Starting phenix.real_space_refine on Thu Jan 15 11:00:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z8g_14550/01_2026/7z8g_14550.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z8g_14550/01_2026/7z8g_14550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z8g_14550/01_2026/7z8g_14550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z8g_14550/01_2026/7z8g_14550.map" model { file = "/net/cci-nas-00/data/ceres_data/7z8g_14550/01_2026/7z8g_14550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z8g_14550/01_2026/7z8g_14550.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 11 5.49 5 Mg 1 5.21 5 S 122 5.16 5 C 15662 2.51 5 N 4256 2.21 5 O 4604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24656 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 24535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3047, 24535 Classifications: {'peptide': 3047} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 130, 'TRANS': 2913} Chain breaks: 3 Chain: "A" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 121 Unusual residues: {' MG': 1, 'ADP': 1, 'ANP': 2, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.41, per 1000 atoms: 0.22 Number of scatterers: 24656 At special positions: 0 Unit cell: (139.384, 180.453, 128.184, 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 11 15.00 Mg 1 11.99 O 4604 8.00 N 4256 7.00 C 15662 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: 2.42 Conformation dependent library (CDL) restraints added in 1.2 seconds 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5796 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 19 sheets defined 62.5% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 1327 through 1348 removed outlier: 4.183A pdb=" N LYS A1338 " --> pdb=" O SER A1334 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL A1339 " --> pdb=" O GLU A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1354 removed outlier: 3.503A pdb=" N VAL A1354 " --> pdb=" O TRP A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1371 Processing helix chain 'A' and resid 1374 through 1379 removed outlier: 3.716A pdb=" N GLN A1379 " --> pdb=" O ALA A1375 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1396 removed outlier: 3.515A pdb=" N GLU A1384 " --> pdb=" O TYR A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1404 Processing helix chain 'A' and resid 1409 through 1421 Processing helix chain 'A' and resid 1430 through 1437 removed outlier: 3.624A pdb=" N ILE A1434 " --> pdb=" O THR A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1473 Processing helix chain 'A' and resid 1489 through 1508 Processing helix chain 'A' and resid 1516 through 1552 removed outlier: 4.329A pdb=" N VAL A1536 " --> pdb=" O ALA A1532 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP A1539 " --> pdb=" O ASP A1535 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP A1544 " --> pdb=" O VAL A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1561 Processing helix chain 'A' and resid 1561 through 1584 removed outlier: 3.629A pdb=" N GLU A1574 " --> pdb=" O SER A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1593 Processing helix chain 'A' and resid 1596 through 1626 Processing helix chain 'A' and resid 1627 through 1632 Processing helix chain 'A' and resid 1633 through 1643 Processing helix chain 'A' and resid 1646 through 1652 removed outlier: 4.051A pdb=" N LYS A1652 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1658 removed outlier: 3.613A pdb=" N MET A1657 " --> pdb=" O HIS A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1729 removed outlier: 4.256A pdb=" N ILE A1726 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE A1727 " --> pdb=" O GLU A1723 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1745 Processing helix chain 'A' and resid 1746 through 1770 Processing helix chain 'A' and resid 1775 through 1798 removed outlier: 3.570A pdb=" N LEU A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1829 removed outlier: 3.657A pdb=" N HIS A1817 " --> pdb=" O THR A1813 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1840 Processing helix chain 'A' and resid 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 removed outlier: 3.510A pdb=" N LEU A1963 " --> pdb=" O PHE A1960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1964 through 1984 Processing helix chain 'A' and resid 1985 through 1987 No H-bonds generated for 'chain 'A' and resid 1985 through 1987' Processing helix chain 'A' and resid 2045 through 2057 Processing helix chain 'A' and resid 2062 through 2080 Proline residue: A2071 - end of helix removed outlier: 3.531A pdb=" N LYS A2074 " --> pdb=" O VAL A2070 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2118 Processing helix chain 'A' and resid 2123 through 2130 removed outlier: 3.793A pdb=" N ASN A2130 " --> pdb=" O GLU A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2132 through 2146 Processing helix chain 'A' and resid 2147 through 2149 No H-bonds generated for 'chain 'A' and resid 2147 through 2149' Processing helix chain 'A' and resid 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 removed outlier: 3.763A pdb=" N ARG A2243 " --> pdb=" O LYS A2239 " (cutoff:3.500A) Processing helix chain 'A' and resid 2260 through 2266 Processing helix chain 'A' and resid 2278 through 2290 Processing helix chain 'A' and resid 2309 through 2311 No H-bonds generated for 'chain 'A' and resid 2309 through 2311' Processing helix chain 'A' and resid 2312 through 2320 removed outlier: 4.277A pdb=" N SER A2317 " --> pdb=" O GLU A2313 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL A2318 " --> pdb=" O ASN A2314 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2359 removed outlier: 3.594A pdb=" N ARG A2358 " --> pdb=" O ALA A2354 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS A2359 " --> pdb=" O THR A2355 " (cutoff:3.500A) Processing helix chain 'A' and resid 2365 through 2369 removed outlier: 3.669A pdb=" N LEU A2369 " --> pdb=" O GLU A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2385 removed outlier: 3.654A pdb=" N SER A2384 " --> pdb=" O ALA A2380 " (cutoff:3.500A) Processing helix chain 'A' and resid 2395 through 2400 removed outlier: 3.576A pdb=" N LYS A2399 " --> pdb=" O GLN A2395 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A2400 " --> pdb=" O ARG A2396 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2395 through 2400' Processing helix chain 'A' and resid 2410 through 2424 removed outlier: 3.516A pdb=" N GLN A2414 " --> pdb=" O SER A2410 " (cutoff:3.500A) Processing helix chain 'A' and resid 2425 through 2428 removed outlier: 4.002A 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: 3.692A pdb=" N GLN A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A2443 " --> pdb=" O HIS A2439 " (cutoff:3.500A) Processing helix chain 'A' and resid 2450 through 2476 Processing helix chain 'A' and resid 2482 through 2503 removed outlier: 3.596A pdb=" N VAL A2495 " --> pdb=" O GLN A2491 " (cutoff:3.500A) Processing helix chain 'A' and resid 2504 through 2506 No H-bonds generated for 'chain 'A' and resid 2504 through 2506' 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 removed outlier: 3.713A pdb=" N VAL A2552 " --> pdb=" O GLN A2549 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2549 through 2552' Processing helix chain 'A' and resid 2571 through 2587 removed outlier: 4.016A pdb=" N GLU A2587 " --> pdb=" O THR A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2612 removed outlier: 3.605A pdb=" N LEU A2612 " --> pdb=" O ALA A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2627 through 2638 removed outlier: 4.076A pdb=" N LEU A2631 " --> pdb=" O THR A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2677 through 2690 Processing helix chain 'A' and resid 2724 through 2729 Processing helix chain 'A' and resid 2739 through 2756 removed outlier: 4.315A pdb=" N SER A2743 " --> pdb=" O PRO A2739 " (cutoff:3.500A) Processing helix chain 'A' and resid 2762 through 2764 No H-bonds generated for 'chain 'A' and resid 2762 through 2764' Processing helix chain 'A' and resid 2765 through 2784 removed outlier: 3.596A pdb=" N TYR A2777 " --> pdb=" O MET A2773 " (cutoff:3.500A) Processing helix chain 'A' and resid 2795 through 2811 removed outlier: 3.797A pdb=" N MET A2799 " --> pdb=" O SER A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2834 Processing helix chain 'A' and resid 2839 through 2858 removed outlier: 3.637A pdb=" N ASP A2851 " --> pdb=" O ASP