Starting phenix.real_space_refine on Fri Feb 6 13:46:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ynf_73176/02_2026/9ynf_73176.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ynf_73176/02_2026/9ynf_73176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ynf_73176/02_2026/9ynf_73176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ynf_73176/02_2026/9ynf_73176.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ynf_73176/02_2026/9ynf_73176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ynf_73176/02_2026/9ynf_73176.map" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.037 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 10 5.49 5 Mg 1 5.21 5 S 122 5.16 5 C 15626 2.51 5 N 4246 2.21 5 O 4583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24588 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 24471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3038, 24471 Classifications: {'peptide': 3038} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 133, 'TRANS': 2904} Chain breaks: 4 Chain: "A" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 117 Unusual residues: {' MG': 1, 'ADP': 2, 'ANP': 1, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.72, per 1000 atoms: 0.23 Number of scatterers: 24588 At special positions: 0 Unit cell: (121.52, 145.824, 180.544, 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 10 15.00 Mg 1 11.99 O 4583 8.00 N 4246 7.00 C 15626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 884.6 milliseconds 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5780 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 17 sheets defined 63.5% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 1327 through 1348 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 1405 removed outlier: 4.042A pdb=" N MET A1398 " --> pdb=" O MET A1394 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LEU A1399 " --> pdb=" O LYS A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1421 Processing helix chain 'A' and resid 1425 through 1429 removed outlier: 3.687A pdb=" N LEU A1429 " --> pdb=" O VAL A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1437 Processing helix chain 'A' and resid 1442 through 1473 removed outlier: 3.503A pdb=" N GLY A1455 " --> pdb=" O LEU A1451 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1509 removed outlier: 3.685A pdb=" N LEU A1493 " --> pdb=" O GLY A1489 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A1509 " --> pdb=" O SER A1505 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1554 removed outlier: 3.902A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A1553 " --> pdb=" O GLY A1549 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER A1554 " --> pdb=" O ILE A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1561 Processing helix chain 'A' and resid 1561 through 1585 removed outlier: 3.757A pdb=" N SER A1585 " --> pdb=" O LYS A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1594 Processing helix chain 'A' and resid 1596 through 1626 Processing helix chain 'A' and resid 1627 through 1632 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1646 through 1657 removed outlier: 3.683A pdb=" N LYS A1649 " --> pdb=" O ASN A1646 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE A1654 " --> pdb=" O GLN A1651 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LYS A1655 " --> pdb=" O LYS A1652 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1729 removed outlier: 4.419A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE A1727 " --> pdb=" O GLU A1723 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 removed outlier: 3.591A pdb=" N TYR A1745 " --> pdb=" O TRP A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1773 removed outlier: 4.051A pdb=" N GLY A1771 " --> pdb=" O SER A1767 " (cutoff:3.500A) Processing helix chain 'A' and resid 1775 through 1798 removed outlier: 3.735A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1828 removed outlier: 3.774A pdb=" N HIS A1817 " --> pdb=" O THR A1813 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1841 Processing helix chain 'A' and resid 1882 through 1898 Processing helix chain 'A' and resid 1911 through 1923 Processing helix chain 'A' and resid 1940 through 1952 Processing helix chain 'A' and resid 1959 through 1963 Processing helix chain 'A' and resid 1964 through 1984 Processing helix chain 'A' and resid 2029 through 2034 removed outlier: 5.152A pdb=" N LYS A2034 " --> pdb=" O ASN A2031 " (cutoff:3.500A) 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: 4.348A pdb=" N GLU A2078 " --> pdb=" O LYS A2074 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2118 Processing helix chain 'A' and resid 2123 through 2130 removed outlier: 3.587A pdb=" N ASN A2130 " --> pdb=" O GLU A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2133 through 2146 Processing helix chain 'A' and resid 2147 through 2149 No H-bonds generated for 'chain 'A' and resid 2147 through 2149' Processing helix chain 'A' and resid 2153 through 2165 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 removed outlier: 3.627A pdb=" N TYR A2265 " --> pdb=" O LYS A2261 " (cutoff:3.500A) Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2293 through 2297 Processing helix chain 'A' and resid 2315 through 2320 Processing helix chain 'A' and resid 2352 through 2359 Processing helix chain 'A' and resid 2370 through 2385 Processing helix chain 'A' and resid 2394 through 2400 removed outlier: 3.966A 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: 3.748A 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: 3.548A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 Processing helix chain 'A' and resid 2482 through 2504 Processing helix chain 'A' and resid 2507 through 2522 Processing helix chain 'A' and resid 2533 through 2535 No H-bonds generated for 'chain 'A' and resid 2533 through 2535' Processing helix chain 'A' and resid 2549 through 2552 Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 3.727A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2612 Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.034A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2690 removed outlier: 3.692A pdb=" N HIS A2689 " --> pdb=" O GLN A2685 " (cutoff:3.500A) Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2740 through 2757 Processing helix chain 'A' and resid 2761 through 2764 removed outlier: 4.304A pdb=" N THR A2764 " --> pdb=" O SER A2761 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2761 through 2764' Processing helix chain 'A' and resid 2765 through 2784 Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.879A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 removed outlier: 3.625A pdb=" N LEU A2821 " --> pdb=" O PRO A2817 " (cutoff:3.500A) Processing helix chain 'A' and resid 2839 through 2858 Processing helix chain 'A' and resid 2885 