Starting phenix.real_space_refine on Thu Jun 4 13:30:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xd5_66755/06_2026/9xd5_66755.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xd5_66755/06_2026/9xd5_66755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xd5_66755/06_2026/9xd5_66755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xd5_66755/06_2026/9xd5_66755.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xd5_66755/06_2026/9xd5_66755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xd5_66755/06_2026/9xd5_66755.map" } resolution = 2.72 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= 0.001 sd= 0.028 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 Zn 1 6.06 5 P 10 5.49 5 S 91 5.16 5 C 8059 2.51 5 N 2221 2.21 5 O 2428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12810 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1571, 12577 Classifications: {'peptide': 1571} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 1525} Chain breaks: 14 Chain: "C" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 232 Classifications: {'RNA': 11} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna3p_pur': 3, 'rna3p_pyr': 4} Link IDs: {'rna2p': 3, 'rna3p': 7} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 816 SG CYS A1028 53.121 17.087 88.623 1.00 59.72 S ATOM 835 SG CYS A1031 56.892 17.034 89.053 1.00 93.27 S ATOM 1078 SG CYS A1062 55.319 14.302 87.182 1.00 74.60 S ATOM 1098 SG CYS A1065 55.188 17.484 85.456 1.00 83.14 S Time building chain proxies: 3.10, per 1000 atoms: 0.24 Number of scatterers: 12810 At special positions: 0 Unit cell: (96.36, 104.244, 127.02, 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) Zn 1 29.99 S 91 16.00 P 10 15.00 O 2428 8.00 N 2221 7.00 C 8059 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: 1.24 Conformation dependent library (CDL) restraints added in 767.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A4001 " pdb="ZN ZN A4001 " - pdb=" SG CYS A1062 " pdb="ZN ZN A4001 " - pdb=" SG CYS A1028 " pdb="ZN ZN A4001 " - pdb=" SG CYS A1031 " pdb="ZN ZN A4001 " - pdb=" SG CYS A1065 " Number of angles added : 6 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3010 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 11 sheets defined 61.8% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 930 through 941 removed outlier: 3.503A pdb=" N VAL A 934 " --> pdb=" O SER A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 947 removed outlier: 3.559A pdb=" N ASN A 947 " --> pdb=" O GLU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 967 Processing helix chain 'A' and resid 973 through 987 Processing helix chain 'A' and resid 987 through 997 Processing helix chain 'A' and resid 1006 through 1024 removed outlier: 3.574A pdb=" N THR A1010 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N SER A1011 " --> pdb=" O ASN A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1041 removed outlier: 3.578A pdb=" N LYS A1036 " --> pdb=" O LEU A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1056 Processing helix chain 'A' and resid 1084 through 1088 removed outlier: 3.532A pdb=" N VAL A1088 " --> pdb=" O ILE A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1111 Processing helix chain 'A' and resid 1118 through 1140 removed outlier: 3.569A pdb=" N MET A1138 " --> pdb=" O LEU A1134 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY A1140 " --> pdb=" O MET A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1182 removed outlier: 4.372A pdb=" N ALA A1177 " --> pdb=" O ASP A1173 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU A1178 " --> pdb=" O GLN A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1187 Processing helix chain 'A' and resid 1191 through 1196 removed outlier: 3.743A pdb=" N SER A1196 " --> pdb=" O LYS A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1204 removed outlier: 3.545A pdb=" N SER A1204 " --> pdb=" O ARG A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1232 Processing helix chain 'A' and resid 1237 through 1254 removed outlier: 3.849A pdb=" N VAL A1241 " --> pdb=" O LYS A1237 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A1242 " --> pdb=" O ASP A1238 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1281 removed outlier: 3.524A pdb=" N LEU A1270 " --> pdb=" O SER A1266 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A1277 " --> pdb=" O CYS A1273 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE A1279 " --> pdb=" O ASP A1275 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS A1280 " --> pdb=" O VAL A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1296 removed outlier: 3.791A pdb=" N ILE A1295 " --> pdb=" O GLN A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1307 Processing helix chain 'A' and resid 1315 through 1328 Processing helix chain 'A' and resid 1330 through 1352 Processing helix chain 'A' and resid 1401 through 1409 removed outlier: 3.891A pdb=" N LEU A1407 " --> pdb=" O ARG A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1426 removed outlier: 3.928A pdb=" N GLN A1424 " --> pdb=" O ILE A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1429 through 1434 removed outlier: 3.804A pdb=" N ASN A1433 " --> pdb=" O GLU A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1463 Processing helix chain 'A' and resid 1465 through 1481 removed outlier: 3.762A pdb=" N SER A1469 " --> pdb=" O ARG A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1505 Processing helix chain 'A' and resid 1507 through 1512 Processing helix chain 'A' and resid 1515 through 1524 removed outlier: 3.532A pdb=" N MET A1524 " --> pdb=" O LYS A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1524 through 1530 Processing helix chain 'A' and resid 1531 through 1534 Processing helix chain 'A' and resid 1538 through 1543 Processing helix chain 'A' and resid 1544 through 1547 removed outlier: 3.515A pdb=" N SER A1547 " --> pdb=" O LYS A1544 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1544 through 1547' Processing helix chain 'A' and resid 1552 through 1570 Processing helix chain 'A' and resid 1572 through 1581 removed outlier: 3.939A pdb=" N LYS A1581 " --> pdb=" O VAL A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1605 through 1612 Processing helix chain 'A' and resid 1613 through 1616 removed outlier: 3.557A pdb=" N ILE A1616 " --> pdb=" O ASN A1613 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1613 through 1616' Processing helix chain 'A' and resid 1629 through 1645 Processing helix chain 'A' and resid 1661 through 1666 Processing helix chain 'A' and resid 1758 through 1772 Processing helix chain 'A' and resid 1780 through 1792 removed outlier: 3.566A pdb=" N GLU A1789 " --> pdb=" O GLN A1785 " (cutoff:3.500A) Processing helix chain 'A' and resid 1796 through 1806 Processing helix chain 'A' and resid 1838 through 1852 Processing helix chain 'A' and resid 2295 through 2305 Processing helix chain 'A' and resid 2316 through 2335 Processing helix chain 'A' and resid 2367 through 2379 removed outlier: 3.712A pdb=" N GLN A2377 " --> pdb=" O GLY A2373 " (cutoff:3.500A) Processing helix chain 'A' and resid 2382 through 2397 