A2847 " (cutoff:3.500A) Processing helix chain 'A' and resid 2862 through 2867 Processing helix chain 'A' and resid 2885 through 2902 removed outlier: 3.995A pdb=" N GLU A2902 " --> pdb=" O LYS A2898 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2928 removed outlier: 4.012A pdb=" N ASP A2917 " --> pdb=" O ASN A2913 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N HIS A2918 " --> pdb=" O GLU A2914 " (cutoff:3.500A) Processing helix chain 'A' and resid 2945 through 2954 Processing helix chain 'A' and resid 2968 through 2985 removed outlier: 3.529A pdb=" N PHE A2972 " --> pdb=" O THR A2968 " (cutoff:3.500A) Processing helix chain 'A' and resid 3006 through 3015 removed outlier: 4.178A pdb=" N THR A3010 " --> pdb=" O GLU A3006 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A3011 " --> pdb=" O ARG A3007 " (cutoff:3.500A) Processing helix chain 'A' and resid 3023 through 3041 removed outlier: 3.738A pdb=" N ALA A3027 " --> pdb=" O GLY A3023 " (cutoff:3.500A) Processing helix chain 'A' and resid 3046 through 3061 Processing helix chain 'A' and resid 3082 through 3089 Processing helix chain 'A' and resid 3098 through 3108 Processing helix chain 'A' and resid 3138 through 3164 removed outlier: 3.730A pdb=" N HIS A3151 " --> pdb=" O CYS A3147 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 3220 removed outlier: 3.781A pdb=" N TYR A3176 " --> pdb=" O THR A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3471 through 3516 removed outlier: 3.608A pdb=" N SER A3475 " --> pdb=" O LYS A3471 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR A3476 " --> pdb=" O VAL A3472 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA A3477 " --> pdb=" O ASN A3473 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA A3484 " --> pdb=" O LYS A3480 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA A3504 " --> pdb=" O MET A3500 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLY A3505 " --> pdb=" O SER A3501 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP A3506 " --> pdb=" O THR A3502 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE A3513 " --> pdb=" O LEU A3509 " (cutoff:3.500A) Processing helix chain 'A' and resid 3521 through 3539 Processing helix chain 'A' and resid 3548 through 3553 Processing helix chain 'A' and resid 3555 through 3565 Processing helix chain 'A' and resid 3570 through 3580 Processing helix chain 'A' and resid 3594 through 3604 removed outlier: 3.772A pdb=" N GLU A3598 " --> pdb=" O GLY A3594 " (cutoff:3.500A) Processing helix chain 'A' and resid 3605 through 3608 Processing helix chain 'A' and resid 3616 through 3618 No H-bonds generated for 'chain 'A' and resid 3616 through 3618' Processing helix chain 'A' and resid 3619 through 3630 Processing helix chain 'A' and resid 3637 through 3641 removed outlier: 3.725A pdb=" N SER A3640 " --> pdb=" O ASP A3637 " (cutoff:3.500A) Processing helix chain 'A' and resid 3642 through 3644 No H-bonds generated for 'chain 'A' and resid 3642 through 3644' Processing helix chain 'A' and resid 3645 through 3651 Processing helix chain 'A' and resid 3689 through 3695 removed outlier: 3.543A pdb=" N SER A3694 " --> pdb=" O PRO A3690 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A3695 " --> pdb=" O ASP A3691 " (cutoff:3.500A) Processing helix chain 'A' and resid 3704 through 3721 Processing helix chain 'A' and resid 3721 through 3730 Processing helix chain 'A' and resid 3735 through 3752 removed outlier: 4.232A pdb=" N GLN A3739 " --> pdb=" O GLN A3735 " (cutoff:3.500A) Processing helix chain 'A' and resid 3766 through 3786 removed outlier: 3.903A pdb=" N LEU A3773 " --> pdb=" O THR A3769 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU A3776 " --> pdb=" O ASN A3772 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A3777 " --> pdb=" O LEU A3773 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A3778 " --> pdb=" O LYS A3774 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A3784 " --> pdb=" O VAL A3780 " (cutoff:3.500A) Processing helix chain 'A' and resid 3788 through 3801 removed outlier: 3.599A pdb=" N GLN A3800 " --> pdb=" O THR A3796 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A3801 " --> pdb=" O VAL A3797 " (cutoff:3.500A) Processing helix chain 'A' and resid 3801 through 3818 removed outlier: 3.586A pdb=" N SER A3805 " --> pdb=" O TYR A3801 " (cutoff:3.500A) Processing helix chain 'A' and resid 3819 through 3821 No H-bonds generated for 'chain 'A' and resid 3819 through 3821' Processing helix chain 'A' and resid 3828 through 3841 removed outlier: 3.642A pdb=" N PHE A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3847 Processing helix chain 'A' and resid 3851 through 3873 Processing helix chain 'A' and resid 3874 through 3875 No H-bonds generated for 'chain 'A' and resid 3874 through 3875' Processing helix chain 'A' and resid 3876 through 3878 No H-bonds generated for 'chain 'A' and resid 3876 through 3878' Processing helix chain 'A' and resid 3879 through 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 3946 through 3954 Processing helix chain 'A' and resid 3956 through 3962 removed outlier: 3.623A pdb=" N TRP A3960 " --> pdb=" O GLN A3956 " (cutoff:3.500A) Processing helix chain 'A' and resid 3965 through 3970 removed outlier: 3.519A pdb=" N GLN A3968 " --> pdb=" O SER A3965 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL A3970 " --> pdb=" O GLU A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3981 through 3997 Processing helix chain 'A' and resid 4000 through 4013 Processing helix chain 'A' and resid 4026 through 4034 removed outlier: 3.746A pdb=" N ILE A4030 " --> pdb=" O ASP A4026 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4063 removed outlier: 3.814A pdb=" N VAL A4055 " --> pdb=" O ALA A4051 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4091 removed outlier: 3.651A pdb=" N PHE A4077 " --> pdb=" O SER A4073 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN A4078 " --> pdb=" O ALA A4074 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS A4089 " --> pdb=" O ASN A4085 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4101 No H-bonds generated for 'chain 'A' and resid 4099 through 4101' Processing helix chain 'A' and resid 4102 through 4114 Processing helix chain 'A' and resid 4135 through 4141 Processing helix chain 'A' and resid 4152 through 4164 Processing helix chain 'A' and resid 4165 through 4171 removed outlier: 3.576A pdb=" N ILE A4169 " --> pdb=" O PRO A4165 " (cutoff:3.500A) Processing helix chain 'A' and resid 4175 through 4194 Processing helix chain 'A' and resid 4195 through 4197 No H-bonds generated for 'chain 'A' and resid 4195 through 4197' Processing helix chain 'A' and resid 4208 through 4228 removed outlier: 3.614A pdb=" N LEU A4212 " --> pdb=" O GLY A4208 " (cutoff:3.500A) Processing helix chain 'A' and resid 4239 through 4250 Processing helix chain 'A' and resid 4258 through 4273 Processing helix chain 'A' and resid 4274 through 4279 Processing helix chain 'A' and resid 4289 through 4291 No H-bonds generated for 'chain 'A' and resid 4289 through 4291' Processing helix chain 'A' and resid 4301 through 4311 removed outlier: 3.532A pdb=" N PHE A4305 " --> pdb=" O ARG A4301 " (cutoff:3.500A) Processing helix chain 'A' and resid 4317 through 4322 Processing helix chain 'A' and resid 4325 through 4345 removed outlier: 3.898A pdb=" N ARG A4329 " --> pdb=" O ASN A4325 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A4333 " --> pdb=" O ARG A4329 " (cutoff:3.500A) Processing helix chain 'A' and resid 4376 through 4391 removed outlier: 3.757A pdb=" N THR A4382 " --> pdb=" O ARG A4378 " (cutoff:3.500A) Processing helix chain 'A' and resid 4401 through 4406 removed outlier: 4.238A pdb=" N LYS A4406 " --> pdb=" O VAL A4402 " (cutoff:3.500A) Processing helix chain 'A' and resid 4407 through 4439 Processing helix chain 'A' and resid 4445 through 4458 Processing helix chain 'A' and resid 4461 through 4465 Processing helix chain 'A' and resid 4474 through 4500 removed outlier: 3.666A pdb=" N TRP A4478 " --> pdb=" O THR A4474 " (cutoff:3.500A) Processing helix chain 'A' and resid 4502 through 4507 removed outlier: 4.367A pdb=" N ASN A4506 " --> pdb=" O LYS A4502 " (cutoff:3.500A) Processing helix chain 'A' and resid 4512 through 4514 No H-bonds generated for 'chain 'A' and resid 4512 through 4514' Processing helix chain 'A' and resid 4516 through 4533 removed outlier: 3.666A pdb=" N TYR A4520 " --> pdb=" O VAL