through 2903 removed outlier: 3.933A pdb=" N GLU A2902 " --> pdb=" O LYS A2898 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU A2903 " --> pdb=" O VAL A2899 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2927 Processing helix chain 'A' and resid 2942 through 2954 Processing helix chain 'A' and resid 2968 through 2985 Processing helix chain 'A' and resid 3001 through 3015 removed outlier: 4.161A pdb=" N LEU A3005 " --> pdb=" O ASP A3001 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR A3010 " --> pdb=" O GLU A3006 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU A3011 " --> pdb=" O ARG A3007 " (cutoff:3.500A) Processing helix chain 'A' and resid 3022 through 3041 Processing helix chain 'A' and resid 3046 through 3062 Processing helix chain 'A' and resid 3082 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: 3.731A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3471 through 3516 removed outlier: 4.977A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 5.392A 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: 3.533A 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 Processing helix chain 'A' and resid 3618 through 3630 Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3651 Processing helix chain 'A' and resid 3689 through 3696 Processing helix chain 'A' and resid 3704 through 3721 Processing helix chain 'A' and resid 3721 through 3734 Processing helix chain 'A' and resid 3736 through 3755 removed outlier: 3.878A pdb=" N GLU A3755 " --> pdb=" O GLN A3751 " (cutoff:3.500A) Processing helix chain 'A' and resid 3758 through 3762 removed outlier: 3.631A pdb=" N ASP A3762 " --> pdb=" O ARG A3759 " (cutoff:3.500A) Processing helix chain 'A' and resid 3766 through 3786 removed outlier: 3.783A pdb=" N LEU A3770 " --> pdb=" O ILE A3766 " (cutoff:3.500A) Processing helix chain 'A' and resid 3786 through 3817 Proline residue: A3803 - end of helix Processing helix chain 'A' and resid 3818 through 3821 Processing helix chain 'A' and resid 3828 through 3841 Processing helix chain 'A' and resid 3843 through 3847 Processing helix chain 'A' and resid 3851 through 3874 removed outlier: 3.549A pdb=" N ARG A3873 " --> pdb=" O ASN A3869 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY A3874 " --> pdb=" O ARG A3870 " (cutoff:3.500A) Processing helix chain 'A' and resid 3875 through 3878 removed outlier: 5.944A pdb=" N GLN A3878 " --> pdb=" O MET A3875 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3875 through 3878' Processing helix chain 'A' and resid 3879 through 3895 Processing helix chain 'A' and resid 3901 through 3911 Processing helix chain 'A' and resid 3928 through 3939 Processing helix chain 'A' and resid 3940 through 3945 removed outlier: 6.316A pdb=" N ALA A3943 " --> pdb=" O CYS A3940 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A3945 " --> pdb=" O PRO A3942 " (cutoff:3.500A) Processing helix chain 'A' and resid 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 Processing helix chain 'A' and resid 3965 through 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 4018 through 4023 removed outlier: 3.906A pdb=" N GLU A4022 " --> pdb=" O MET A4018 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN A4023 " --> pdb=" O SER A4019 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4018 through 4023' Processing helix chain 'A' and resid 4026 through 4034 removed outlier: 3.912A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4063 removed outlier: 3.864A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4089 removed outlier: 3.906A pdb=" N LYS A4089 " --> pdb=" O ASN A4085 " (cutoff:3.500A) Processing helix chain 'A' and resid 4098 through 4101 removed outlier: 3.766A pdb=" N LEU A4101 " --> pdb=" O ASN A4098 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4098 through 4101' Processing helix chain 'A' and resid 4102 through 4116 removed outlier: 3.741A pdb=" N SER A4115 " --> pdb=" O LYS A4111 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4141 removed outlier: 3.529A pdb=" N LEU A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4170 Processing helix chain 'A' and resid 4175 through 4193 Processing helix chain 'A' and resid 4194 through 4197 Processing helix chain 'A' and resid 4208 through 4228 removed outlier: 3.750A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4234 through 4238 Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4252 through 4256 removed outlier: 3.737A pdb=" N ARG A4255 " --> pdb=" O TYR A4252 " (cutoff:3.500A) Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 removed outlier: 3.682A pdb=" N PHE A4278 " --> pdb=" O THR A4275 " (cutoff:3.500A) Processing helix chain 'A' and resid 4287 through 4291 Processing helix chain 'A' and resid 4301 through 4311 Processing helix chain 'A' and resid 4326 through 4346 Processing helix chain 'A' and resid 4376 through 4391 Processing helix chain 'A' and resid 4401 through 4406 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 4505 removed outlier: 8.458A pdb=" N ALA A4501 " --> pdb=" O ALA A4497 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N LYS A4502 " --> pdb=" O SER A4498 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A4504 " --> pdb=" O GLY A4500 " (cutoff:3.500A) Processing helix chain 'A' and resid 4516 through 4533 Processing helix chain 'A' and resid 4535 through 4537 No H-bonds generated for 'chain 'A' and resid 4535 through 4537' Processing helix chain 'A' and resid 4631 through 4638 Processing sheet with id=AA1, first strand: chain 'A' and resid 1477 through 1480 removed outlier: 3.952A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1661 through 1666 removed outlier: 10.799A pdb=" N VAL A1672 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 11.279A pdb=" N THR A1688 " --> pdb=" O VAL A1672 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU A1674 " --> pdb=" O PHE A1686 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846 removed outlier: 3.599A pdb=" N GLN A1860 " --> pdb=" O ARG A1843 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1930 removed outlier: 5.875A pdb=" N LEU A1928 " --> pdb=" O CYS A1956 " (cutoff:3.500A) removed outlier: 6.690A 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 2219 through 2223 removed outlier: 6.746A pdb=" N LEU A2220 " --> pdb=" O PHE A2343 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL A2345 " --> pdb=" O LEU A2220 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N MET A2222 " --> pdb=" O VAL A2345 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE A2303 " --> pdb=" O GLU A2344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2324 through 2325 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 2615 through 2620 removed outlier: 6.559A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A2591 " --> pdb=" O PHE A2708 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL A2592 " --> pdb=" O VAL A2734 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2639 through 2644 removed outlier: 3.530A pdb=" N THR A2644 " --> pdb=" O GLY A2647 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A2648 " --> pdb=" O LYS A2702 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 3.528A pdb=" N MET A2994 " --> pdb=" O VAL A3065 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.620A pdb=" N LEU A3633 " --> pdb=" O PHE A3678 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N SER A3680 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL A3635 " --> pdb=" O SER A3680 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N THR A3681 " --> pdb=" O PRO A3587 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE A3589 " --> pdb=" O THR A3681 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.049A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 4283 through 4285 removed outlier: 3.992A pdb=" N ALA A4285 " --> pdb=" O ILE A4294 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 3.587A pdb=" N VAL A4509 " --> pdb=" O GLY A4559 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A4561 " --> pdb=" O VAL A4509 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A4587 " --> pdb=" O THR A4546 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 4563 through 4570 removed outlier: 4.318A pdb=" N LEU A4563 " --> pdb=" O LEU A4585 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY A4567 " --> pdb=" O ILE A4581 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE A4581 " --> pdb=" O GLY A4567 " (cutoff:3.500A) removed outlier: 9.762A pdb=" N THR A4569 " --> pdb=" O ASN A4579 " (cutoff:3.500A) removed outlier: 9.924A pdb=" N ASN A4579 " --> pdb=" O THR A4569 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N VAL A4642 " --> pdb=" O THR A4606 " (cutoff:3.500A) 1455 hydrogen bonds defined for protein. 4245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.16 Time building geometry restraints manager: 2.74 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: 8084 1.34 - 1.46: 4149 1.46 - 1.58: 12660 1.58 - 1.70: 12 1.70 - 1.82: 208 Bond restraints: 25113 Sorted by residual: bond pdb=" CB MET A2603 " pdb=" CG MET A2603 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.86e+00 bond pdb=" CG1 ILE A4486 " pdb=" CD1 ILE A4486 " ideal model delta sigma weight residual 1.513 1.440 0.073 3.90e-02 6.57e+02 3.51e+00 bond pdb=" C PRO A2596 " pdb=" N PRO A2597 " ideal model delta sigma weight residual 1.332 1.353 -0.021 1.34e-02 5.57e+03 2.51e+00 bond pdb=" CD GLU A3217 " pdb=" OE1 GLU A3217 " ideal model delta sigma weight residual 1.249 1.220 0.029 1.90e-02 2.77e+03 2.39e+00 bond pdb=" SD MET A2603 " pdb=" CE MET A2603 " ideal model delta sigma weight residual 1.791 1.757 0.034 2.50e-02 1.60e+03 1.89e+00 ... (remaining 25108 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 33648 2.57 - 5.13: 358 5.13 - 7.70: 40 7.70 - 10.27: 5 10.27 - 12.84: 1 Bond angle restraints: 34052 Sorted by residual: angle pdb=" N GLU A3217 " pdb=" CA GLU A3217 " pdb=" CB GLU A3217 " ideal model delta sigma weight residual 110.30 117.16 -6.86 1.54e+00 4.22e-01 1.98e+01 angle pdb=" CB MET A2603 " pdb=" CG MET A2603 " pdb=" SD MET A2603 " ideal model delta sigma weight residual 112.70 99.86 12.84 3.00e+00 1.11e-01 1.83e+01 angle pdb=" C THR A1430 " pdb=" CA THR A1430 " pdb=" CB THR A1430 " ideal model delta sigma weight residual 115.79 110.72 5.07 1.19e+00 7.06e-01 1.81e+01 angle pdb=" C GLU A3216 " pdb=" N GLU A3217 " pdb=" CA GLU A3217 " ideal model delta sigma weight residual 120.68 114.20 6.48 1.70e+00 3.46e-01 1.45e+01 angle pdb=" CB LYS A4457 " pdb=" CG LYS A4457 " pdb=" CD LYS A4457 " ideal model delta sigma weight residual 111.30 119.87 -8.57 2.30e+00 1.89e-01 1.39e+01 ... (remaining 34047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.02: 14187 22.02 - 44.03: 896 44.03 - 66.05: 107 66.05 - 88.07: 60 88.07 - 110.08: 7 Dihedral angle restraints: 15257 sinusoidal: 6361 harmonic: 8896 Sorted by residual: dihedral pdb=" CA PRO A2597 " pdb=" C PRO A2597 " pdb=" N GLY A2598 " pdb=" CA GLY A2598 " ideal model delta harmonic sigma weight residual -180.00 -149.31 -30.69 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" O1B ADP A4704 " pdb=" O3A ADP A4704 " pdb=" PB ADP A4704 " pdb=" PA ADP A4704 " ideal model delta sinusoidal sigma weight residual -60.00 -170.08 110.08 1 2.00e+01 2.50e-03 3.22e+01 dihedral pdb=" CA ILE A3662 " pdb=" C ILE A3662 " pdb=" N THR A3663 " pdb=" CA THR A3663 " ideal model delta harmonic sigma weight residual 180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 15254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2616 0.036 - 0.073: 881 0.073 - 0.109: 265 0.109 - 0.146: 52 0.146 - 0.182: 2 Chirality restraints: 3816 Sorted by residual: chirality pdb=" CG LEU A4423 " pdb=" CB LEU A4423 " pdb=" CD1 LEU A4423 " pdb=" CD2 LEU A4423 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.29e-01 chirality pdb=" C1' ANP A4703 " pdb=" C2' ANP A4703 " pdb=" N9 ANP A4703 " pdb=" O4' ANP A4703 " both_signs ideal model delta sigma weight residual False 2.42 2.26 0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CA LYS A1391 " pdb=" N LYS A1391 " pdb=" C LYS A1391 " pdb=" CB LYS A1391 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.20e-01 ... (remaining 3813 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1435 " -0.032 2.00e-02 2.50e+03 2.66e-02 1.77e+01 pdb=" CG TRP A1435 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP A1435 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A1435 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A1435 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A1435 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1435 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1435 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1435 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A1435 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A4117 " -0.042 5.00e-02 4.00e+02 6.34e-02 6.42e+00 pdb=" N PRO A4118 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A4118 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A4118 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A3172 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO A3173 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A3173 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A3173 " -0.029 5.00e-02 4.00e+02 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1030 2.72 - 3.27: 26751 3.27 - 3.81: 42150 3.81 - 4.36: 49215 4.36 - 4.90: 82421 Nonbonded interactions: 201567 Sorted by model distance: nonbonded pdb=" NE2 GLN A1361 " pdb=" OD1 ASN A1362 " model vdw 2.175 3.120 nonbonded pdb=" OH TYR A4205 " pdb=" OD1 ASP A4257 " model vdw 2.176 3.040 nonbonded pdb=" O3A ATP A4702 " pdb="MG MG A4705 " model vdw 2.195 