Processing helix chain 'A' and resid 2404 through 2419 removed outlier: 3.568A pdb=" N LEU A2415 " --> pdb=" O ILE A2411 " (cutoff:3.500A) Processing helix chain 'A' and resid 2429 through 2434 Processing helix chain 'A' and resid 2435 through 2440 removed outlier: 3.775A pdb=" N ASP A2439 " --> pdb=" O ARG A2435 " (cutoff:3.500A) Processing helix chain 'A' and resid 2441 through 2445 removed outlier: 3.697A pdb=" N ASP A2445 " --> pdb=" O ASP A2442 " (cutoff:3.500A) Processing helix chain 'A' and resid 2447 through 2457 Processing helix chain 'A' and resid 2458 through 2461 Processing helix chain 'A' and resid 2476 through 2503 removed outlier: 4.033A pdb=" N VAL A2489 " --> pdb=" O SER A2485 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A2490 " --> pdb=" O LEU A2486 " (cutoff:3.500A) Processing helix chain 'A' and resid 2530 through 2540 removed outlier: 3.536A pdb=" N THR A2540 " --> pdb=" O GLN A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2540 through 2558 removed outlier: 3.596A pdb=" N HIS A2544 " --> pdb=" O THR A2540 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS A2558 " --> pdb=" O ALA A2554 " (cutoff:3.500A) Processing helix chain 'A' and resid 2589 through 2594 removed outlier: 3.658A pdb=" N MET A2594 " --> pdb=" O ILE A2591 " (cutoff:3.500A) Processing helix chain 'A' and resid 2595 through 2600 removed outlier: 3.584A pdb=" N ILE A2599 " --> pdb=" O PHE A2595 " (cutoff:3.500A) Processing helix chain 'A' and resid 2607 through 2623 Processing helix chain 'A' and resid 2626 through 2645 removed outlier: 3.693A pdb=" N PHE A2641 " --> pdb=" O ARG A2637 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N HIS A2644 " --> pdb=" O ILE A2640 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A2645 " --> pdb=" O PHE A2641 " (cutoff:3.500A) Processing helix chain 'A' and resid 2645 through 2652 Processing helix chain 'A' and resid 2652 through 2657 removed outlier: 3.859A pdb=" N THR A2656 " --> pdb=" O TYR A2652 " (cutoff:3.500A) Processing helix chain 'A' and resid 2658 through 2659 No H-bonds generated for 'chain 'A' and resid 2658 through 2659' Processing helix chain 'A' and resid 2660 through 2664 Processing helix chain 'A' and resid 2671 through 2675 removed outlier: 3.887A pdb=" N VAL A2675 " --> pdb=" O SER A2672 " (cutoff:3.500A) Processing helix chain 'A' and resid 2678 through 2697 Processing helix chain 'A' and resid 2753 through 2764 Processing helix chain 'A' and resid 2770 through 2783 Processing helix chain 'A' and resid 2806 through 2816 Processing helix chain 'A' and resid 2818 through 2836 Processing helix chain 'A' and resid 2899 through 2910 removed outlier: 3.540A pdb=" N LYS A2906 " --> pdb=" O LEU A2902 " (cutoff:3.500A) Processing helix chain 'A' and resid 2950 through 2954 Processing helix chain 'A' and resid 2993 through 3003 Processing helix chain 'A' and resid 3043 through 3060 removed outlier: 3.672A pdb=" N ASN A3057 " --> pdb=" O PHE A3053 " (cutoff:3.500A) Processing helix chain 'A' and resid 3062 through 3073 Processing helix chain 'A' and resid 3094 through 3100 removed outlier: 3.679A pdb=" N GLN A3098 " --> pdb=" O SER A3094 " (cutoff:3.500A) Processing helix chain 'A' and resid 3104 through 3112 removed outlier: 3.964A pdb=" N LEU A3112 " --> pdb=" O VAL A3108 " (cutoff:3.500A) Processing helix chain 'A' and resid 3116 through 3120 removed outlier: 3.624A pdb=" N SER A3119 " --> pdb=" O SER A3116 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A3120 " --> pdb=" O ALA A3117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3116 through 3120' Processing helix chain 'A' and resid 3130 through 3141 removed outlier: 3.538A pdb=" N GLN A3140 " --> pdb=" O PHE A3136 " (cutoff:3.500A) Processing helix chain 'A' and resid 3142 through 3157 removed outlier: 3.596A pdb=" N PHE A3146 " --> pdb=" O PHE A3142 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A3157 " --> pdb=" O THR A3153 " (cutoff:3.500A) Processing helix chain 'A' and resid 3169 through 3185 removed outlier: 3.545A pdb=" N ARG A3173 " --> pdb=" O GLN A3169 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN A3176 " --> pdb=" O ALA A3172 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET A3184 " --> pdb=" O LEU A3180 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A3185 " --> pdb=" O LEU A3181 " (cutoff:3.500A) Processing helix chain 'A' and resid 3208 through 3217 removed outlier: 3.704A pdb=" N LEU A3212 " --> pdb=" O THR A3208 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A3213 " --> pdb=" O VAL A3209 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A3217 " --> pdb=" O VAL A3213 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 971 through 972 removed outlier: 6.929A pdb=" N VAL A 971 " --> pdb=" O TYR A1755 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1003 through 1004 Processing sheet with id=AA3, first strand: chain 'A' and resid 1151 through 1153 removed outlier: 3.948A pdb=" N CYS A1143 " --> pdb=" O VAL A1220 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1357 through 1362 removed outlier: 4.176A pdb=" N LEU A1383 " --> pdb=" O LYS A1373 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A1386 " --> pdb=" O GLY A1396 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N GLY A1396 " --> pdb=" O LEU A1386 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2507 through 2511 Processing sheet with id=AA6, first strand: chain 'A' and resid 2399 through 2400 removed outlier: 3.508A pdb=" N ARG A2399 " --> pdb=" O SER A2467 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2574 through 2576 removed outlier: 4.412A pdb=" N PHE A2580 " --> pdb=" O THR A2587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2958 through 2960 removed outlier: 3.660A pdb=" N ILE A2990 " --> pdb=" O ASP A2960 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 3005 through 3009 removed outlier: 6.246A pdb=" N SER A3005 " --> pdb=" O LEU A3039 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL A3041 " --> pdb=" O SER A3005 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER A3007 " --> pdb=" O VAL A3041 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 3078 through 3081 removed outlier: 3.912A pdb=" N SER A3078 " --> pdb=" O ARG A3224 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 3086 through 3089 653 hydrogen bonds defined for protein. 