A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4631 through 4639 removed outlier: 3.990A pdb=" N PHE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1477 through 1480 removed outlier: 3.886A pdb=" N CYS A1484 " --> pdb=" O TYR A1480 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1663 through 1666 removed outlier: 6.899A pdb=" N SER A1663 " --> pdb=" O ILE A1676 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ILE A1676 " --> pdb=" O SER A1663 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE A1665 " --> pdb=" O LEU A1674 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLY A1675 " --> pdb=" O THR A1688 " (cutoff:3.500A) removed outlier: 10.518A pdb=" N THR A1688 " --> pdb=" O GLY A1675 " (cutoff:3.500A) removed outlier: 11.638A pdb=" N SER A1677 " --> pdb=" O PHE A1686 " (cutoff:3.500A) removed outlier: 11.454A pdb=" N PHE A1686 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846 Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905 removed outlier: 6.458A pdb=" N GLY A1901 " --> pdb=" O ARG A2037 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU A2039 " --> pdb=" O GLY A1901 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N SER A1903 " --> pdb=" O LEU A2039 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1931 removed outlier: 6.154A pdb=" N GLY A1955 " --> pdb=" O PHE A2015 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2001 Processing sheet with id=AA7, first strand: chain 'A' and resid 2249 through 2254 removed outlier: 7.412A pdb=" N GLN A2299 " --> pdb=" O ARG A2340 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N MET A2342 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE A2301 " --> pdb=" O MET A2342 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLU A2344 " --> pdb=" O ILE A2301 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE A2303 " --> pdb=" O GLU A2344 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLY A2219 " --> pdb=" O GLY A2360 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N VAL A2362 " --> pdb=" O GLY A2219 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N MET A2221 " --> pdb=" O VAL A2362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2324 through 2326 Processing sheet with id=AA9, first strand: chain 'A' and resid 2537 through 2539 Processing sheet with id=AB1, first strand: chain 'A' and resid 2616 through 2620 removed outlier: 5.879A pdb=" N GLU A2616 " --> pdb=" O VAL A2660 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N PHE A2662 " --> pdb=" O GLU A2616 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A2618 " --> pdb=" O PHE A2662 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU A2659 " --> pdb=" O GLN A2707 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL A2709 " --> pdb=" O LEU A2659 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU A2661 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA A2711 " --> pdb=" O LEU A2661 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N CYS A2663 " --> pdb=" O ALA A2711 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A2591 " --> pdb=" O GLY A2710 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2639 through 2643 removed outlier: 4.433A pdb=" N VAL A2648 " --> pdb=" O TRP A2700 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2873 through 2874 removed outlier: 3.601A pdb=" N SER A2874 " --> pdb=" O ILE A2882 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE A2882 " --> pdb=" O SER A2874 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 2957 through 2960 removed outlier: 6.392A pdb=" N LEU A2934 " --> pdb=" O ASN A3092 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3610 through 3613 removed outlier: 6.365A pdb=" N THR A3610 " --> pdb=" O LEU A3634 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N GLN A3636 " --> pdb=" O THR A3610 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR A3612 " --> pdb=" O GLN A3636 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 3654 through 3656 Processing sheet with id=AB7, first strand: chain 'A' and resid 4066 through 4070 removed outlier: 6.368A pdb=" N THR A4067 " --> pdb=" O MET A4095 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LYS A4097 " --> pdb=" O THR A4067 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE A4069 " --> pdb=" O LYS A4097 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL A4094 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N THR A4127 " --> pdb=" O VAL A4094 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU A4096 " --> pdb=" O THR A4127 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N GLU A4129 " --> pdb=" O LEU A4096 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL A4041 " --> pdb=" O LEU A4126 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N MET A4128 " --> pdb=" O VAL A4041 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N MET A4043 " --> pdb=" O MET A4128 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A4042 " --> pdb=" O PHE A4145 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N PHE A4147 " --> pdb=" O LEU A4042 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N CYS A4044 " --> pdb=" O PHE A4147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 4283 through 4288 removed outlier: 5.738A pdb=" N CYS A4286 " --> pdb=" O ILE A4294 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE A4294 " --> pdb=" O CYS A4286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 4509 through 4510 removed outlier: 3.578A pdb=" N THR A4561 " --> pdb=" O VAL A4509 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4568 through 4571 removed outlier: 3.807A pdb=" N PHE A4620 " --> pdb=" O VAL A4609 " (cutoff:3.500A) 1379 hydrogen bonds defined for protein. 4026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.56 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8125 1.34 - 1.46: 5523 1.46 - 1.58: 11318 1.58 - 1.70: 10 1.70 - 1.82: 206 Bond restraints: 25182 Sorted by residual: bond pdb=" O3A ANP A4704 " pdb=" PB ANP A4704 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" O3A ANP A4705 " pdb=" PB ANP A4705 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" N3B ANP A4705 " pdb=" PG ANP A4705 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" N3B ANP A4704 " pdb=" PG ANP A4704 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" O5' ANP A4704 " pdb=" PA ANP A4704 " ideal model delta sigma weight residual 1.655 1.577 0.078 2.00e-02 2.50e+03 1.53e+01 ... (remaining 25177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.80: 33911 3.80 - 7.60: 224 7.60 - 11.40: 11 11.40 - 15.20: 0 15.20 - 19.00: 2 Bond angle restraints: 34148 Sorted by residual: angle pdb=" PB ANP A4705 " pdb=" N3B ANP A4705 " pdb=" PG ANP A4705 " ideal model delta sigma weight residual 126.95 107.95 19.00 3.00e+00 1.11e-01 4.01e+01 angle pdb=" PB ANP A4704 " pdb=" N3B ANP A4704 " pdb=" PG ANP A4704 " ideal model delta sigma weight residual 126.95 108.38 18.57 3.00e+00 1.11e-01 3.83e+01 angle pdb=" N ARG A2273 " pdb=" CA ARG A2273 " pdb=" C ARG A2273 " ideal model delta sigma weight residual 110.30 115.91 -5.61 1.50e+00 4.44e-01 1.40e+01 angle pdb=" CB ARG A2273 " pdb=" CG ARG A2273 " pdb=" CD ARG A2273 " ideal model delta sigma weight residual 111.30 119.73 -8.43 2.30e+00 1.89e-01 1.34e+01 angle pdb=" O1B ANP A4705 " pdb=" PB ANP A4705 " pdb=" O2B ANP A4705 " ideal model delta sigma weight residual 120.08 109.19 10.89 3.00e+00 1.11e-01 1.32e+01 ... (remaining 34143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.10: 14653 32.10 - 64.20: 597 64.20 - 96.30: 67 96.30 - 128.39: 0 128.39 - 160.49: 2 Dihedral angle restraints: 15319 sinusoidal: 6397 harmonic: 8922 Sorted by residual: dihedral pdb=" CA CYS A2712 " pdb=" C CYS A2712 " pdb=" N ASN A2713 " pdb=" CA ASN A2713 " ideal model delta harmonic sigma weight residual 180.00 157.03 22.97 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" O1A ANP A4705 " pdb=" O3A ANP A4705 " pdb=" PA ANP A4705 " pdb=" PB ANP A4705 " ideal model delta sinusoidal sigma weight residual 83.11 -77.38 160.49 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" O1A ANP A4704 " pdb=" O3A ANP A4704 " pdb=" PA ANP A4704 " pdb=" PB ANP A4704 " ideal model delta sinusoidal sigma weight residual 83.11 -55.13 138.24 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 15316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3338 0.058 - 0.116: 417 0.116 - 0.174: 64 0.174 - 0.232: 2 0.232 - 0.291: 4 Chirality restraints: 3825 Sorted by residual: chirality