2.170 nonbonded pdb=" O LEU A2499 " pdb=" OG SER A2503 " model vdw 2.216 3.040 nonbonded pdb=" O MET A2053 " pdb=" OG SER A2056 " model vdw 2.216 3.040 ... (remaining 201562 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.210 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 0.073 25113 Z= 0.132 Angle : 0.639 12.837 34052 Z= 0.323 Chirality : 0.040 0.182 3816 Planarity : 0.004 0.063 4362 Dihedral : 14.776 110.082 9477 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.16), residues: 3028 helix: 1.83 (0.12), residues: 1772 sheet: -1.00 (0.35), residues: 226 loop : -0.05 (0.21), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A3219 TYR 0.023 0.001 TYR A1513 PHE 0.016 0.001 PHE A1686 TRP 0.072 0.002 TRP A1435 HIS 0.007 0.001 HIS A4006 Details of bonding type rmsd covalent geometry : bond 0.00289 (25113) covalent geometry : angle 0.63946 (34052) hydrogen bonds : bond 0.09788 ( 1455) hydrogen bonds : angle 5.16728 ( 4245) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1431 LEU cc_start: 0.8970 (tp) cc_final: 0.8768 (tp) REVERT: A 1941 MET cc_start: 0.7716 (tpp) cc_final: 0.7439 (tpp) REVERT: A 2232 MET cc_start: 0.5511 (ptt) cc_final: 0.4912 (ptt) REVERT: A 2481 MET cc_start: 0.7598 (tpt) cc_final: 0.6712 (tpt) REVERT: A 2867 MET cc_start: 0.7696 (mmm) cc_final: 0.7184 (mmp) REVERT: A 2897 LEU cc_start: 0.8162 (mt) cc_final: 0.7869 (mt) REVERT: A 3508 LEU cc_start: 0.9097 (tp) cc_final: 0.8882 (tp) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1685 time to fit residues: 60.0519 Evaluate side-chains 165 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.0030 chunk 261 optimal weight: 0.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.0470 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.1894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1863 ASN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2554 GLN ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2752 ASN A2964 HIS A3499 GLN A4532 ASN A4549 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.097464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.078810 restraints weight = 70916.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.081340 restraints weight = 38944.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.083012 restraints weight = 26061.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.084171 restraints weight = 19838.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.084883 restraints weight = 16401.026| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25113 Z= 0.150 Angle : 0.591 8.472 34052 Z= 0.298 Chirality : 0.040 0.179 3816 Planarity : 0.004 0.056 4362 Dihedral : 7.264 102.763 3391 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.70 % Allowed : 6.07 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.16), residues: 3028 helix: 1.85 (0.12), residues: 1782 sheet: -1.11 (0.35), residues: 227 loop : -0.12 (0.21), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A3219 TYR 0.018 0.001 TYR A1513 PHE 0.017 0.001 PHE A1836 TRP 0.040 0.001 TRP A1435 HIS 0.006 0.001 HIS A2964 Details of bonding type rmsd covalent geometry : bond 0.00339 (25113) covalent geometry : angle 0.59067 (34052) hydrogen bonds : bond 0.03872 ( 1455) hydrogen bonds : angle 4.57831 ( 4245) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1685 MET cc_start: 0.8346 (mmm) cc_final: 0.7950 (mmm) REVERT: A 2012 MET cc_start: 0.9120 (ppp) cc_final: 0.8916 (ppp) REVERT: A 2041 MET cc_start: 0.8577 (mtp) cc_final: 0.8176 (mtp) REVERT: A 3875 MET cc_start: 0.7977 (tmm) cc_final: 0.7082 (tmm) REVERT: A 4021 MET cc_start: 0.8232 (mmp) cc_final: 0.8021 (mmp) REVERT: A 4189 ILE cc_start: 0.9598 (mm) cc_final: 0.9333 (mt) REVERT: A 4296 MET cc_start: 0.8669 (tmm) cc_final: 0.8142 (tmm) outliers start: 19 outliers final: 11 residues processed: 193 average time/residue: 0.1535 time to fit residues: 48.4891 Evaluate side-chains 165 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1413 TRP Chi-restraints excluded: chain A residue 2207 VAL Chi-restraints excluded: chain A residue 2377 ASN Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3570 ASP Chi-restraints excluded: chain A residue 3599 PHE Chi-restraints excluded: chain A residue 3712 CYS Chi-restraints excluded: chain A residue 3991 LEU Chi-restraints excluded: chain A residue 4330 VAL Chi-restraints excluded: chain A residue 4460 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 276 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 268 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 109 optimal weight: 0.0980 chunk 264 optimal weight: 0.1980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2079 GLN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3069 ASN A3584 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.098567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.080132 restraints weight = 70679.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.082704 restraints weight = 38297.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.084377 restraints weight = 25439.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.085537 restraints weight = 19320.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.086326 restraints weight = 15922.001| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25113 Z= 0.109 Angle : 0.535 7.893 34052 Z= 0.268 Chirality : 0.039 0.176 3816 Planarity : 0.004 0.054 4362 Dihedral : 7.017 98.623 3391 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.63 % Allowed : 7.58 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.16), residues: 3028 helix: 1.96 (0.12), residues: 1782 sheet: -0.87 (0.33), residues: 249 loop : -0.08 (0.21), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A4462 TYR 0.016 0.001 TYR A1513 PHE 0.012 0.001 PHE A1836 TRP 0.022 0.001 TRP A1435 HIS 0.003 0.001 HIS A4100 Details of bonding type rmsd covalent geometry : bond 0.00236 (25113) covalent geometry : angle 0.53468 (34052) hydrogen bonds : bond 0.03651 ( 1455) hydrogen bonds : angle 4.33390 ( 4245) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1420 LEU cc_start: 0.8445 (tp) cc_final: 0.8187 (tp) REVERT: A 1507 MET cc_start: 0.8938 (tpp) cc_final: 0.8681 (tpp) REVERT: A 2012 MET cc_start: 0.9101 (ppp) cc_final: 0.8781 (ppp) REVERT: A 2041 MET cc_start: 0.8568 (mtp) cc_final: 0.8116 (mtp) REVERT: A 2481 MET cc_start: 0.7955 (tpp) cc_final: 0.6379 (tmm) REVERT: A 2755 MET cc_start: 0.8156 (tpt) cc_final: 0.7803 (tpt) REVERT: A 3875 MET cc_start: 0.7509 (tmm) cc_final: 0.7041 (tmm) REVERT: A 4007 MET cc_start: 0.7716 (ttp) cc_final: 0.7508 (ttp) REVERT: A 4189 ILE cc_start: 0.9572 (mm) cc_final: 0.9339 (mt) REVERT: A 4296 MET cc_start: 0.8699 (tmm) cc_final: 0.8144 (tmm) outliers start: 17 outliers final: 12 residues processed: 194 average time/residue: 0.1572 time to fit residues: 49.2779 Evaluate side-chains 