1884 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: 3.00 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4017 1.34 - 1.46: 1919 1.46 - 1.58: 6951 1.58 - 1.69: 20 1.69 - 1.81: 132 Bond restraints: 13039 Sorted by residual: bond pdb=" C VAL A1288 " pdb=" N PRO A1289 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.83e+00 bond pdb=" CG LEU A2391 " pdb=" CD1 LEU A2391 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.14e+00 bond pdb=" C PHE A2593 " pdb=" N MET A2594 " ideal model delta sigma weight residual 1.332 1.318 0.015 1.40e-02 5.10e+03 1.11e+00 bond pdb=" CB CYS A1667 " pdb=" SG CYS A1667 " ideal model delta sigma weight residual 1.808 1.776 0.032 3.30e-02 9.18e+02 9.35e-01 bond pdb=" N9 A C 5 " pdb=" C4 A C 5 " ideal model delta sigma weight residual 1.374 1.393 -0.019 2.00e-02 2.50e+03 9.07e-01 ... (remaining 13034 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 17438 2.38 - 4.75: 157 4.75 - 7.13: 17 7.13 - 9.50: 2 9.50 - 11.88: 2 Bond angle restraints: 17616 Sorted by residual: angle pdb=" CA LEU A1056 " pdb=" CB LEU A1056 " pdb=" CG LEU A1056 " ideal model delta sigma weight residual 116.30 128.18 -11.88 3.50e+00 8.16e-02 1.15e+01 angle pdb=" C SER A3159 " pdb=" N GLU A3160 " pdb=" CA GLU A3160 " ideal model delta sigma weight residual 121.54 127.57 -6.03 1.91e+00 2.74e-01 9.98e+00 angle pdb=" C ASP A1657 " pdb=" N THR A1658 " pdb=" CA THR A1658 " ideal model delta sigma weight residual 121.54 127.50 -5.96 1.91e+00 2.74e-01 9.74e+00 angle pdb=" C ARG A1659 " pdb=" N THR A1660 " pdb=" CA THR A1660 " ideal model delta sigma weight residual 121.54 127.39 -5.85 1.91e+00 2.74e-01 9.39e+00 angle pdb=" CA LEU A1418 " pdb=" CB LEU A1418 " pdb=" CG LEU A1418 " ideal model delta sigma weight residual 116.30 126.44 -10.14 3.50e+00 8.16e-02 8.40e+00 ... (remaining 17611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 7443 17.90 - 35.79: 482 35.79 - 53.69: 62 53.69 - 71.59: 12 71.59 - 89.49: 5 Dihedral angle restraints: 8004 sinusoidal: 3391 harmonic: 4613 Sorted by residual: dihedral pdb=" CA ARG A1027 " pdb=" C ARG A1027 " pdb=" N CYS A1028 " pdb=" CA CYS A1028 " ideal model delta harmonic sigma weight residual -180.00 -159.07 -20.93 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA LEU A1644 " pdb=" C LEU A1644 " pdb=" N ASP A1645 " pdb=" CA ASP A1645 " ideal model delta harmonic sigma weight residual 180.00 159.98 20.02 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA PHE A1505 " pdb=" C PHE A1505 " pdb=" N LEU A1506 " pdb=" CA LEU A1506 " ideal model delta harmonic sigma weight residual -180.00 -160.77 -19.23 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 8001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1438 0.041 - 0.082: 493 0.082 - 0.123: 90 0.123 - 0.164: 15 0.164 - 0.206: 1 Chirality restraints: 2037 Sorted by residual: chirality pdb=" CG LEU A1056 " pdb=" CB LEU A1056 " pdb=" CD1 LEU A1056 " pdb=" CD2 LEU A1056 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA PHE A2633 " pdb=" N PHE A2633 " pdb=" C PHE A2633 " pdb=" CB PHE A2633 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA ILE A2403 " pdb=" N ILE A2403 " pdb=" C ILE A2403 " pdb=" CB ILE A2403 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 ... (remaining 2034 not shown) Planarity restraints: 2189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A2633 " 0.020 2.00e-02 2.50e+03 2.01e-02 7.05e+00 pdb=" CG PHE A2633 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A2633 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A2633 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A2633 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A2633 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A2633 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A3049 " 0.015 2.00e-02 2.50e+03 1.55e-02 4.18e+00 pdb=" CG PHE A3049 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A3049 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A3049 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A3049 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A3049 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A3049 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1311 " 0.033 5.00e-02 4.00e+02 4.92e-02 3.88e+00 pdb=" N PRO A1312 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A1312 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1312 " 0.027 5.00e-02 4.00e+02 ... (remaining 2186 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 7848 3.05 - 3.52: 13210 3.52 - 3.98: 20696 3.98 - 4.44: 25517 4.44 - 4.90: 38356 Nonbonded interactions: 105627 Sorted by model distance: nonbonded pdb=" O4' C C 2 " pdb=" C6 C C 2 " model vdw 2.593 2.672 nonbonded pdb=" N1 G C 8 " pdb=" C4 G C 8 " model vdw 2.604 2.672 nonbonded pdb=" N GLY A2337 " pdb=" N LYS A2338 " model vdw 2.609 2.560 nonbonded pdb=" N ILE A1616 " pdb=" N TYR A1617 " model vdw 2.618 2.560 nonbonded pdb=" N THR A1660 " pdb=" N ALA A1661 " model vdw 2.638 2.560 ... (remaining 105622 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.830 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 0.035 13043 Z= 0.158 Angle : 0.597 11.881 17622 Z= 0.304 Chirality : 0.042 0.206 2037 Planarity : 0.005 0.049 2189 Dihedral : 11.820 89.486 4994 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.53 (0.21), residues: 1541 helix: 0.26 (0.17), residues: 879 sheet: 0.54 (0.72), residues: 69 loop : -1.31 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1184 TYR 0.014 0.001 TYR A2994 PHE 0.046 0.002 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.005 0.001 HIS A1491 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (13039) covalent geometry : angle 0.58934 / 0.30 (17616) hydrogen bonds : bond 0.13902 / 8.97 ( 653) hydrogen bonds : angle 5.50710 / 3.89 ( 1884) metal coordination : bond 0.00943 / 0.39 ( 4) metal coordination : angle 5.22355 / 2.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 943 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7633 (mm-30) REVERT: A 975 GLU cc_start: 0.7630 (pt0) cc_final: 0.7403 (pt0) REVERT: A 982 ASN cc_start: 0.7907 (m-40) cc_final: 0.7620 (m-40) REVERT: A 1031 CYS cc_start: 0.7340 (m) cc_final: 0.7093 (m) REVERT: A 1084 LYS cc_start: 0.8482 (mtpt) cc_final: 0.8105 (mtpt) REVERT: A 1245 ILE cc_start: 0.7984 (pt) cc_final: 0.7743 (mt) REVERT: A 1277 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7216 (mp10) REVERT: A 1282 LYS cc_start: 0.8876 (mttt) cc_final: 0.8655 (mttm) REVERT: A 1379 LYS cc_start: 0.8328 (mttt) cc_final: 0.8108 (mttt) REVERT: A 1434 SER cc_start: 0.8324 (p) cc_final: 0.7977 (t) REVERT: A 1448 MET cc_start: 0.8575 (mmt) cc_final: 0.8108 (mpp) REVERT: A 1452 GLU cc_start: 0.7337 (mt-10) cc_final: 0.7112 (mp0) REVERT: A 1509 ASP cc_start: 0.8091 (m-30) cc_final: 0.7849 (m-30) REVERT: A 1519 ASN cc_start: 0.8258 (t0) cc_final: 0.7988 (t0) REVERT: A 1524 MET cc_start: 0.8398 (mmt) cc_final: 0.8173 (mmm) REVERT: A 1534 SER cc_start: 0.8727 (t) cc_final: 0.8504 (p) REVERT: A 1634 GLU cc_start: 0.7724 (tp30) cc_final: 0.7361 (tp30) REVERT: A 1647 MET cc_start: 0.8166 (ttt) cc_final: 0.7947 (ttm) REVERT: A 1669 ASN cc_start: 0.8348 (t0) cc_final: 0.8109 (t0) REVERT: A 1789 GLU cc_start: 0.7861 (tp30) cc_final: 0.7527 (tp30) REVERT: A 1850 MET cc_start: 0.6247 (mtt) cc_final: 0.5760 (mtt) REVERT: A 2298 MET cc_start: 0.8008 (ttp) cc_final: 0.7728 (tpp) REVERT: A 2319 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6990 (mt-10) REVERT: A 2345 ASN cc_start: 0.8119 (t0) cc_final: 0.7783 (t0) REVERT: A 2438 THR cc_start: 0.7587 (m) cc_final: 0.7238 (p) REVERT: A 2459 SER cc_start: 0.8527 (p) cc_final: 0.8280 (m) REVERT: A 2460 LYS cc_start: 0.8519 (mttt) cc_final: 0.8252 (mttp) REVERT: A 2493 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7155 (tp30) REVERT: A 2501 ARG cc_start: 0.8205 (ttp-170) cc_final: 0.8004 (tmm160) REVERT: A 2538 ASP cc_start: 0.8181 (t0) cc_final: 0.7922 (t0) REVERT: A 2581 MET