A 2461 MET cc_start: 0.7759 (ttm) cc_final: 0.7115 (ttm) REVERT: A 2464 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8594 (tm-30) REVERT: A 2603 MET cc_start: 0.8084 (ttp) cc_final: 0.7771 (tpp) REVERT: A 2752 ASN cc_start: 0.6882 (m-40) cc_final: 0.6420 (m110) REVERT: A 3043 MET cc_start: 0.6447 (mmp) cc_final: 0.5837 (mmp) REVERT: A 3552 TYR cc_start: 0.8251 (t80) cc_final: 0.7699 (t80) REVERT: A 3799 GLN cc_start: 0.7590 (tm-30) cc_final: 0.7286 (tm-30) REVERT: A 4004 MET cc_start: 0.7575 (tpp) cc_final: 0.7360 (tpp) REVERT: A 4484 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8100 (mp0) outliers start: 37 outliers final: 32 residues processed: 262 average time/residue: 0.3618 time to fit residues: 156.5803 Evaluate side-chains 252 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 218 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2226 SER Chi-restraints excluded: chain A residue 2310 GLU Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2623 SER Chi-restraints excluded: chain A residue 2799 MET Chi-restraints excluded: chain A residue 2871 ILE Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3489 TRP Chi-restraints excluded: chain A residue 3600 ILE Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3716 VAL Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4043 MET Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4250 SER Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4445 THR Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4516 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 159 optimal weight: 1.9990 chunk 119 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 204 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 179 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 255 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1482 ASN ** A1502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3057 GLN ** A3175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.135310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.100498 restraints weight = 43963.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.104422 restraints weight = 22432.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.107017 restraints weight = 14698.741| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25142 Z= 0.115 Angle : 0.551 11.862 34089 Z= 0.267 Chirality : 0.038 0.169 3821 Planarity : 0.004 0.051 4367 Dihedral : 4.972 74.014 3377 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.33 % Allowed : 13.90 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.16), residues: 3035 helix: 2.36 (0.12), residues: 1772 sheet: -0.84 (0.32), residues: 262 loop : 0.41 (0.22), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2234 HIS 0.013 0.001 HIS A3880 PHE 0.032 0.001 PHE A3149 TYR 0.015 0.001 TYR A2748 ARG 0.006 0.000 ARG A2292 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 1434) hydrogen bonds : angle 3.80209 ( 4182) covalent geometry : bond 0.00260 (25142) covalent geometry : angle 0.55075 (34089) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6070 Ramachandran restraints generated. 3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 2.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1417 MET cc_start: 0.7066 (tmm) cc_final: 0.6817 (tmm) REVERT: A 2292 ARG cc_start: 0.6982 (mtm-85) cc_final: 0.6371 (mtm110) REVERT: A 2310 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8016 (mp0) REVERT: A 2461 MET cc_start: 0.7729 (ttm) cc_final: 0.7047 (ttm) REVERT: A 2464 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8609 (tm-30) REVERT: A 2603 MET cc_start: 0.8038 (ttp) cc_final: 0.7784 (tpp) REVERT: A 2642 ARG cc_start: 0.7132 (ttp-110) cc_final: 0.6797 (ptp-110) REVERT: A 2644 THR cc_start: 0.6774 (p) cc_final: 0.6294 (p) REVERT: A 2752 ASN cc_start: 0.6864 (m-40) cc_final: 0.6397 (m110) REVERT: A 3552 TYR cc_start: 0.8261 (t80) cc_final: 0.7739 (t80) REVERT: A 3799 GLN cc_start: 0.7599 (tm-30) cc_final: 0.7297 (tm-30) REVERT: A 4004 MET cc_start: 0.7602 (tpp) cc_final: 0.7378 (tpp) REVERT: A 4429 GLN cc_start: 0.8219 (tp40) cc_final: 0.7802 (tt0) REVERT: A 4484 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8095 (mp0) outliers start: 36 outliers final: 30 residues processed: 258 average time/residue: 0.3722 time to fit residues: 156.0577 Evaluate side-chains 252 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1797 LEU Chi-restraints excluded: chain A residue 2189 MET Chi-restraints excluded: chain A residue 2226 SER Chi-restraints excluded: chain A residue 2310 GLU Chi-restraints excluded: chain A residue 2352 THR Chi-restraints excluded: chain A residue 2623 SER Chi-restraints excluded: chain A residue 2799 MET Chi-restraints excluded: chain A residue 2871 ILE Chi-restraints excluded: chain A residue 2910 VAL Chi-restraints excluded: chain A residue 3005 LEU Chi-restraints excluded: chain A residue 3155 HIS Chi-restraints excluded: chain A residue 3168 THR Chi-restraints excluded: chain A residue 3489 TRP Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3716 VAL Chi-restraints excluded: chain A residue 3770 LEU Chi-restraints excluded: chain A residue 3772 ASN Chi-restraints excluded: chain A residue 3835 ILE Chi-restraints excluded: chain A residue 3836 TYR Chi-restraints excluded: chain A residue 3929 VAL Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4011 THR Chi-restraints excluded: chain A residue 4043 MET Chi-restraints excluded: chain A residue 4055 VAL Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain A residue 4250 SER Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4445 THR Chi-restraints excluded: chain A residue 4448 LEU Chi-restraints excluded: chain A residue 4484 GLU Chi-restraints excluded: chain A residue 4516 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 104 optimal weight: 0.6980 chunk 303 optimal weight: 1.9990 chunk 292 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 126 optimal weight: 0.6980 chunk 250 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 32 optimal weight: 0.1980 chunk 42 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3057 GLN ** A3175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.135430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.100747 restraints weight = 43671.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.104669 restraints weight = 22286.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.107288 restraints weight = 14580.535| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25142 Z= 0.116 Angle : 0.561 11.970 34089 Z= 0.271 Chirality : 0.039 0.172 3821 Planarity : 0.004 0.051 4367 Dihedral : 4.916 68.333 3377 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.44 % Allowed : 14.19 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.16), residues: 3035 helix: 2.39 (0.12), residues: 1765 sheet: -0.84 (0.33), residues: 260 loop : 0.45 (0.22), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2234 HIS 0.010 0.001 HIS A3880 PHE 0.030 0.001 PHE A3149 TYR 0.019 0.001 TYR A4527 ARG 0.011 0.000 ARG A2332 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 1434) hydrogen bonds : angle 3.81077 ( 4182) covalent geometry : bond 0.00264 (25142) covalent geometry : angle 0.56051 (34089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8410.90 seconds wall clock time: 146 minutes 7.76 seconds (8767.76 seconds total)