162 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1413 TRP Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2377 ASN Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3205 LEU Chi-restraints excluded: chain A residue 3570 ASP Chi-restraints excluded: chain A residue 3599 PHE Chi-restraints excluded: chain A residue 3786 GLU Chi-restraints excluded: chain A residue 3991 LEU Chi-restraints excluded: chain A residue 4330 VAL Chi-restraints excluded: chain A residue 4460 LEU Chi-restraints excluded: chain A residue 4509 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 32 optimal weight: 0.4980 chunk 66 optimal weight: 0.0170 chunk 274 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 296 optimal weight: 0.9980 chunk 190 optimal weight: 0.8980 chunk 212 optimal weight: 1.9990 chunk 128 optimal weight: 0.0670 chunk 151 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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** ** A2707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2849 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.100636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.082510 restraints weight = 70027.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.085096 restraints weight = 37548.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.086816 restraints weight = 24788.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.087970 restraints weight = 18678.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.088754 restraints weight = 15346.561| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 25113 Z= 0.103 Angle : 0.520 8.433 34052 Z= 0.259 Chirality : 0.038 0.170 3816 Planarity : 0.004 0.054 4362 Dihedral : 6.779 93.996 3391 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.07 % Allowed : 9.29 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.16), residues: 3028 helix: 2.01 (0.12), residues: 1789 sheet: -0.82 (0.33), residues: 250 loop : -0.04 (0.21), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A4462 TYR 0.015 0.001 TYR A2748 PHE 0.015 0.001 PHE A1938 TRP 0.017 0.001 TRP A1435 HIS 0.003 0.001 HIS A4100 Details of bonding type rmsd covalent geometry : bond 0.00221 (25113) covalent geometry : angle 0.51978 (34052) hydrogen bonds : bond 0.03474 ( 1455) hydrogen bonds : angle 4.20821 ( 4245) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1420 LEU cc_start: 0.8461 (tp) cc_final: 0.8157 (tp) REVERT: A 2012 MET cc_start: 0.9094 (ppp) cc_final: 0.8718 (ppp) REVERT: A 2041 MET cc_start: 0.8537 (mtp) cc_final: 0.8096 (mtp) REVERT: A 2799 MET cc_start: 0.8227 (tpp) cc_final: 0.8006 (tpp) REVERT: A 2867 MET cc_start: 0.7939 (mmm) cc_final: 0.7654 (mmp) REVERT: A 3068 MET cc_start: 0.8507 (ttp) cc_final: 0.8093 (ppp) REVERT: A 3217 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7928 (pp20) REVERT: A 3875 MET cc_start: 0.7596 (tmm) cc_final: 0.7098 (tmm) REVERT: A 3885 MET cc_start: 0.8921 (tpt) cc_final: 0.8603 (tpt) REVERT: A 4189 ILE cc_start: 0.9592 (mm) cc_final: 0.9349 (mt) REVERT: A 4296 MET cc_start: 0.8684 (tmm) cc_final: 0.8153 (tmm) REVERT: A 4377 MET cc_start: 0.6897 (tpt) cc_final: 0.6669 (tpp) outliers start: 29 outliers final: 15 residues processed: 194 average time/residue: 0.1547 time to fit residues: 49.1502 Evaluate side-chains 170 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1413 TRP Chi-restraints excluded: chain A residue 2207 VAL Chi-restraints excluded: chain A residue 2377 ASN Chi-restraints excluded: chain A residue 2441 PHE Chi-restraints excluded: chain A residue 2816 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3205 LEU Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3570 ASP Chi-restraints excluded: chain A residue 3599 PHE Chi-restraints excluded: chain A residue 3786 GLU Chi-restraints excluded: chain A residue 3991 LEU Chi-restraints excluded: chain A residue 4330 VAL Chi-restraints excluded: chain A residue 4460 LEU Chi-restraints excluded: chain A residue 4546 THR Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 206 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 119 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 246 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- 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** ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2707 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.097534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.079203 restraints weight = 70520.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.081904 restraints weight = 41833.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.084839 restraints weight = 24428.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.085129 restraints weight = 16820.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.085071 restraints weight = 14479.745| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25113 Z= 0.121 Angle : 0.534 9.648 34052 Z= 0.264 Chirality : 0.039 0.185 3816 Planarity : 0.004 0.054 4362 Dihedral : 6.490 88.158 3391 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.15 % Allowed : 10.36 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.16), residues: 3028 helix: 2.07 (0.12), residues: 1783 sheet: -0.80 (0.34), residues: 250 loop : -0.02 (0.21), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A4462 TYR 0.015 0.001 TYR A2748 PHE 0.016 0.001 PHE A4008 TRP 0.015 0.001 TRP A1701 HIS 0.004 0.001 HIS A1412 Details of bonding type rmsd covalent geometry : bond 0.00269 (25113) covalent geometry : angle 0.53373 (34052) hydrogen bonds : bond 0.03453 ( 1455) hydrogen bonds : angle 4.16396 ( 4245) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2012 MET cc_start: 0.9124 (ppp) cc_final: 0.8663 (ppp) REVERT: A 2041 MET cc_start: 0.8550 (mtp) cc_final: 0.8101 (mtp) REVERT: A 2113 ARG cc_start: 0.7906 (ptt180) cc_final: 0.7620 (ptt-90) REVERT: A 2232 MET cc_start: 0.8393 (ptm) cc_final: 0.8150 (ptm) REVERT: A 2361 MET cc_start: 0.7913 (mmm) cc_final: 0.7629 (mtp) REVERT: A 2481 MET cc_start: 0.8295 (mmm) cc_final: 0.7034 (tmm) REVERT: A 2755 MET cc_start: 0.7906 (tpt) cc_final: 0.7309 (tpt) REVERT: A 3068 MET cc_start: 0.8452 (ttp) cc_final: 0.7342 (ppp) REVERT: A 3217 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7957 (pp20) REVERT: A 3875 MET cc_start: 0.7639 (tmm) cc_final: 0.7130 (tmm) REVERT: A 4296 MET cc_start: 0.8704 (tmm) cc_final: 0.8184 (tmm) REVERT: A 4348 MET cc_start: 0.7062 (tpp) cc_final: 0.6764 (tpp) REVERT: A 4377 MET cc_start: 0.6984 (tpt) cc_final: 0.6717 (tpp) outliers start: 31 outliers final: 18 residues processed: 189 average time/residue: 0.1501 time to fit residues: 46.5176 Evaluate side-chains 172 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1413 TRP Chi-restraints excluded: chain A residue 2207 VAL Chi-restraints excluded: chain A residue 2377 ASN Chi-restraints excluded: chain