pdb=" C2' ATP A4702 " pdb=" C1' ATP A4702 " pdb=" C3' ATP A4702 " pdb=" O2' ATP A4702 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C3' ATP A4702 " pdb=" C2' ATP A4702 " pdb=" C4' ATP A4702 " pdb=" O3' ATP A4702 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' ANP A4704 " pdb=" C2' ANP A4704 " pdb=" C4' ANP A4704 " pdb=" O3' ANP A4704 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 3822 not shown) Planarity restraints: 4376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A4376 " -0.020 2.00e-02 2.50e+03 2.52e-02 1.59e+01 pdb=" CG TRP A4376 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP A4376 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A4376 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A4376 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A4376 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A4376 " -0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP A4376 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A4376 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A4376 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A2668 " 0.046 5.00e-02 4.00e+02 6.90e-02 7.63e+00 pdb=" N PRO A2669 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A2669 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A2669 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A2627 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO A2628 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A2628 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A2628 " 0.035 5.00e-02 4.00e+02 ... (remaining 4373 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 91 2.50 - 3.10: 17762 3.10 - 3.70: 38105 3.70 - 4.30: 54220 4.30 - 4.90: 91227 Nonbonded interactions: 201405 Sorted by model distance: nonbonded pdb=" NH2 ARG A2726 " pdb="MG MG A4703 " model vdw 1.902 2.250 nonbonded pdb=" O ILE A2747 " pdb=" OG1 THR A2750 " model vdw 2.177 3.040 nonbonded pdb=" O1G ANP A4705 " pdb=" O2B ANP A4705 " model vdw 2.179 3.040 nonbonded pdb=" O THR A3492 " pdb=" OG1 THR A3495 " model vdw 2.210 3.040 nonbonded pdb=" NH1 ARG A2729 " pdb=" O2G ATP A4702 " model vdw 2.219 3.120 ... (remaining 201400 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: 29.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.530 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 25182 Z= 0.190 Angle : 0.734 19.001 34148 Z= 0.360 Chirality : 0.041 0.291 3825 Planarity : 0.005 0.069 4376 Dihedral : 16.837 160.493 9523 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.18 % Allowed : 13.14 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: 0.93 (0.15), residues: 3039 helix: 1.21 (0.12), residues: 1720 sheet: -1.26 (0.31), residues: 243 loop : 0.31 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A2844 TYR 0.021 0.001 TYR A2748 PHE 0.014 0.001 PHE A4410 TRP 0.067 0.002 TRP A4376 HIS 0.008 0.001 HIS A2637 Details of bonding type rmsd covalent geometry : bond 0.00424 (25182) covalent geometry : angle 0.73379 (34148) hydrogen bonds : bond 0.13821 ( 1379) hydrogen bonds : angle 5.67017 ( 4026) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 210 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 2055 TYR cc_start: 0.7973 (t80) cc_final: 0.7496 (t80) REVERT: A 4419 MET cc_start: 0.6329 (ttt) cc_final: 0.6073 (ttt) REVERT: A 4422 LYS cc_start: 0.7341 (ttmm) cc_final: 0.7087 (mmtm) outliers start: 5 outliers final: 4 residues processed: 215 average time/residue: 0.1728 time to fit residues: 59.1774 Evaluate side-chains 196 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 192 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1871 GLU Chi-restraints excluded: chain A residue 3154 LEU Chi-restraints excluded: chain A residue 3588 LEU Chi-restraints excluded: chain A residue 4078 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1387 GLN A1784 ASN A1894 GLN A2377 ASN A2560 HIS A2637 HIS A2930 GLN A2987 ASN A3155 HIS A3175 HIS A3200 HIS A3822 HIS A4006 HIS A4065 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.088915 restraints weight = 45133.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.091498 restraints weight = 24633.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.093185 restraints weight = 16675.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.094290 restraints weight = 12933.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.094991 restraints weight = 10968.609| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25182 Z= 0.136 Angle : 0.532 7.117 34148 Z= 0.270 Chirality : 0.040 0.162 3825 Planarity : 0.004 0.060 4376 Dihedral : 8.863 175.389 3431 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.73 % Allowed : 12.92 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: 3039 helix: 1.63 (0.12), residues: 1740 sheet: -1.03 (0.31), residues: 251 loop : 0.43 (0.21), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2726 TYR 0.022 0.001 TYR A2748 PHE 0.015 0.002 PHE A2912 TRP 0.029 0.001 TRP A4376 HIS 0.004 0.001 HIS A4187 Details of bonding type rmsd covalent geometry : bond 0.00312 (25182) covalent geometry : angle 0.53222 (34148) hydrogen bonds : bond 0.04223 ( 1379) hydrogen bonds : angle 4.24078 ( 4026) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 213 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 2223 VAL cc_start: 0.8315 (OUTLIER) cc_final: 0.7919 (t) REVERT: A 2481 MET cc_start: 0.6908 (tpt) cc_final: 0.6701 (tpt) REVERT: A 2869 ARG cc_start: 0.6122 (mmm160) cc_final: 0.5783 (mtt-85) REVERT: A 3862 ASP cc_start: 0.7415 (m-30) cc_final: 0.6840 (m-30) REVERT: A 4063 ASN cc_start: 0.7364 (t0) cc_final: 0.7153 (t0) REVERT: A 4192 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7560 (tp30) REVERT: A 4419 MET cc_start: 0.6286 (ttt) cc_final: 0.6039 (ttt) REVERT: A 4494 LEU cc_start: 0.8269 (mt) cc_final: 0.7823 (tp) outliers start: 47 outliers final: 19 residues processed: 243 average time/residue: 0.1626 time to fit residues: 64.1368 Evaluate side-chains 203 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 2221 MET Chi-restraints excluded: chain A residue 2223 VAL Chi-restraints excluded: chain A residue 2234 TRP Chi-restraints excluded: chain A residue 2502 LEU Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 3000 LEU Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3196 GLU Chi-restraints excluded: chain A residue 3588 LEU Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3670 ASP Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3686 VAL Chi-restraints excluded: chain A residue 3691 ASP Chi-restraints excluded: chain A residue 3757 LYS Chi-restraints excluded: chain A residue 3981 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 282 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 268 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 212 optimal weight: 0.9980 chunk 257 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 221 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 chunk 254 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1387 GLN A1541 GLN A1855 GLN A3155 HIS A4453 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.108415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.087396 restraints weight = 45076.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.089948 restraints weight = 24760.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.091606 restraints weight = 16812.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.092687 restraints weight = 13097.