cc_start: 0.7874 (tmm) cc_final: 0.7391 (tmm) REVERT: A 2641 PHE cc_start: 0.8238 (m-80) cc_final: 0.7992 (m-80) REVERT: A 2663 PHE cc_start: 0.8879 (m-80) cc_final: 0.8653 (m-80) REVERT: A 2683 ASP cc_start: 0.7612 (m-30) cc_final: 0.7399 (m-30) REVERT: A 2788 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6959 (mm-30) REVERT: A 2835 TYR cc_start: 0.8069 (m-80) cc_final: 0.7675 (m-80) REVERT: A 2993 LYS cc_start: 0.7545 (mttt) cc_final: 0.6989 (mttp) REVERT: A 3025 ARG cc_start: 0.8028 (mtt180) cc_final: 0.7811 (mpp80) REVERT: A 3037 ARG cc_start: 0.7945 (mtm180) cc_final: 0.7604 (ttm110) REVERT: A 3041 VAL cc_start: 0.8196 (t) cc_final: 0.7904 (m) REVERT: A 3077 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7697 (mt-10) REVERT: A 3089 LYS cc_start: 0.8382 (ttmt) cc_final: 0.8177 (ttmt) REVERT: A 3226 SER cc_start: 0.8516 (t) cc_final: 0.8292 (p) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.6115 time to fit residues: 260.3395 Evaluate side-chains 319 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1006 GLN A1044 ASN ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1247 ASN A1325 ASN A1424 GLN A2359 ASN A2477 HIS A2505 GLN A2644 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.146849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.126128 restraints weight = 17146.448| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.85 r_work: 0.3557 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13043 Z= 0.132 Angle : 0.509 9.278 17622 Z= 0.261 Chirality : 0.039 0.151 2037 Planarity : 0.004 0.045 2189 Dihedral : 7.160 73.291 1840 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.00 % Allowed : 10.23 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.22 (0.22), residues: 1541 helix: 0.99 (0.17), residues: 886 sheet: 0.74 (0.65), residues: 76 loop : -1.23 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2416 TYR 0.014 0.001 TYR A2994 PHE 0.033 0.001 PHE A2633 TRP 0.015 0.001 TRP A2542 HIS 0.005 0.001 HIS A2477 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (13039) covalent geometry : angle 0.50559 / 0.26 (17616) hydrogen bonds : bond 0.03861 / 2.49 ( 653) hydrogen bonds : angle 4.22691 / 3.04 ( 1884) metal coordination : bond 0.00717 / 0.30 ( 4) metal coordination : angle 3.41999 / 1.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 320 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 932 LYS cc_start: 0.7831 (mppt) cc_final: 0.7614 (mppt) REVERT: A 968 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7758 (mp0) REVERT: A 975 GLU cc_start: 0.7644 (pt0) cc_final: 0.7428 (pt0) REVERT: A 982 ASN cc_start: 0.8008 (m-40) cc_final: 0.7765 (m-40) REVERT: A 999 LYS cc_start: 0.8704 (pttp) cc_final: 0.8446 (pttp) REVERT: A 1031 CYS cc_start: 0.7343 (m) cc_final: 0.7126 (m) REVERT: A 1041 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: A 1084 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7944 (mtpt) REVERT: A 1252 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7712 (ttm170) REVERT: A 1272 LYS cc_start: 0.7994 (mtpp) cc_final: 0.7771 (mttp) REVERT: A 1277 GLN cc_start: 0.7706 (mm-40) cc_final: 0.7143 (mm-40) REVERT: A 1279 PHE cc_start: 0.8410 (m-80) cc_final: 0.8186 (m-80) REVERT: A 1348 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7555 (ttm-80) REVERT: A 1379 LYS cc_start: 0.8261 (mttt) cc_final: 0.8054 (mttt) REVERT: A 1434 SER cc_start: 0.8199 (p) cc_final: 0.7903 (t) REVERT: A 1448 MET cc_start: 0.8615 (mmt) cc_final: 0.8130 (mpp) REVERT: A 1519 ASN cc_start: 0.8175 (t0) cc_final: 0.7963 (t0) REVERT: A 1534 SER cc_start: 0.8623 (t) cc_final: 0.8286 (p) REVERT: A 1541 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7664 (mm-30) REVERT: A 1633 GLU cc_start: 0.7788 (tp30) cc_final: 0.7453 (tp30) REVERT: A 1634 GLU cc_start: 0.7687 (tp30) cc_final: 0.7400 (tp30) REVERT: A 1640 MET cc_start: 0.8252 (ttp) cc_final: 0.8041 (ttt) REVERT: A 1647 MET cc_start: 0.8326 (ttt) cc_final: 0.8072 (ttp) REVERT: A 1789 GLU cc_start: 0.7823 (tp30) cc_final: 0.7429 (tp30) REVERT: A 1850 MET cc_start: 0.6132 (mtt) cc_final: 0.5692 (mtt) REVERT: A 2298 MET cc_start: 0.8136 (ttp) cc_final: 0.7899 (tpp) REVERT: A 2345 ASN cc_start: 0.8134 (t0) cc_final: 0.7877 (t0) REVERT: A 2438 THR cc_start: 0.7569 (m) cc_final: 0.7248 (p) REVERT: A 2459 SER cc_start: 0.8549 (p) cc_final: 0.8318 (m) REVERT: A 2493 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7177 (tp30) REVERT: A 2500 LYS cc_start: 0.8491 (mttp) cc_final: 0.8255 (mptm) REVERT: A 2502 SER cc_start: 0.8495 (p) cc_final: 0.8238 (m) REVERT: A 2538 ASP cc_start: 0.8127 (t0) cc_final: 0.7878 (t0) REVERT: A 2581 MET cc_start: 0.7896 (tmm) cc_final: 0.7253 (tmm) REVERT: A 2622 TYR cc_start: 0.8390 (m-10) cc_final: 0.8187 (m-10) REVERT: A 2683 ASP cc_start: 0.7582 (m-30) cc_final: 0.7369 (m-30) REVERT: A 2760 ILE cc_start: 0.8283 (mm) cc_final: 0.8046 (mt) REVERT: A 2788 GLU cc_start: 0.7295 (mm-30) cc_final: 0.7045 (mm-30) REVERT: A 2835 TYR cc_start: 0.8006 (m-80) cc_final: 0.7738 (m-80) REVERT: A 2993 LYS cc_start: 0.7426 (mttt) cc_final: 0.6938 (mttp) REVERT: A 3037 ARG cc_start: 0.8051 (mtm180) cc_final: 0.7597 (ttm110) REVERT: A 3091 LYS cc_start: 0.8091 (mmpt) cc_final: 0.7886 (mmpt) REVERT: A 3203 MET cc_start: 0.6535 (mpp) cc_final: 0.6177 (mpp) outliers start: 29 outliers final: 10 residues processed: 330 average time/residue: 0.6367 time to fit residues: 226.8345 Evaluate side-chains 307 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 295 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain A residue 1252 ARG Chi-restraints excluded: chain A residue 1393 LEU Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 2391 LEU Chi-restraints excluded: chain A residue 2579 GLU Chi-restraints excluded: chain A residue 3006 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 39 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2366 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.145099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.124376 restraints weight = 17358.117| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.86 r_work: 0.3535 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13043 Z= 0.162 Angle : 0.513 8.389 17622 Z= 0.264 Chirality : 0.040 0.161 2037 Planarity : 0.004 0.043 2189 Dihedral : 7.214 73.208 1840 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.49 % Allowed : 13.82 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.36 (0.22), residues: 1541 helix: 1.18 (0.17), residues: 890 sheet: 0.52 (0.62), residues: 81 loop : -1.31 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1403 TYR 0.014 0.001 TYR A2994 PHE 0.032 0.001 PHE A2633 TRP 0.016 0.001 TRP A2542 HIS 0.004 0.001 HIS A1090 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (13039) covalent geometry : angle 0.50920 / 0.26 (17616) hydrogen bonds : bond 0.03925 / 2.53 ( 653) hydrogen bonds : angle 4.12374 / 2.97 ( 1884) metal coordination : bond 0.00931 / 0.41 ( 4) metal coordination : angle 3.47046 / 1.