A residue 2441 PHE Chi-restraints excluded: chain A residue 2816 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3205 LEU Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3570 ASP Chi-restraints excluded: chain A residue 3599 PHE Chi-restraints excluded: chain A residue 3786 GLU Chi-restraints excluded: chain A residue 3991 LEU Chi-restraints excluded: chain A residue 4291 HIS Chi-restraints excluded: chain A residue 4330 VAL Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4460 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4546 THR Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 148 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 243 optimal weight: 0.0970 chunk 181 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 255 optimal weight: 2.9990 chunk 297 optimal weight: 0.0170 overall best weight: 0.5416 ------------------------------------------------------------------------------- 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** ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3865 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.098403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.079966 restraints weight = 70699.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.082525 restraints weight = 38618.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.084228 restraints weight = 25728.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.085365 restraints weight = 19490.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.086139 restraints weight = 16127.862| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25113 Z= 0.102 Angle : 0.517 9.012 34052 Z= 0.255 Chirality : 0.038 0.205 3816 Planarity : 0.003 0.053 4362 Dihedral : 6.286 89.038 3391 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.96 % Allowed : 11.32 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.16), residues: 3028 helix: 2.12 (0.12), residues: 1789 sheet: -0.84 (0.33), residues: 243 loop : 0.08 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A4462 TYR 0.016 0.001 TYR A2748 PHE 0.010 0.001 PHE A1836 TRP 0.015 0.001 TRP A2234 HIS 0.003 0.001 HIS A1412 Details of bonding type rmsd covalent geometry : bond 0.00218 (25113) covalent geometry : angle 0.51743 (34052) hydrogen bonds : bond 0.03343 ( 1455) hydrogen bonds : angle 4.06069 ( 4245) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1447 LYS cc_start: 0.8807 (mtmt) cc_final: 0.8533 (mtmm) REVERT: A 2012 MET cc_start: 0.9054 (ppp) cc_final: 0.8612 (ppp) REVERT: A 2041 MET cc_start: 0.8645 (mtp) cc_final: 0.8211 (mtp) REVERT: A 2232 MET cc_start: 0.7999 (ptm) cc_final: 0.7623 (ptm) REVERT: A 2481 MET cc_start: 0.8437 (mmm) cc_final: 0.7392 (tmm) REVERT: A 3068 MET cc_start: 0.8413 (ttp) cc_final: 0.7303 (ppp) REVERT: A 3217 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.8022 (pp20) REVERT: A 4296 MET cc_start: 0.8693 (tmm) cc_final: 0.8160 (tmm) REVERT: A 4326 ASN cc_start: 0.7799 (p0) cc_final: 0.7414 (p0) REVERT: A 4348 MET cc_start: 0.7002 (tpp) cc_final: 0.6719 (tpp) outliers start: 26 outliers final: 19 residues processed: 189 average time/residue: 0.1493 time to fit residues: 45.7983 Evaluate side-chains 175 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1413 TRP Chi-restraints excluded: chain A residue 2207 VAL Chi-restraints excluded: chain A residue 2377 ASN Chi-restraints excluded: chain A residue 2441 PHE Chi-restraints excluded: chain A residue 2816 LEU Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3205 LEU Chi-restraints excluded: chain A residue 3217 GLU Chi-restraints excluded: chain A residue 3570 ASP Chi-restraints excluded: chain A residue 3599 PHE Chi-restraints excluded: chain A residue 3786 GLU Chi-restraints excluded: chain A residue 3991 LEU Chi-restraints excluded: chain A residue 4291 HIS Chi-restraints excluded: chain A residue 4330 VAL Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4460 LEU Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4546 THR Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 129 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 294 optimal weight: 0.1980 chunk 161 optimal weight: 0.8980 chunk 230 optimal weight: 8.9990 chunk 61 optimal weight: 0.2980 chunk 213 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 147 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.100908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.082990 restraints weight = 70544.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.085693 restraints weight = 41454.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.087914 restraints weight = 24584.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.088225 restraints weight = 18394.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.088442 restraints weight = 16019.009| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25113 Z= 0.105 Angle : 0.536 10.242 34052 Z= 0.262 Chirality : 0.038 0.199 3816 Planarity : 0.003 0.053 4362 Dihedral : 6.202 85.750 3391 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.26 % Allowed : 11.76 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.16), residues: 3028 helix: 2.12 (0.12), residues: 1790 sheet: -0.81 (0.33), residues: 243 loop : 0.12 (0.21), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A4462 TYR 0.015 0.001 TYR A2748 PHE 0.011 0.001 PHE A1836 TRP 0.015 0.001 TRP A2234 HIS 0.003 0.001 HIS A3047 Details of bonding type rmsd covalent geometry : bond 0.00231 (25113) covalent geometry : angle 0.53570 (34052) hydrogen bonds : bond 0.03323 ( 1455) hydrogen bonds : angle 4.04788 ( 4245) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1447 LYS cc_start: 0.8793 (mtmt) cc_final: 0.8531 (mtmm) REVERT: A 1507 MET cc_start: 0.8912 (tpp) cc_final: 0.8648 (tpp) REVERT: A 2012 MET cc_start: 0.9053 (ppp) cc_final: 0.8562 (ppp) REVERT: A 2041 MET cc_start: 0.8620 (mtp) cc_final: 0.8175 (mtp) REVERT: A 2232 MET cc_start: 0.7903 (ptm) cc_final: 0.7570 (ptm) REVERT: A 2481 MET cc_start: 0.8440 (mmm) cc_final: 0.7517 (tmm) REVERT: A 2755 MET cc_start: 0.7917 (tpt) cc_final: 0.7322 (tpt) REVERT: A 2799 MET cc_start: 0.8187 (tpp) cc_final: 0.7655 (tpp) REVERT: A 3068 MET cc_start: 0.8418 (ttp) cc_final: 0.7326 (ppp) REVERT: A 3743 ARG cc_start: 0.7542 (mmp80) cc_final: 0.6323 (mmm160) REVERT: A 4296 MET cc_start: 0.8681 (tmm) cc_final: 0.8158 (tmm) REVERT: A 4326 ASN cc_start: 0.7761 (p0) cc_final: 0.7390 (p0) REVERT: A 4348 MET cc_start: 0.7023 (tpp) cc_final: 0.6767 (tpp) REVERT: A 4419 MET cc_start: 0.8770 (ttt) cc_final: 0.8155 (mtt) outliers start: 34 outliers final: 25 residues processed: 188 average time/residue: 0.1643 time to fit residues: 49.8860 Evaluate side-chains 180 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1411 ARG Chi-restraints excluded: chain A residue 1413 TRP Chi-restraints excluded: chain A residue 2207 VAL Chi-restraints