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.093387 restraints weight = 11151.308| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25182 Z= 0.147 Angle : 0.511 7.891 34148 Z= 0.259 Chirality : 0.040 0.157 3825 Planarity : 0.004 0.059 4376 Dihedral : 8.335 178.529 3424 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.62 % Allowed : 13.87 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: 1.56 (0.16), residues: 3039 helix: 1.78 (0.12), residues: 1737 sheet: -0.93 (0.30), residues: 264 loop : 0.46 (0.21), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3741 TYR 0.020 0.001 TYR A2748 PHE 0.013 0.001 PHE A2912 TRP 0.019 0.001 TRP A3489 HIS 0.003 0.001 HIS A2577 Details of bonding type rmsd covalent geometry : bond 0.00341 (25182) covalent geometry : angle 0.51125 (34148) hydrogen bonds : bond 0.04030 ( 1379) hydrogen bonds : angle 4.10365 ( 4026) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 1.057 Fit side-chains REVERT: A 1419 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7403 (ttm170) REVERT: A 2053 MET cc_start: 0.7629 (mtp) cc_final: 0.7273 (mtp) REVERT: A 2869 ARG cc_start: 0.6130 (mmm160) cc_final: 0.5858 (mtt-85) REVERT: A 2886 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7268 (tp-100) REVERT: A 3862 ASP cc_start: 0.7409 (m-30) cc_final: 0.6839 (m-30) REVERT: A 4063 ASN cc_start: 0.7262 (t0) cc_final: 0.7049 (t0) REVERT: A 4192 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7624 (tp30) REVERT: A 4419 MET cc_start: 0.6360 (ttt) cc_final: 0.6126 (ttt) REVERT: A 4494 LEU cc_start: 0.8211 (mt) cc_final: 0.7774 (tp) outliers start: 44 outliers final: 22 residues processed: 228 average time/residue: 0.1660 time to fit residues: 60.8608 Evaluate side-chains 215 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1419 ARG Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 2039 LEU Chi-restraints excluded: chain A residue 2234 TRP Chi-restraints excluded: chain A residue 2502 LEU Chi-restraints excluded: chain A residue 2541 ILE Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2886 GLN Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 3000 LEU Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3196 GLU Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3670 ASP Chi-restraints excluded: chain A residue 3681 THR Chi-restraints excluded: chain A residue 3686 VAL Chi-restraints excluded: chain A residue 3691 ASP Chi-restraints excluded: chain A residue 3820 GLN Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4453 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 271 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 156 optimal weight: 0.7980 chunk 245 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 254 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 193 optimal weight: 0.5980 chunk 185 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1355 GLN A1387 GLN A1479 ASN A1643 ASN A2560 HIS A3063 HIS A3473 ASN A4453 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.108159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.087171 restraints weight = 44930.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.089717 restraints weight = 24773.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.091378 restraints weight = 16842.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.092466 restraints weight = 13123.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.093103 restraints weight = 11157.411| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25182 Z= 0.140 Angle : 0.502 7.262 34148 Z= 0.254 Chirality : 0.039 0.154 3825 Planarity : 0.004 0.057 4376 Dihedral : 8.060 175.007 3422 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.85 % Allowed : 14.13 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: 1.62 (0.16), residues: 3039 helix: 1.84 (0.12), residues: 1738 sheet: -0.89 (0.30), residues: 264 loop : 0.46 (0.20), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3741 TYR 0.023 0.001 TYR A4467 PHE 0.011 0.001 PHE A2912 TRP 0.019 0.001 TRP A1701 HIS 0.004 0.001 HIS A4466 Details of bonding type rmsd covalent geometry : bond 0.00326 (25182) covalent geometry : angle 0.50209 (34148) hydrogen bonds : bond 0.03873 ( 1379) hydrogen bonds : angle 4.01780 ( 4026) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 200 time to evaluate : 0.886 Fit side-chains REVERT: A 2032 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7553 (mt) REVERT: A 2835 ASP cc_start: 0.7976 (m-30) cc_final: 0.7465 (m-30) REVERT: A 2886 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7300 (tp-100) REVERT: A 3075 LEU cc_start: 0.4648 (OUTLIER) cc_final: 0.4082 (mp) REVERT: A 3862 ASP cc_start: 0.7380 (m-30) cc_final: 0.6834 (m-30) REVERT: A 4192 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7702 (tp30) REVERT: A 4419 MET cc_start: 0.6228 (ttt) cc_final: 0.5862 (ttt) REVERT: A 4494 LEU cc_start: 0.8208 (mt) cc_final: 0.7775 (tp) outliers start: 50 outliers final: 28 residues processed: 232 average time/residue: 0.1695 time to fit residues: 63.2813 Evaluate side-chains 218 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1768 SER Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2039 LEU Chi-restraints excluded: chain A residue 2234 TRP Chi-restraints excluded: chain A residue 2502 LEU Chi-restraints excluded: chain A residue 2541 ILE Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2886 GLN Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 3000 LEU Chi-restraints excluded: chain A residue 3075 LEU Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3196 GLU Chi-restraints excluded: chain A residue 3472 VAL Chi-restraints excluded: chain A residue 3668 ASP Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3686 VAL Chi-restraints excluded: chain A residue 3691 ASP Chi-restraints excluded: chain A residue 3696 VAL Chi-restraints excluded: chain A residue 3757 LYS Chi-restraints excluded: chain A residue 3820 GLN Chi-restraints excluded: chain A residue 3824 LEU Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4476 ILE Chi-restraints excluded: chain A residue 4611 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 294 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 177 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 278 optimal weight: 0.9980 chunk 161 optimal weight: 0.0030 chunk 218 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3522 GLN A4453 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.108675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.087542 restraints weight = 45052.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.090102 restraints weight = 24818.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.091784 restraints weight = 16872.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.092872 restraints weight = 13112.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.093566 restraints weight = 11173.534| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25182 Z= 0.127 Angle : 0.493 6.188 34148 Z= 0.250 Chirality : 0.039 0.149 3825 Planarity : 0.004 0.057 4376 Dihedral : 7.829 174.451 3422 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.36 % Allowed : 14.21 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: 1.75 (0.16), residues: 3039 helix: 1.96 (0.12), residues: 1733 sheet: -0.72 (0.31), residues: 249 loop : 0.44 (0.20), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2273 TYR 0.019 0.001 TYR A2748 PHE 0.012 0.001 PHE A4410 TRP 0.019 0.001 TRP A1701 HIS 0.003 0.001 HIS A4466 Details of bonding type rmsd covalent geometry : bond 0.00291 (25182) covalent geometry : angle 0.49331 (34148) hydrogen bonds : bond 0.03704 ( 1379) hydrogen bonds : angle 3.93790 ( 4026) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 199 time to evaluate : 1.089 Fit side-chains REVERT: A 1417 MET cc_start: 0.7336 (ptm) cc_final: 0.7011 (ptm) REVERT: A 2032 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7521 (mt) REVERT: A 2053 MET cc_start: 0.7675 (mtp) cc_final: 0.7350 (mtp) REVERT: A 2335 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8417 (tt) REVERT: A 2835 ASP cc_start: 0.7960 (m-30) cc_final: 0.7410 (m-30) REVERT: A 2886 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7270 (tp-100) REVERT: A 3075 LEU cc_start: 0.4631 (OUTLIER) cc_final: 0.4070 (mp) REVERT: A 3764 ASP cc_start: 0.6798 (OUTLIER) cc_final: 0.6497 (t0) REVERT: A 3862 ASP cc_start: 0.7397 (m-30) cc_final: 0.6815 (m-30) REVERT: A 4110 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: A 4192 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7729 (tp30) REVERT: A 4419 MET cc_start: 0.6167 (ttt) cc_final: 0.5851 (ttt) REVERT: A 4473 MET cc_start: 0.5045 (ptm) cc_final: 0.4744 (ttp) REVERT: A 4494 LEU cc_start: 0.8350 (mt) cc_final: 0.7930 (tp) outliers start: 64 outliers final: 32 residues processed: 246 average time/residue: 0.1665 time to fit residues: 66.1551 Evaluate side-chains 227 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2039 LEU Chi-restraints excluded: chain A residue 2234 TRP Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2335 LEU Chi-restraints excluded: chain A residue 2502 LEU Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2872 LEU Chi-restraints excluded: chain A residue 2886 GLN Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 3000 LEU Chi-restraints excluded: chain A residue 3075 LEU Chi-restraints excluded: chain A residue 3094 PHE Chi-restraints excluded: chain A residue 3196 GLU Chi-restraints excluded: chain A residue 3218 LEU Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3670 ASP Chi-restraints excluded: chain A residue 3686 VAL Chi-restraints excluded: chain A residue 3691 ASP Chi-restraints excluded: chain A residue 3696 VAL Chi-restraints excluded: chain A residue 3757 LYS Chi-restraints excluded: chain A residue 3764 ASP Chi-restraints excluded: chain A residue 3820 GLN Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4110 GLU Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4453 ASN Chi-restraints excluded: chain A residue 4476 ILE Chi-restraints excluded: chain A residue 4546 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 104 optimal weight: 0.5980 chunk 200 optimal weight: 0.6980 chunk 185 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 227 optimal weight: 0.0980 chunk 133 optimal weight: 0.4980 chunk 103 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2083 GLN A2376 ASN A2463 HIS A2637 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.088743 restraints weight = 44681.