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 305 time to evaluate : 0.522 Fit side-chains REVERT: A 932 LYS cc_start: 0.8005 (mppt) cc_final: 0.7780 (mppt) REVERT: A 968 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7776 (mp0) REVERT: A 975 GLU cc_start: 0.7638 (pt0) cc_final: 0.7416 (pt0) REVERT: A 982 ASN cc_start: 0.8078 (m-40) cc_final: 0.7876 (m-40) REVERT: A 1031 CYS cc_start: 0.7285 (m) cc_final: 0.7065 (m) REVERT: A 1041 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7386 (mt-10) REVERT: A 1249 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8405 (mm) REVERT: A 1272 LYS cc_start: 0.8029 (mtpp) cc_final: 0.7826 (mttp) REVERT: A 1277 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7098 (mm-40) REVERT: A 1279 PHE cc_start: 0.8430 (m-80) cc_final: 0.8161 (m-80) REVERT: A 1348 ARG cc_start: 0.8028 (ttm-80) cc_final: 0.7499 (ttm-80) REVERT: A 1379 LYS cc_start: 0.8244 (mttt) cc_final: 0.8040 (mttt) REVERT: A 1434 SER cc_start: 0.8140 (p) cc_final: 0.7861 (t) REVERT: A 1448 MET cc_start: 0.8532 (mmt) cc_final: 0.7855 (mpp) REVERT: A 1452 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: A 1519 ASN cc_start: 0.8192 (t0) cc_final: 0.7944 (t0) REVERT: A 1633 GLU cc_start: 0.7849 (tp30) cc_final: 0.7531 (tp30) REVERT: A 1640 MET cc_start: 0.8251 (ttp) cc_final: 0.7980 (ttt) REVERT: A 1647 MET cc_start: 0.8341 (ttt) cc_final: 0.8094 (ttp) REVERT: A 1763 LEU cc_start: 0.8376 (tp) cc_final: 0.8141 (tp) REVERT: A 1772 LYS cc_start: 0.8508 (ptpp) cc_final: 0.8278 (ptmm) REVERT: A 1789 GLU cc_start: 0.7781 (tp30) cc_final: 0.7440 (tp30) REVERT: A 1850 MET cc_start: 0.6243 (mtt) cc_final: 0.5909 (mtt) REVERT: A 2298 MET cc_start: 0.8170 (ttp) cc_final: 0.7913 (tpp) REVERT: A 2338 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7926 (mmtp) REVERT: A 2345 ASN cc_start: 0.8163 (t0) cc_final: 0.7843 (t0) REVERT: A 2438 THR cc_start: 0.7557 (m) cc_final: 0.7218 (p) REVERT: A 2459 SER cc_start: 0.8533 (p) cc_final: 0.8288 (m) REVERT: A 2493 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7232 (tp30) REVERT: A 2538 ASP cc_start: 0.8157 (t0) cc_final: 0.7910 (t0) REVERT: A 2580 PHE cc_start: 0.8697 (m-80) cc_final: 0.8291 (m-80) REVERT: A 2622 TYR cc_start: 0.8405 (m-10) cc_final: 0.8174 (m-10) REVERT: A 2683 ASP cc_start: 0.7662 (m-30) cc_final: 0.7456 (m-30) REVERT: A 2760 ILE cc_start: 0.8359 (mm) cc_final: 0.8072 (mt) REVERT: A 2788 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6588 (mm-30) REVERT: A 2835 TYR cc_start: 0.8043 (m-80) cc_final: 0.7741 (m-80) REVERT: A 2993 LYS cc_start: 0.7428 (mttt) cc_final: 0.6971 (mttp) REVERT: A 3037 ARG cc_start: 0.7987 (mtm180) cc_final: 0.7558 (ttm110) REVERT: A 3091 LYS cc_start: 0.8059 (mmpt) cc_final: 0.7828 (mmpt) REVERT: A 3203 MET cc_start: 0.6552 (mpp) cc_final: 0.6220 (mpp) outliers start: 36 outliers final: 19 residues processed: 319 average time/residue: 0.6410 time to fit residues: 221.1374 Evaluate side-chains 313 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 290 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1393 LEU Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1452 GLU Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 1801 ASP Chi-restraints excluded: chain A residue 2338 LYS Chi-restraints excluded: chain A residue 2391 LEU Chi-restraints excluded: chain A residue 2463 MET Chi-restraints excluded: chain A residue 2475 ILE Chi-restraints excluded: chain A residue 2528 ILE Chi-restraints excluded: chain A residue 2579 GLU Chi-restraints excluded: chain A residue 2677 SER Chi-restraints excluded: chain A residue 3006 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 53 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 136 optimal weight: 1.9990 chunk 58 optimal weight: 0.0770 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 944 HIS ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1247 ASN A2366 HIS A2825 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.146185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.125347 restraints weight = 17139.287| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.88 r_work: 0.3550 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13043 Z= 0.129 Angle : 0.493 5.950 17622 Z= 0.253 Chirality : 0.039 0.151 2037 Planarity : 0.004 0.044 2189 Dihedral : 7.047 73.269 1840 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.42 % Allowed : 15.76 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.56 (0.22), residues: 1541 helix: 1.40 (0.18), residues: 889 sheet: 0.47 (0.63), residues: 79 loop : -1.30 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1403 TYR 0.011 0.001 TYR A2417 PHE 0.028 0.001 PHE A2633 TRP 0.015 0.001 TRP A2542 HIS 0.003 0.001 HIS A1090 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (13039) covalent geometry : angle 0.49081 / 0.25 (17616) hydrogen bonds : bond 0.03558 / 2.30 ( 653) hydrogen bonds : angle 4.00766 / 2.88 ( 1884) metal coordination : bond 0.00676 / 0.29 ( 4) metal coordination : angle 2.75807 / 1.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 299 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 968 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7843 (mp0) REVERT: A 975 GLU cc_start: 0.7666 (pt0) cc_final: 0.7445 (pt0) REVERT: A 999 LYS cc_start: 0.8635 (pttp) cc_final: 0.8419 (pttp) REVERT: A 1041 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7373 (mt-10) REVERT: A 1277 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7054 (mm-40) REVERT: A 1279 PHE cc_start: 0.8453 (m-80) cc_final: 0.8178 (m-80) REVERT: A 1348 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7762 (ttm-80) REVERT: A 1391 MET cc_start: 0.8248 (mmt) cc_final: 0.8039 (mmp) REVERT: A 1434 SER cc_start: 0.8097 (p) cc_final: 0.7843 (t) REVERT: A 1448 MET cc_start: 0.8513 (mmt) cc_final: 0.7843 (mpp) REVERT: A 1452 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: A 1647 MET cc_start: 0.8336 (ttt) cc_final: 0.8090 (ttp) REVERT: A 1772 LYS cc_start: 0.8507 (ptpp) cc_final: 0.8278 (ptmm) REVERT: A 1789 GLU cc_start: 0.7748 (tp30) cc_final: 0.7360 (tp30) REVERT: A 1850 MET cc_start: 0.6324 (mtt) cc_final: 0.6020 (mtt) REVERT: A 2298 MET cc_start: 0.8210 (ttp) cc_final: 0.7951 (tpp) REVERT: A 2345 ASN cc_start: 0.8132 (t0) cc_final: 0.7791 (t0) REVERT: A 2375 MET cc_start: 0.8301 (mmt) cc_final: 0.8088 (mmm) REVERT: A 2438 THR cc_start: 0.7584 (m) cc_final: 0.7252 (p) REVERT: A 2459 SER cc_start: 0.8495 (p) cc_final: 0.8243 (m) REVERT: A 2493 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7193 (tp30) REVERT: A 2580 PHE cc_start: 0.8664 (m-80) cc_final: 0.8273 (m-80) REVERT: A 2622 TYR cc_start: 0.8409 (m-10) cc_final: 0.8171 (m-10) REVERT: A 2683 ASP cc_start: 0.7582 (m-30) cc_final: 0.7373 (m-30) REVERT: A 2744 PHE cc_start: 0.7649 (t80) cc_final: 0.7378 (m-80) REVERT: A 2747 GLU cc_start: 0.7723 (tp30) cc_final: 0.7515 (tp30) REVERT: A 2788 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6496 (mm-30) REVERT: A 2818 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8524 (mt) REVERT: A 2993 LYS cc_start: 0.7387 (mttt) cc_final: 0.6898 (mttp) REVERT: A 3091 LYS cc_start: 0.8057 (mmpt) cc_final: 0.7818 (mmpt) REVERT: A 3203 MET cc_start: 0.6561 (mpp) cc_final: 0.6235 (mpp) outliers start: 35 outliers final: 20 residues processed: 