excluded: chain A residue 2377 ASN Chi-restraints excluded: chain A residue 2441 PHE Chi-restraints excluded: chain A residue 2461 MET Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2816 LEU Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3205 LEU Chi-restraints excluded: chain A residue 3570 ASP Chi-restraints excluded: chain A residue 3599 PHE Chi-restraints excluded: chain A residue 3786 GLU Chi-restraints excluded: chain A residue 3875 MET Chi-restraints excluded: chain A residue 3991 LEU Chi-restraints excluded: chain A residue 4291 HIS Chi-restraints excluded: chain A residue 4330 VAL Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4460 LEU Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4546 THR Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 39 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 258 optimal weight: 0.9990 chunk 289 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 175 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 97 optimal weight: 0.0970 chunk 4 optimal weight: 7.9990 chunk 210 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3631 ASN A4078 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.099928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.081955 restraints weight = 70718.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.084581 restraints weight = 41704.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.086928 restraints weight = 24832.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.087216 restraints weight = 18271.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.087306 restraints weight = 15958.976| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25113 Z= 0.114 Angle : 0.542 10.203 34052 Z= 0.265 Chirality : 0.039 0.221 3816 Planarity : 0.003 0.053 4362 Dihedral : 6.113 86.096 3391 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.04 % Allowed : 12.50 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.16), residues: 3028 helix: 2.16 (0.12), residues: 1785 sheet: -0.75 (0.33), residues: 247 loop : 0.05 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A4462 TYR 0.015 0.001 TYR A2748 PHE 0.012 0.001 PHE A1836 TRP 0.015 0.001 TRP A2234 HIS 0.003 0.001 HIS A2827 Details of bonding type rmsd covalent geometry : bond 0.00256 (25113) covalent geometry : angle 0.54216 (34052) hydrogen bonds : bond 0.03341 ( 1455) hydrogen bonds : angle 4.06414 ( 4245) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1447 LYS cc_start: 0.8771 (mtmt) cc_final: 0.8518 (mtmm) REVERT: A 1685 MET cc_start: 0.8453 (mmm) cc_final: 0.7862 (mmm) REVERT: A 2012 MET cc_start: 0.9058 (ppp) cc_final: 0.8546 (ppp) REVERT: A 2041 MET cc_start: 0.8621 (mtp) cc_final: 0.8189 (mtp) REVERT: A 2232 MET cc_start: 0.7949 (ptm) cc_final: 0.7557 (ptm) REVERT: A 2481 MET cc_start: 0.8057 (mmm) cc_final: 0.7067 (tmm) REVERT: A 3743 ARG cc_start: 0.7589 (mmp80) cc_final: 0.6334 (mmm160) REVERT: A 4296 MET cc_start: 0.8694 (tmm) cc_final: 0.8171 (tmm) REVERT: A 4326 ASN cc_start: 0.7783 (p0) cc_final: 0.7421 (p0) REVERT: A 4348 MET cc_start: 0.7106 (tpp) cc_final: 0.6803 (tpp) REVERT: A 4419 MET cc_start: 0.8779 (ttt) cc_final: 0.8124 (mtm) outliers start: 28 outliers final: 26 residues processed: 184 average time/residue: 0.1702 time to fit residues: 50.0876 Evaluate side-chains 184 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1411 ARG Chi-restraints excluded: chain A residue 1413 TRP Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 2207 VAL Chi-restraints excluded: chain A residue 2377 ASN Chi-restraints excluded: chain A residue 2441 PHE Chi-restraints excluded: chain A residue 2461 MET Chi-restraints excluded: chain A residue 2800 THR Chi-restraints excluded: chain A residue 2816 LEU Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3205 LEU Chi-restraints excluded: chain A residue 3570 ASP Chi-restraints excluded: chain A residue 3599 PHE Chi-restraints excluded: chain A residue 3786 GLU Chi-restraints excluded: chain A residue 3875 MET Chi-restraints excluded: chain A residue 3991 LEU Chi-restraints excluded: chain A residue 4291 HIS Chi-restraints excluded: chain A residue 4330 VAL Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4460 LEU Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4546 THR Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 105 optimal weight: 3.9990 chunk 239 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 214 optimal weight: 6.9990 chunk 266 optimal weight: 0.6980 chunk 290 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 302 optimal weight: 0.8980 chunk 165 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.099888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.081778 restraints weight = 70884.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.084272 restraints weight = 43531.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.087215 restraints weight = 25718.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.087273 restraints weight = 18154.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.087355 restraints weight = 15929.618| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25113 Z= 0.114 Angle : 0.557 11.266 34052 Z= 0.271 Chirality : 0.039 0.320 3816 Planarity : 0.003 0.053 4362 Dihedral : 6.132 92.454 3391 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.96 % Allowed : 13.02 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.16), residues: 3028 helix: 2.15 (0.12), residues: 1785 sheet: -0.74 (0.33), residues: 250 loop : 0.02 (0.21), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A4462 TYR 0.015 0.001 TYR A2748 PHE 0.011 0.001 PHE A1836 TRP 0.015 0.001 TRP A2234 HIS 0.003 0.000 HIS A2827 Details of bonding type rmsd covalent geometry : bond 0.00255 (25113) covalent geometry : angle 0.55726 (34052) hydrogen bonds : bond 0.03333 ( 1455) hydrogen bonds : angle 4.06216 ( 4245) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1408 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8353 (mt) REVERT: A 1447 LYS cc_start: 0.8739 (mtmt) cc_final: 0.8491 (mtmm) REVERT: A 1531 MET cc_start: 0.8637 (tpp) cc_final: 0.8381 (mmm) REVERT: A 1602 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7253 (mp0) REVERT: A 1685 MET cc_start: 0.8489 (mmm) cc_final: 0.7917 (mmm) REVERT: A 2012 MET cc_start: 0.9036 (ppp) cc_final: 0.8535 (ppp) REVERT: A 2041 MET cc_start: 0.8606 (mtp) cc_final: 0.8172 (mtp) REVERT: A 2113 ARG cc_start: 0.7933 (ptt180) cc_final: 0.7702 (ptt-90) REVERT: A 2232 MET cc_start: 0.8131 (ptm) cc_final: 0.7519 (ptm) REVERT: A 2481 MET cc_start: 0.8058 (mmm) cc_final: 0.7132 (tmm) REVERT: A 2603 MET cc_start: 0.6676 (ptm) cc_final: 0.6469 (ptt) REVERT: A 2755 MET cc_start: 0.7976 (tpt) cc_final: 0.7384 (tpt) REVERT: A 3068 MET cc_start: 0.7923 (tmm) cc_final: 0.6471 (ppp) REVERT: A 4296 MET cc_start: 0.8704 (tmm) cc_final: 0.8179 (tmm) REVERT: A 4326 ASN cc_start: 0.7754 (p0) cc_final: 0.7399 (p0) REVERT: A 4348 MET cc_start: 0.7150 (tpp) cc_final: 0.6906 (tpp) REVERT: A 4419 MET cc_start: 0.8750 (ttt) cc_final: 0.8165 (mtm) outliers start: 26 outliers final: 23 residues processed: 183 average time/residue: 0.1732 time to fit residues: 50.9226 Evaluate side-chains 177 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1411 ARG Chi-restraints excluded: chain A residue 1413 TRP Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 2207 VAL Chi-restraints excluded: chain A residue 2377 ASN Chi-restraints excluded: chain A residue 2441 PHE Chi-restraints excluded: chain A residue 2461 MET Chi-restraints excluded: chain A residue 2816 LEU Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3570 ASP Chi-restraints excluded: chain A residue 3786 GLU Chi-restraints excluded: chain A residue 3875 MET Chi-restraints excluded: chain A residue 3991 LEU Chi-restraints excluded: chain A residue 4291 HIS Chi-restraints excluded: chain A residue 4330 VAL Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4460 LEU Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4546 THR Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 14 optimal weight: 0.0470 chunk 198 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 93 optimal weight: 0.0030 chunk 162 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 47 optimal weight: 0.0060 overall best weight: 0.3904 ------------------------------------------------------------------------------- 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** ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.104448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.087309 restraints weight = 71249.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.089358 restraints weight = 38205.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.091646 restraints weight = 23232.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.091675 restraints weight = 17786.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.091851 restraints weight = 15751.522| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25113 Z= 0.104 Angle : 0.561 11.225 34052 Z= 0.272 Chirality : 0.039 0.309 3816 Planarity : 0.003 0.053 4362 Dihedral : 6.102 93.459 3391 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.85 % Allowed : 13.36 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.16), residues: 3028 helix: 2.15 (0.12), residues: 1785 sheet: -0.69 (0.34), residues: 240 loop : 0.03 (0.21), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4092 TYR 0.015 0.001 TYR A2748 PHE 0.010 0.001 PHE A1836 TRP 0.015 0.001 TRP A1701 HIS 0.002 0.000 HIS A2085 Details of bonding type rmsd covalent geometry : bond 0.00227 (25113) covalent geometry : angle 0.56137 (34052) hydrogen bonds : bond 0.03298 ( 1455) hydrogen bonds : angle 4.02173 ( 4245) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1408 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8305 (mt) REVERT: A 1602 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7256 (mp0) REVERT: A 1685 MET cc_start: 0.8508 (mmm) cc_final: 0.7906 (mmm) REVERT: A 1967 MET cc_start: 0.8812 (mmm) cc_final: 0.8530 (mmt) REVERT: A 2012 MET cc_start: 0.9055 (ppp) cc_final: 0.8545 (ppp) REVERT: A 2041 MET cc_start: 0.8494 (mtp) cc_final: 0.8095 (mtp) REVERT: A 2481 MET cc_start: 0.8017 (mmm) cc_final: 0.7153 (tmm) REVERT: A 2799 MET cc_start: 0.8184 (tpp) cc_final: 0.7733 (tpp) REVERT: A 3048 GLU cc_start: 0.7959 (pm20) cc_final: 0.7208 (pt0) REVERT: A 3068 MET cc_start: 0.7946 (tmm) cc_final: 0.6483 (ppp) REVERT: A 4296 MET cc_start: 0.8738 (tmm) cc_final: 0.8192 (tmm) REVERT: A 4326 ASN cc_start: 0.7550 (p0) cc_final: 0.7195 (p0) REVERT: A 4419 MET cc_start: 0.8730 (ttt) cc_final: 0.8205 (mtt) REVERT: A 4454 GLU cc_start: 0.7969 (tt0) cc_final: 0.7472 (tm-30) REVERT: A 4462 ARG cc_start: 0.8655 (mmm-85) cc_final: 0.8301 (mmm160) outliers start: 23 outliers final: 21 residues processed: 179 average time/residue: 0.1720 time to fit residues: 49.9669 Evaluate side-chains 171 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1411 ARG Chi-restraints excluded: chain A residue 1413 TRP Chi-restraints excluded: chain A residue 2207 VAL Chi-restraints excluded: chain A residue 2377 ASN Chi-restraints excluded: chain A residue 2441 PHE Chi-restraints excluded: chain A residue 2461 MET Chi-restraints excluded: chain A residue 2816 LEU Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 2953 MET Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3570 ASP Chi-restraints excluded: chain A residue 3786 GLU Chi-restraints excluded: chain A residue 3875 MET Chi-restraints excluded: chain A residue 4291 HIS Chi-restraints excluded: chain A residue 4330 VAL Chi-restraints excluded: chain A residue 4423 LEU Chi-restraints excluded: chain A residue 4460 LEU Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4509 VAL Chi-restraints excluded: chain A residue 4546 THR Chi-restraints excluded: chain A residue 4617 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 249 optimal weight: 0.9990 chunk 191 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 6 optimal weight: 0.0980 chunk 254 optimal weight: 0.2980 chunk 217 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 chunk 295 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2329 ASN ** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2730 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 = 0.3702 r_free = 0.3702 target = 0.099746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.082471 restraints weight = 69467.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.085384 restraints weight = 39902.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.087566 restraints weight = 22163.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.087876 restraints weight = 16468.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.088090 restraints weight = 13983.611| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25113 Z= 0.109 Angle : 0.565 13.390 34052 Z= 0.274 Chirality : 0.039 0.353 3816 Planarity : 0.003 0.053 4362 Dihedral : 6.111 95.209 3391 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.92 % Allowed : 13.69 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.16), residues: 3028 helix: 2.16 (0.12), residues: 1785 sheet: -0.76 (0.34), residues: 234 loop : 0.03 (0.21), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3191 TYR 0.015 0.001 TYR A2748 PHE 0.011 0.001 PHE A1836 TRP 0.015 0.001 TRP A1701 HIS 0.002 0.000 HIS A2827 Details of bonding type rmsd covalent geometry : bond 0.00243 (25113) covalent geometry : angle 0.56468 (34052) hydrogen bonds : bond 0.03293 ( 1455) hydrogen bonds : angle 4.01044 ( 4245) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3195.22 seconds wall clock time: 56 minutes 31.86 seconds (3391.86 seconds total)