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.091326 restraints weight = 24513.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.093012 restraints weight = 16585.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.094100 restraints weight = 12885.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.094777 restraints weight = 10946.998| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25182 Z= 0.102 Angle : 0.478 8.036 34148 Z= 0.240 Chirality : 0.038 0.141 3825 Planarity : 0.004 0.057 4376 Dihedral : 7.547 171.851 3422 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.03 % Allowed : 14.69 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: 1.93 (0.16), residues: 3039 helix: 2.11 (0.12), residues: 1735 sheet: -0.66 (0.32), residues: 247 loop : 0.49 (0.20), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3741 TYR 0.019 0.001 TYR A2748 PHE 0.014 0.001 PHE A4482 TRP 0.020 0.001 TRP A1701 HIS 0.004 0.000 HIS A2637 Details of bonding type rmsd covalent geometry : bond 0.00227 (25182) covalent geometry : angle 0.47821 (34148) hydrogen bonds : bond 0.03489 ( 1379) hydrogen bonds : angle 3.83495 ( 4026) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 206 time to evaluate : 0.989 Fit side-chains REVERT: A 1360 ARG cc_start: 0.6879 (ttt90) cc_final: 0.6559 (ttt-90) REVERT: A 1417 MET cc_start: 0.7341 (ptm) cc_final: 0.6944 (ptm) REVERT: A 2053 MET cc_start: 0.7626 (mtp) cc_final: 0.7288 (mtp) REVERT: A 2335 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8390 (tt) REVERT: A 2632 LEU cc_start: 0.8745 (mt) cc_final: 0.8509 (mt) REVERT: A 2835 ASP cc_start: 0.7955 (m-30) cc_final: 0.7416 (m-30) REVERT: A 2886 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7246 (tp-100) REVERT: A 3075 LEU cc_start: 0.4594 (OUTLIER) cc_final: 0.4048 (mp) REVERT: A 3500 MET cc_start: 0.7126 (tpt) cc_final: 0.6923 (tpp) REVERT: A 3764 ASP cc_start: 0.6640 (OUTLIER) cc_final: 0.6366 (t0) REVERT: A 3815 MET cc_start: 0.7935 (mtp) cc_final: 0.7688 (ttm) REVERT: A 3862 ASP cc_start: 0.7412 (m-30) cc_final: 0.6823 (m-30) REVERT: A 4110 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: A 4192 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7727 (tp30) REVERT: A 4347 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.7196 (tp40) REVERT: A 4419 MET cc_start: 0.6154 (ttt) cc_final: 0.5784 (ttt) REVERT: A 4494 LEU cc_start: 0.8342 (mt) cc_final: 0.7920 (tp) REVERT: A 4581 ILE cc_start: 0.8938 (mp) cc_final: 0.8656 (mm) outliers start: 55 outliers final: 35 residues processed: 247 average time/residue: 0.1529 time to fit residues: 61.9416 Evaluate side-chains 234 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1768 SER Chi-restraints excluded: chain A residue 2039 LEU Chi-restraints excluded: chain A residue 2234 TRP Chi-restraints excluded: chain A residue 2335 LEU Chi-restraints excluded: chain A residue 2502 LEU Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2872 LEU Chi-restraints excluded: chain A residue 2886 GLN Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 3075 LEU Chi-restraints excluded: chain A residue 3196 GLU Chi-restraints excluded: chain A residue 3218 LEU Chi-restraints excluded: chain A residue 3524 MET Chi-restraints excluded: chain A residue 3668 ASP Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3670 ASP Chi-restraints excluded: chain A residue 3686 VAL Chi-restraints excluded: chain A residue 3691 ASP Chi-restraints excluded: chain A residue 3696 VAL Chi-restraints excluded: chain A residue 3764 ASP Chi-restraints excluded: chain A residue 3820 GLN Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4095 MET Chi-restraints excluded: chain A residue 4110 GLU Chi-restraints excluded: chain A residue 4212 LEU Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4347 GLN Chi-restraints excluded: chain A residue 4349 LEU Chi-restraints excluded: chain A residue 4476 ILE Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4546 THR Chi-restraints excluded: chain A residue 4611 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 143 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 189 optimal weight: 0.0050 chunk 260 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 265 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 187 optimal weight: 0.6980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1387 GLN A2083 GLN A2085 HIS A2560 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.109105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.088097 restraints weight = 44848.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.090673 restraints weight = 24680.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.092337 restraints weight = 16708.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.093432 restraints weight = 13019.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.094132 restraints weight = 11060.169| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25182 Z= 0.118 Angle : 0.483 6.849 34148 Z= 0.244 Chirality : 0.038 0.142 3825 Planarity : 0.004 0.058 4376 Dihedral : 7.182 172.233 3422 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.07 % Allowed : 15.39 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: 1.95 (0.16), residues: 3039 helix: 2.12 (0.12), residues: 1736 sheet: -0.64 (0.32), residues: 254 loop : 0.52 (0.21), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3741 TYR 0.018 0.001 TYR A2748 PHE 0.011 0.001 PHE A4410 TRP 0.030 0.001 TRP A4478 HIS 0.006 0.001 HIS A4466 Details of bonding type rmsd covalent geometry : bond 0.00272 (25182) covalent geometry : angle 0.48318 (34148) hydrogen bonds : bond 0.03486 ( 1379) hydrogen bonds : angle 3.82916 ( 4026) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 196 time to evaluate : 1.103 Fit side-chains REVERT: A 1360 ARG cc_start: 0.6923 (ttt90) cc_final: 0.6539 (ttt-90) REVERT: A 2032 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7524 (mt) REVERT: A 2053 MET cc_start: 0.7652 (mtp) cc_final: 0.7279 (mtp) REVERT: A 2149 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.7677 (mm) REVERT: A 2632 LEU cc_start: 0.8740 (mt) cc_final: 0.8519 (mt) REVERT: A 2835 ASP cc_start: 0.7910 (m-30) cc_final: 0.7351 (m-30) REVERT: A 2886 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7270 (tp-100) REVERT: A 3075 LEU cc_start: 0.4804 (OUTLIER) cc_final: 0.4266 (mp) REVERT: A 3500 MET cc_start: 0.7118 (tpt) cc_final: 0.6887 (tpp) REVERT: A 3764 ASP cc_start: 0.6615 (OUTLIER) cc_final: 0.6290 (t0) REVERT: A 3815 MET cc_start: 0.7967 (mtp) cc_final: 0.7739 (ttm) REVERT: A 3862 ASP cc_start: 0.7387 (m-30) cc_final: 0.6810 (m-30) REVERT: A 4110 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: A 4192 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7749 (tp30) REVERT: A 4347 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7354 (tp40) REVERT: A 4419 MET cc_start: 0.6021 (ttt) cc_final: 0.5722 (ttt) REVERT: A 4473 MET cc_start: 0.4980 (ptm) cc_final: 0.4613 (ttp) REVERT: A 4494 LEU cc_start: 0.8340 (mt) cc_final: 0.7917 (tp) REVERT: A 4581 ILE cc_start: 0.8943 (mp) cc_final: 0.8667 (mm) outliers start: 56 outliers final: 43 residues processed: 237 average time/residue: 0.1605 time to fit residues: 62.4889 Evaluate side-chains 236 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 186 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1768 SER Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2039 LEU Chi-restraints excluded: chain A residue 2130 ASN