313 average time/residue: 0.6623 time to fit residues: 223.5410 Evaluate side-chains 311 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 288 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 943 GLU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain A residue 1320 LEU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1393 LEU Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1452 GLU Chi-restraints excluded: chain A residue 2391 LEU Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2475 ILE Chi-restraints excluded: chain A residue 2579 GLU Chi-restraints excluded: chain A residue 2677 SER Chi-restraints excluded: chain A residue 2818 LEU Chi-restraints excluded: chain A residue 3006 VAL Chi-restraints excluded: chain A residue 3226 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 0.0970 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 36 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 144 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2302 ASN A2366 HIS A2505 GLN A2644 HIS ** A2825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.146236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.125312 restraints weight = 17234.354| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.89 r_work: 0.3553 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13043 Z= 0.129 Angle : 0.503 9.216 17622 Z= 0.256 Chirality : 0.039 0.178 2037 Planarity : 0.004 0.044 2189 Dihedral : 7.029 73.268 1840 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.63 % Allowed : 16.03 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.70 (0.22), residues: 1541 helix: 1.51 (0.18), residues: 889 sheet: 0.49 (0.62), residues: 79 loop : -1.25 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2418 TYR 0.012 0.001 TYR A2417 PHE 0.027 0.001 PHE A2633 TRP 0.015 0.001 TRP A2542 HIS 0.002 0.001 HIS A2794 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (13039) covalent geometry : angle 0.50090 / 0.26 (17616) hydrogen bonds : bond 0.03502 / 2.28 ( 653) hydrogen bonds : angle 3.98066 / 2.86 ( 1884) metal coordination : bond 0.00670 / 0.29 ( 4) metal coordination : angle 2.65050 / 1.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 301 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 932 LYS cc_start: 0.8089 (mppt) cc_final: 0.7882 (mppt) REVERT: A 975 GLU cc_start: 0.7692 (pt0) cc_final: 0.7477 (pt0) REVERT: A 1210 LEU cc_start: 0.7914 (tm) cc_final: 0.7705 (tt) REVERT: A 1249 LEU cc_start: 0.8654 (mt) cc_final: 0.8406 (mm) REVERT: A 1277 GLN cc_start: 0.7485 (mm-40) cc_final: 0.7009 (mm110) REVERT: A 1279 PHE cc_start: 0.8448 (m-80) cc_final: 0.8149 (m-80) REVERT: A 1434 SER cc_start: 0.8085 (p) cc_final: 0.7837 (t) REVERT: A 1442 ASP cc_start: 0.7733 (m-30) cc_final: 0.7482 (m-30) REVERT: A 1448 MET cc_start: 0.8504 (mmt) cc_final: 0.7848 (mpp) REVERT: A 1452 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: A 1534 SER cc_start: 0.8677 (OUTLIER) cc_final: 0.8326 (p) REVERT: A 1647 MET cc_start: 0.8341 (ttt) cc_final: 0.8093 (ttp) REVERT: A 1763 LEU cc_start: 0.8418 (tp) cc_final: 0.8193 (tp) REVERT: A 1772 LYS cc_start: 0.8505 (ptpp) cc_final: 0.8283 (ptmm) REVERT: A 1789 GLU cc_start: 0.7769 (tp30) cc_final: 0.7375 (tp30) REVERT: A 1801 ASP cc_start: 0.7192 (p0) cc_final: 0.6978 (p0) REVERT: A 1806 ASP cc_start: 0.7983 (t0) cc_final: 0.7752 (t0) REVERT: A 1850 MET cc_start: 0.6321 (mtt) cc_final: 0.5989 (mtt) REVERT: A 2298 MET cc_start: 0.8239 (ttp) cc_final: 0.7953 (tpp) REVERT: A 2345 ASN cc_start: 0.8152 (t0) cc_final: 0.7809 (t0) REVERT: A 2375 MET cc_start: 0.8299 (mmt) cc_final: 0.8076 (mmm) REVERT: A 2438 THR cc_start: 0.7578 (m) cc_final: 0.7245 (p) REVERT: A 2449 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.7867 (p) REVERT: A 2459 SER cc_start: 0.8470 (p) cc_final: 0.8237 (m) REVERT: A 2493 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7191 (tp30) REVERT: A 2538 ASP cc_start: 0.8192 (t0) cc_final: 0.7938 (t0) REVERT: A 2580 PHE cc_start: 0.8651 (m-80) cc_final: 0.8286 (m-80) REVERT: A 2622 TYR cc_start: 0.8423 (m-10) cc_final: 0.8184 (m-10) REVERT: A 2683 ASP cc_start: 0.7592 (m-30) cc_final: 0.7388 (m-30) REVERT: A 2744 PHE cc_start: 0.7636 (t80) cc_final: 0.7389 (m-80) REVERT: A 2747 GLU cc_start: 0.7766 (tp30) cc_final: 0.7535 (tp30) REVERT: A 2788 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6529 (mm-30) REVERT: A 2818 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8528 (mt) REVERT: A 2993 LYS cc_start: 0.7368 (mttt) cc_final: 0.6871 (mttp) REVERT: A 3089 LYS cc_start: 0.8394 (ttmt) cc_final: 0.8184 (ttmt) REVERT: A 3091 LYS cc_start: 0.8094 (mmpt) cc_final: 0.7845 (mmpt) REVERT: A 3203 MET cc_start: 0.6567 (mpp) cc_final: 0.6215 (mpp) outliers start: 38 outliers final: 22 residues processed: 318 average time/residue: 0.6568 time to fit residues: 225.1445 Evaluate side-chains 320 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 294 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain A residue 1320 LEU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1393 LEU Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1452 GLU Chi-restraints excluded: chain A residue 1534 SER Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 2391 LEU Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2475 ILE Chi-restraints excluded: chain A residue 2579 GLU Chi-restraints excluded: chain A residue 2758 GLN Chi-restraints excluded: chain A residue 2793 ARG Chi-restraints excluded: chain A residue 2818 LEU Chi-restraints excluded: chain A residue 3006 VAL Chi-restraints excluded: chain A residue 3145 VAL Chi-restraints excluded: chain A residue 3226 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 64 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1773 ASN A2366 HIS A2505 GLN A2644 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.145235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.124228 restraints weight = 17027.740| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.89 r_work: 0.3537 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13043 Z= 0.162 Angle : 0.534 7.680 17622 Z= 0.272 Chirality : 0.040 0.165 2037 Planarity : 0.004 0.055 2189 Dihedral : 7.092 73.184 1840 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.70 % Allowed : 16.24 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.68 (0.22), residues: 1541 helix: 1.51 (0.18), residues: 884 sheet: 0.41 (0.61), residues: 79 loop : -1.22 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1348 TYR 0.011 0.001 TYR A1617 PHE 0.027 0.001 PHE A2633 TRP 0.016 0.001 TRP A2542 HIS 0.004 0.001 HIS A2794 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (13039) covalent geometry : angle 0.53078 / 0.27 (17616) hydrogen bonds : bond 0.03740 / 2.43 ( 653) hydrogen bonds : angle 4.01364 / 2.88 ( 1884) metal coordination : bond 0.00917 / 0.41 ( 4) metal coordination : angle 3.30769 / 1.