Chi-restraints excluded: chain A residue 2149 LEU Chi-restraints excluded: chain A residue 2234 TRP Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2502 LEU Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2872 LEU Chi-restraints excluded: chain A residue 2886 GLN Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 2923 ASP Chi-restraints excluded: chain A residue 3075 LEU Chi-restraints excluded: chain A residue 3196 GLU Chi-restraints excluded: chain A residue 3218 LEU Chi-restraints excluded: chain A residue 3524 MET Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3668 ASP Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3670 ASP Chi-restraints excluded: chain A residue 3686 VAL Chi-restraints excluded: chain A residue 3691 ASP Chi-restraints excluded: chain A residue 3696 VAL Chi-restraints excluded: chain A residue 3764 ASP Chi-restraints excluded: chain A residue 3820 GLN Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4095 MET Chi-restraints excluded: chain A residue 4110 GLU Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4347 GLN Chi-restraints excluded: chain A residue 4349 LEU Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4476 ILE Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4546 THR Chi-restraints excluded: chain A residue 4611 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 5 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 296 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 287 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 210 optimal weight: 0.0770 chunk 94 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 overall best weight: 0.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1387 GLN A2005 GLN A2560 HIS A2637 HIS A4062 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.108507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.087532 restraints weight = 45035.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.090075 restraints weight = 24861.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.091748 restraints weight = 16878.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.092815 restraints weight = 13127.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.093511 restraints weight = 11176.816| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25182 Z= 0.128 Angle : 0.494 7.771 34148 Z= 0.249 Chirality : 0.039 0.146 3825 Planarity : 0.004 0.058 4376 Dihedral : 6.833 172.469 3422 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.25 % Allowed : 15.68 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: 1.95 (0.16), residues: 3039 helix: 2.11 (0.12), residues: 1736 sheet: -0.59 (0.32), residues: 254 loop : 0.52 (0.20), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3741 TYR 0.019 0.001 TYR A2748 PHE 0.012 0.001 PHE A3094 TRP 0.022 0.001 TRP A4478 HIS 0.004 0.001 HIS A2637 Details of bonding type rmsd covalent geometry : bond 0.00297 (25182) covalent geometry : angle 0.49364 (34148) hydrogen bonds : bond 0.03538 ( 1379) hydrogen bonds : angle 3.82716 ( 4026) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 201 time to evaluate : 0.970 Fit side-chains REVERT: A 1360 ARG cc_start: 0.6874 (ttt90) cc_final: 0.6514 (ttt-90) REVERT: A 2032 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7558 (mt) REVERT: A 2053 MET cc_start: 0.7594 (mtp) cc_final: 0.7284 (mtp) REVERT: A 2149 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.7733 (mm) REVERT: A 2632 LEU cc_start: 0.8720 (mt) cc_final: 0.8500 (mt) REVERT: A 2835 ASP cc_start: 0.7875 (m-30) cc_final: 0.7316 (m-30) REVERT: A 2886 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7345 (tp-100) REVERT: A 2973 ASP cc_start: 0.7987 (t0) cc_final: 0.7363 (t0) REVERT: A 3075 LEU cc_start: 0.4550 (OUTLIER) cc_final: 0.4016 (mp) REVERT: A 3500 MET cc_start: 0.7207 (tpt) cc_final: 0.6958 (tpp) REVERT: A 3862 ASP cc_start: 0.7361 (m-30) cc_final: 0.6800 (m-30) REVERT: A 4110 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: A 4192 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7693 (tp30) REVERT: A 4419 MET cc_start: 0.6099 (ttt) cc_final: 0.5799 (ttt) REVERT: A 4473 MET cc_start: 0.4984 (ptm) cc_final: 0.4567 (ttp) REVERT: A 4494 LEU cc_start: 0.8338 (mt) cc_final: 0.7920 (tp) outliers start: 61 outliers final: 43 residues processed: 247 average time/residue: 0.1648 time to fit residues: 65.0689 Evaluate side-chains 233 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 185 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1556 ASP Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1768 SER Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2039 LEU Chi-restraints excluded: chain A residue 2130 ASN Chi-restraints excluded: chain A residue 2149 LEU Chi-restraints excluded: chain A residue 2234 TRP Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2502 LEU Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2872 LEU Chi-restraints excluded: chain A residue 2886 GLN Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 2923 ASP Chi-restraints excluded: chain A residue 3075 LEU Chi-restraints excluded: chain A residue 3196 GLU Chi-restraints excluded: chain A residue 3218 LEU Chi-restraints excluded: chain A residue 3472 VAL Chi-restraints excluded: chain A residue 3524 MET Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3668 ASP Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3670 ASP Chi-restraints excluded: chain A residue 3686 VAL Chi-restraints excluded: chain A residue 3691 ASP Chi-restraints excluded: chain A residue 3696 VAL Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4095 MET Chi-restraints excluded: chain A residue 4110 GLU Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4349 LEU Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4546 THR Chi-restraints excluded: chain A residue 4611 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 274 optimal weight: 2.9990 chunk 122 optimal weight: 0.1980 chunk 221 optimal weight: 1.9990 chunk 139 optimal weight: 0.4980 chunk 210 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 290 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1387 GLN A2482 GLN A2560 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.107818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.086828 restraints weight = 45128.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.089350 restraints weight = 24957.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.090990 restraints weight = 16984.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.092049 restraints weight = 13255.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.092740 restraints weight = 11295.366| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25182 Z= 0.142 Angle : 0.512 7.064 34148 Z= 0.258 Chirality : 0.039 0.151 3825 Planarity : 0.004 0.058 4376 Dihedral : 6.746 173.395 3422 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.07 % Allowed : 16.16 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.88 (0.16), residues: 3039 helix: 2.05 (0.12), residues: 1737 sheet: -0.58 (0.32), residues: 254 loop : 0.50 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3160 TYR 0.020 0.001 TYR A2748 PHE 0.014 0.001 PHE A3094 TRP 0.021 0.001 TRP A4478 HIS 0.003 0.001 HIS A2577 Details of bonding type rmsd covalent geometry : bond 0.00334 (25182) covalent geometry : angle 0.51159 (34148) hydrogen bonds : bond 0.03632 ( 1379) hydrogen bonds : angle 3.85119 ( 4026) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 188 time to evaluate : 0.961 Fit side-chains REVERT: A 1360 ARG cc_start: 0.6887 (ttt90) cc_final: 0.6517 (ttt-90) REVERT: A 2032 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7597 (mt) REVERT: A 2053 MET cc_start: 0.7573 (mtp) cc_final: 0.7256 (mtp) REVERT: A 2835 ASP cc_start: 0.7864 (m-30) cc_final: 0.7300 (m-30) REVERT: A 2886 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.7367 (tp-100) REVERT: A 2973 ASP cc_start: 0.8003 (t0) cc_final: 0.7376 (t0) REVERT: A 3075 LEU cc_start: 0.4550 (OUTLIER) cc_final: 0.3994 (mp) REVERT: A 3500 MET cc_start: 0.7229 (tpt) cc_final: 0.6972 (tpp) REVERT: A 3862 ASP cc_start: 0.7376 (m-30) cc_final: 0.6809 (m-30) REVERT: A 4110 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7787 (tt0) REVERT: A 4192 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7772 (tp30) REVERT: A 4419 MET cc_start: 0.6246 (ttt) cc_final: 0.5974 (ttt) REVERT: A 4473 MET cc_start: 0.5185 (ptm) cc_final: 0.4828 (ttp) REVERT: A 4494 LEU cc_start: 0.8344 (mt) cc_final: 