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 305 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 968 GLU cc_start: 0.7644 (mp0) cc_final: 0.7318 (mp0) REVERT: A 975 GLU cc_start: 0.7682 (pt0) cc_final: 0.7463 (pt0) REVERT: A 1041 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7398 (mt-10) REVERT: A 1277 GLN cc_start: 0.7564 (mm-40) cc_final: 0.7042 (mm110) REVERT: A 1279 PHE cc_start: 0.8476 (m-80) cc_final: 0.8186 (m-80) REVERT: A 1291 GLN cc_start: 0.8269 (mp10) cc_final: 0.8056 (mp10) REVERT: A 1348 ARG cc_start: 0.8060 (ttm-80) cc_final: 0.7572 (ttm-80) REVERT: A 1434 SER cc_start: 0.8089 (p) cc_final: 0.7843 (t) REVERT: A 1448 MET cc_start: 0.8535 (mmt) cc_final: 0.7868 (mpp) REVERT: A 1452 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: A 1534 SER cc_start: 0.8670 (OUTLIER) cc_final: 0.8336 (p) REVERT: A 1647 MET cc_start: 0.8353 (ttt) cc_final: 0.8100 (ttp) REVERT: A 1763 LEU cc_start: 0.8478 (tp) cc_final: 0.8241 (tp) REVERT: A 1764 LYS cc_start: 0.8383 (mtpp) cc_final: 0.8108 (mtpp) REVERT: A 1789 GLU cc_start: 0.7790 (tp30) cc_final: 0.7388 (tp30) REVERT: A 1806 ASP cc_start: 0.7942 (t0) cc_final: 0.7687 (t0) REVERT: A 1850 MET cc_start: 0.6333 (mtt) cc_final: 0.5989 (mtt) REVERT: A 2298 MET cc_start: 0.8264 (ttp) cc_final: 0.7976 (tpp) REVERT: A 2345 ASN cc_start: 0.8154 (t0) cc_final: 0.7852 (t0) REVERT: A 2375 MET cc_start: 0.8341 (mmt) cc_final: 0.8121 (mmm) REVERT: A 2493 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7220 (tp30) REVERT: A 2580 PHE cc_start: 0.8648 (m-80) cc_final: 0.8312 (m-80) REVERT: A 2581 MET cc_start: 0.8056 (tmm) cc_final: 0.7202 (tmm) REVERT: A 2683 ASP cc_start: 0.7605 (m-30) cc_final: 0.7399 (m-30) REVERT: A 2744 PHE cc_start: 0.7654 (t80) cc_final: 0.7378 (m-80) REVERT: A 2747 GLU cc_start: 0.7800 (tp30) cc_final: 0.7575 (tp30) REVERT: A 2760 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.8047 (mt) REVERT: A 2788 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6558 (mm-30) REVERT: A 2993 LYS cc_start: 0.7407 (mttt) cc_final: 0.6936 (mttp) REVERT: A 3089 LYS cc_start: 0.8403 (ttmt) cc_final: 0.8183 (ttmt) REVERT: A 3091 LYS cc_start: 0.8109 (mmpt) cc_final: 0.7855 (mmpt) REVERT: A 3203 MET cc_start: 0.6522 (mpp) cc_final: 0.6139 (mpp) outliers start: 39 outliers final: 22 residues processed: 321 average time/residue: 0.6710 time to fit residues: 232.1274 Evaluate side-chains 320 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 294 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1393 LEU Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1452 GLU Chi-restraints excluded: chain A residue 1534 SER Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 2391 LEU Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2463 MET Chi-restraints excluded: chain A residue 2475 ILE Chi-restraints excluded: chain A residue 2579 GLU Chi-restraints excluded: chain A residue 2677 SER Chi-restraints excluded: chain A residue 2760 ILE Chi-restraints excluded: chain A residue 2793 ARG Chi-restraints excluded: chain A residue 3006 VAL Chi-restraints excluded: chain A residue 3226 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 122 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 55 optimal weight: 0.2980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2366 HIS A2644 HIS A2758 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.144864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.124037 restraints weight = 16984.425| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.88 r_work: 0.3535 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13043 Z= 0.171 Angle : 0.545 10.137 17622 Z= 0.277 Chirality : 0.041 0.157 2037 Planarity : 0.004 0.052 2189 Dihedral : 7.130 73.170 1840 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.11 % Allowed : 16.86 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.64 (0.22), residues: 1541 helix: 1.49 (0.18), residues: 885 sheet: 0.39 (0.60), residues: 79 loop : -1.27 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2418 TYR 0.012 0.001 TYR A2417 PHE 0.026 0.001 PHE A2633 TRP 0.016 0.001 TRP A2542 HIS 0.003 0.001 HIS A2794 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (13039) covalent geometry : angle 0.54118 / 0.28 (17616) hydrogen bonds : bond 0.03805 / 2.48 ( 653) hydrogen bonds : angle 4.03076 / 2.89 ( 1884) metal coordination : bond 0.00977 / 0.43 ( 4) metal coordination : angle 3.45441 / 1.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 297 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 968 GLU cc_start: 0.7644 (mp0) cc_final: 0.7354 (mp0) REVERT: A 975 GLU cc_start: 0.7708 (pt0) cc_final: 0.7494 (pt0) REVERT: A 1041 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: A 1136 MET cc_start: 0.7397 (mtp) cc_final: 0.7045 (mmm) REVERT: A 1249 LEU cc_start: 0.8653 (mt) cc_final: 0.8416 (mm) REVERT: A 1277 GLN cc_start: 0.7524 (mm-40) cc_final: 0.7051 (mm110) REVERT: A 1279 PHE cc_start: 0.8493 (m-80) cc_final: 0.8207 (m-80) REVERT: A 1348 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7695 (ttm-80) REVERT: A 1350 CYS cc_start: 0.8187 (t) cc_final: 0.7956 (t) REVERT: A 1434 SER cc_start: 0.8094 (p) cc_final: 0.7855 (t) REVERT: A 1442 ASP cc_start: 0.7778 (m-30) cc_final: 0.7529 (m-30) REVERT: A 1448 MET cc_start: 0.8548 (mmt) cc_final: 0.7825 (mpp) REVERT: A 1452 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: A 1534 SER cc_start: 0.8682 (OUTLIER) cc_final: 0.8342 (p) REVERT: A 1647 MET cc_start: 0.8313 (ttt) cc_final: 0.8055 (ttp) REVERT: A 1763 LEU cc_start: 0.8508 (tp) cc_final: 0.8273 (tp) REVERT: A 1764 LYS cc_start: 0.8381 (mtpp) cc_final: 0.8100 (mtpp) REVERT: A 1772 LYS cc_start: 0.8567 (ptmm) cc_final: 0.8316 (ptpp) REVERT: A 1789 GLU cc_start: 0.7841 (tp30) cc_final: 0.7492 (tp30) REVERT: A 1850 MET cc_start: 0.6267 (mtt) cc_final: 0.5929 (mtt) REVERT: A 2298 MET cc_start: 0.8259 (ttp) cc_final: 0.7969 (tpp) REVERT: A 2345 ASN cc_start: 0.8140 (t0) cc_final: 0.7846 (t0) REVERT: A 2493 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7249 (tp30) REVERT: A 2538 ASP cc_start: 0.8194 (t0) cc_final: 0.7939 (t0) REVERT: A 2580 PHE cc_start: 0.8656 (m-80) cc_final: 0.8176 (m-80) REVERT: A 2683 ASP cc_start: 0.7609 (m-30) cc_final: 0.7397 (m-30) REVERT: A 2744 PHE cc_start: 0.7618 (t80) cc_final: 0.7268 (m-80) REVERT: A 2747 GLU cc_start: 0.7764 (tp30) cc_final: 0.7522 (tp30) REVERT: A 2788 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6536 (mm-30) REVERT: A 2993 LYS cc_start: 0.7407 (mttt) cc_final: 0.6940 (mttp) REVERT: A 3089 LYS cc_start: 0.8358 (ttmt) cc_final: 0.8154 (ttmt) REVERT: A 3091 LYS cc_start: 0.8107 (mmpt) cc_final: 0.7818 (mmpt) REVERT: A 3203 MET cc_start: 0.6548 (mpp) cc_final: 0.6216 (mpp) outliers start: 45 outliers final: 27 residues processed: 318 average time/residue: 0.6726 time to fit residues: 230.4259 Evaluate side-chains 324 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 294 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain A residue 1320 LEU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1393 LEU Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1420 ILE Chi-restraints excluded: chain A residue 1452 GLU Chi-restraints excluded: chain A residue 1534 SER Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 2391 LEU Chi-restraints excluded: chain A residue 2442 ASP Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2463 