0.7924 (tp) outliers start: 56 outliers final: 45 residues processed: 231 average time/residue: 0.1598 time to fit residues: 60.4141 Evaluate side-chains 230 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 181 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1556 ASP Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 1768 SER Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2039 LEU Chi-restraints excluded: chain A residue 2130 ASN Chi-restraints excluded: chain A residue 2149 LEU Chi-restraints excluded: chain A residue 2234 TRP Chi-restraints excluded: chain A residue 2250 VAL Chi-restraints excluded: chain A residue 2502 LEU Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2581 LEU Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2676 THR Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2818 VAL Chi-restraints excluded: chain A residue 2872 LEU Chi-restraints excluded: chain A residue 2886 GLN Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 2923 ASP Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 3075 LEU Chi-restraints excluded: chain A residue 3196 GLU Chi-restraints excluded: chain A residue 3218 LEU Chi-restraints excluded: chain A residue 3472 VAL Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3668 ASP Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3670 ASP Chi-restraints excluded: chain A residue 3686 VAL Chi-restraints excluded: chain A residue 3691 ASP Chi-restraints excluded: chain A residue 3696 VAL Chi-restraints excluded: chain A residue 3981 THR Chi-restraints excluded: chain A residue 4095 MET Chi-restraints excluded: chain A residue 4110 GLU Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4340 ILE Chi-restraints excluded: chain A residue 4349 LEU Chi-restraints excluded: chain A residue 4390 LEU Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4546 THR Chi-restraints excluded: chain A residue 4611 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 274 optimal weight: 0.9990 chunk 120 optimal weight: 0.0970 chunk 25 optimal weight: 0.8980 chunk 222 optimal weight: 0.7980 chunk 212 optimal weight: 0.1980 chunk 276 optimal weight: 0.7980 chunk 257 optimal weight: 0.0050 chunk 60 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 279 optimal weight: 0.6980 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4453 ASN ** 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 = 0.3565 r_free = 0.3565 target = 0.110162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.089300 restraints weight = 44819.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.091847 restraints weight = 24470.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.093547 restraints weight = 16567.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.094649 restraints weight = 12837.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.095327 restraints weight = 10882.279| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25182 Z= 0.100 Angle : 0.481 7.497 34148 Z= 0.243 Chirality : 0.038 0.140 3825 Planarity : 0.004 0.063 4376 Dihedral : 6.505 169.326 3422 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.62 % Allowed : 16.57 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % 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: 2.13 (0.16), residues: 3039 helix: 2.28 (0.12), residues: 1734 sheet: -0.50 (0.32), residues: 254 loop : 0.55 (0.20), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3741 TYR 0.018 0.001 TYR A2748 PHE 0.010 0.001 PHE A4410 TRP 0.022 0.001 TRP A1701 HIS 0.002 0.000 HIS A2252 Details of bonding type rmsd covalent geometry : bond 0.00222 (25182) covalent geometry : angle 0.48068 (34148) hydrogen bonds : bond 0.03281 ( 1379) hydrogen bonds : angle 3.73102 ( 4026) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 201 time to evaluate : 0.997 Fit side-chains REVERT: A 1360 ARG cc_start: 0.6838 (ttt90) cc_final: 0.6504 (ttt-90) REVERT: A 1524 GLU cc_start: 0.7656 (tp30) cc_final: 0.7384 (pp20) REVERT: A 2032 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7427 (mt) REVERT: A 2053 MET cc_start: 0.7562 (mtp) cc_final: 0.7318 (mtp) REVERT: A 2149 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.7646 (mm) REVERT: A 2232 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7737 (tpt) REVERT: A 2835 ASP cc_start: 0.7876 (m-30) cc_final: 0.7305 (m-30) REVERT: A 2973 ASP cc_start: 0.7956 (t0) cc_final: 0.7321 (t0) REVERT: A 3691 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7826 (t0) REVERT: A 3815 MET cc_start: 0.8364 (ttm) cc_final: 0.8095 (ttm) REVERT: A 3862 ASP cc_start: 0.7378 (m-30) cc_final: 0.6794 (m-30) REVERT: A 4192 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7737 (tp30) REVERT: A 4419 MET cc_start: 0.6204 (ttt) cc_final: 0.5785 (ttt) REVERT: A 4473 MET cc_start: 0.5139 (ptm) cc_final: 0.4770 (ttp) REVERT: A 4494 LEU cc_start: 0.8345 (mt) cc_final: 0.7916 (tp) REVERT: A 4581 ILE cc_start: 0.8964 (mp) cc_final: 0.8704 (mm) outliers start: 44 outliers final: 32 residues processed: 234 average time/residue: 0.1630 time to fit residues: 62.6539 Evaluate side-chains 223 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2039 LEU Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2130 ASN Chi-restraints excluded: chain A residue 2149 LEU Chi-restraints excluded: chain A residue 2232 MET Chi-restraints excluded: chain A residue 2234 TRP Chi-restraints excluded: chain A residue 2502 LEU Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2666 ILE Chi-restraints excluded: chain A residue 2734 VAL Chi-restraints excluded: chain A residue 2785 THR Chi-restraints excluded: chain A residue 2872 LEU Chi-restraints excluded: chain A residue 2889 LEU Chi-restraints excluded: chain A residue 2911 LEU Chi-restraints excluded: chain A residue 2923 ASP Chi-restraints excluded: chain A residue 2936 ILE Chi-restraints excluded: chain A residue 3196 GLU Chi-restraints excluded: chain A residue 3218 LEU Chi-restraints excluded: chain A residue 3472 VAL Chi-restraints excluded: chain A residue 3612 THR Chi-restraints excluded: chain A residue 3638 VAL Chi-restraints excluded: chain A residue 3669 ILE Chi-restraints excluded: chain A residue 3691 ASP Chi-restraints excluded: chain A residue 3696 VAL Chi-restraints excluded: chain A residue 4095 MET Chi-restraints excluded: chain A residue 4247 MET Chi-restraints excluded: chain A residue 4349 LEU Chi-restraints excluded: chain A residue 4468 THR Chi-restraints excluded: chain A residue 4516 VAL Chi-restraints excluded: chain A residue 4540 CYS Chi-restraints excluded: chain A residue 4546 THR Chi-restraints excluded: chain A residue 4611 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 81 optimal weight: 0.6980 chunk 117 optimal weight: 0.5980 chunk 241 optimal weight: 1.9990 chunk 296 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 237 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 287 optimal weight: 0.3980 chunk 271 optimal weight: 0.0770 chunk 217 optimal weight: 0.9990 chunk 222 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2560 HIS A4526 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.109493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.088655 restraints weight = 44889.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.091189 restraints weight = 24597.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.092883 restraints weight = 16683.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.093966 restraints weight = 12934.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.094687 restraints weight = 10974.632| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25182 Z= 0.114 Angle : 0.494 7.594 34148 Z= 0.249 Chirality : 0.038 0.140 3825 Planarity : 0.004 0.061 4376 Dihedral : 6.480 170.490 3422 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.51 % Allowed : 17.01 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.08 (0.16), residues: 3039 helix: 2.24 (0.12), residues: 1737 sheet: -0.54 (0.32), residues: 262 loop : 0.55 (0.21), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3741 TYR 0.018 0.001 TYR A2748 PHE 0.011 0.001 PHE A4410 TRP 0.056 0.001 TRP A2658 HIS 0.005 0.001 HIS A2964 Details of bonding type rmsd covalent geometry : bond 0.00262 (25182) covalent geometry : angle 0.49437 (34148) hydrogen bonds : bond 0.03350 ( 1379) hydrogen bonds : angle 3.75167 ( 4026) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4363.23 seconds wall clock time: 76 minutes 14.87 seconds (4574.87 seconds total)