MET Chi-restraints excluded: chain A residue 2475 ILE Chi-restraints excluded: chain A residue 2579 GLU Chi-restraints excluded: chain A residue 2677 SER Chi-restraints excluded: chain A residue 2758 GLN Chi-restraints excluded: chain A residue 2793 ARG Chi-restraints excluded: chain A residue 3006 VAL Chi-restraints excluded: chain A residue 3226 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 88 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 111 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2366 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.145375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.124405 restraints weight = 16978.778| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.89 r_work: 0.3539 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13043 Z= 0.158 Angle : 0.559 10.519 17622 Z= 0.279 Chirality : 0.040 0.153 2037 Planarity : 0.004 0.046 2189 Dihedral : 7.117 73.206 1840 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.49 % Allowed : 17.90 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.71 (0.22), residues: 1541 helix: 1.56 (0.18), residues: 886 sheet: 0.38 (0.61), residues: 77 loop : -1.26 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2418 TYR 0.012 0.001 TYR A2994 PHE 0.026 0.001 PHE A2633 TRP 0.016 0.001 TRP A2542 HIS 0.003 0.001 HIS A2794 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (13039) covalent geometry : angle 0.54730 / 0.28 (17616) hydrogen bonds : bond 0.03699 / 2.40 ( 653) hydrogen bonds : angle 4.01783 / 2.89 ( 1884) metal coordination : bond 0.01537 / 0.63 ( 4) metal coordination : angle 6.30126 / 3.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 296 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 968 GLU cc_start: 0.7673 (mp0) cc_final: 0.7365 (mp0) REVERT: A 975 GLU cc_start: 0.7702 (pt0) cc_final: 0.7487 (pt0) REVERT: A 1249 LEU cc_start: 0.8663 (mt) cc_final: 0.8420 (mm) REVERT: A 1277 GLN cc_start: 0.7507 (mm-40) cc_final: 0.7029 (mm110) REVERT: A 1279 PHE cc_start: 0.8477 (m-80) cc_final: 0.8210 (m-80) REVERT: A 1348 ARG cc_start: 0.8062 (ttm-80) cc_final: 0.7740 (ttm-80) REVERT: A 1350 CYS cc_start: 0.8148 (t) cc_final: 0.7925 (t) REVERT: A 1434 SER cc_start: 0.8074 (p) cc_final: 0.7846 (t) REVERT: A 1442 ASP cc_start: 0.7774 (m-30) cc_final: 0.7513 (m-30) REVERT: A 1448 MET cc_start: 0.8542 (mmt) cc_final: 0.7840 (mpp) REVERT: A 1452 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: A 1534 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8335 (p) REVERT: A 1647 MET cc_start: 0.8319 (ttt) cc_final: 0.8063 (ttp) REVERT: A 1763 LEU cc_start: 0.8502 (tp) cc_final: 0.8233 (tp) REVERT: A 1764 LYS cc_start: 0.8381 (mtpp) cc_final: 0.8102 (mtpp) REVERT: A 1772 LYS cc_start: 0.8580 (ptmm) cc_final: 0.8353 (ptpp) REVERT: A 1789 GLU cc_start: 0.7829 (tp30) cc_final: 0.7407 (tp30) REVERT: A 1850 MET cc_start: 0.6286 (mtt) cc_final: 0.5951 (mtt) REVERT: A 2298 MET cc_start: 0.8264 (ttp) cc_final: 0.7971 (tpp) REVERT: A 2345 ASN cc_start: 0.8146 (t0) cc_final: 0.7841 (t0) REVERT: A 2375 MET cc_start: 0.8346 (mmt) cc_final: 0.8130 (mmm) REVERT: A 2493 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7220 (tp30) REVERT: A 2538 ASP cc_start: 0.8178 (t0) cc_final: 0.7928 (t0) REVERT: A 2580 PHE cc_start: 0.8635 (m-80) cc_final: 0.8274 (m-80) REVERT: A 2683 ASP cc_start: 0.7610 (m-30) cc_final: 0.7403 (m-30) REVERT: A 2747 GLU cc_start: 0.7786 (tp30) cc_final: 0.7580 (tp30) REVERT: A 2788 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6522 (mm-30) REVERT: A 2993 LYS cc_start: 0.7372 (mttt) cc_final: 0.6895 (mttp) REVERT: A 3089 LYS cc_start: 0.8349 (ttmt) cc_final: 0.8134 (ttmt) REVERT: A 3091 LYS cc_start: 0.8081 (mmpt) cc_final: 0.7792 (mmpt) REVERT: A 3203 MET cc_start: 0.6618 (mpp) cc_final: 0.6272 (mpp) outliers start: 36 outliers final: 26 residues processed: 311 average time/residue: 0.6947 time to fit residues: 232.6872 Evaluate side-chains 315 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 287 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain A residue 1320 LEU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1393 LEU Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1420 ILE Chi-restraints excluded: chain A residue 1452 GLU Chi-restraints excluded: chain A residue 1534 SER Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 2391 LEU Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2463 MET Chi-restraints excluded: chain A residue 2475 ILE Chi-restraints excluded: chain A residue 2579 GLU Chi-restraints excluded: chain A residue 2677 SER Chi-restraints excluded: chain A residue 2793 ARG Chi-restraints excluded: chain A residue 3006 VAL Chi-restraints excluded: chain A residue 3226 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 74 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 0.0470 chunk 137 optimal weight: 0.9980 chunk 147 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2366 HIS A2758 GLN ** A2825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.144733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.123996 restraints weight = 17068.964| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.86 r_work: 0.3534 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13043 Z= 0.195 Angle : 0.594 11.611 17622 Z= 0.295 Chirality : 0.042 0.181 2037 Planarity : 0.004 0.058 2189 Dihedral : 7.188 73.117 1840 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.56 % Allowed : 18.11 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.58 (0.22), residues: 1541 helix: 1.46 (0.18), residues: 886 sheet: 0.34 (0.61), residues: 77 loop : -1.35 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2418 TYR 0.014 0.001 TYR A2994 PHE 0.027 0.002 PHE A2633 TRP 0.016 0.002 TRP A2542 HIS 0.004 0.001 HIS A2794 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 (13039) covalent geometry : angle 0.58396 / 0.29 (17616) hydrogen bonds : bond 0.03971 / 2.59 ( 653) hydrogen bonds : angle 4.09185 / 2.94 ( 1884) metal coordination : bond 0.01501 / 0.62 ( 4) metal coordination : angle 5.90251 / 2.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 301 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 968 GLU cc_start: 0.7673 (mp0) cc_final: 0.7351 (mp0) REVERT: A 1041 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7386 (mt-10) REVERT: A 1277 GLN cc_start: 0.7547 (mm-40) cc_final: 0.7073 (mm110) REVERT: A 1279 PHE cc_start: 0.8489 (m-80) cc_final: 0.8168 (m-80) REVERT: A 1434 SER cc_start: 0.8091 (p) cc_final: 0.7856 (t) REVERT: A 1442 ASP cc_start: 0.7779 (m-30) cc_final: 0.7538 (m-30) REVERT: A 1448 MET cc_start: 0.8567 (mmt) cc_final: 0.7845 (mpp) REVERT: A 1452 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: A 1534 SER cc_start: 0.8688 (OUTLIER) cc_final: 0.8357 (p) REVERT: A 1647 MET cc_start: 0.8360 (ttt) cc_final: 0.8116 (ttp) REVERT: A 1763 LEU cc_start: 0.8522 (tp) cc_final: 0.8250 (tp) REVERT: A 1789 GLU cc_start: 0.7821 (tp30) cc_final: 0.7472 (tp30) REVERT: A 1850 MET cc_start: 0.6257 (mtt) cc_final: 0.5953 (mtt) REVERT: A 2298 MET cc_start: 0.8270 (ttp) cc_final: 0.7987 (tpp) REVERT: A 2345 ASN cc_start: 0.8128 (t0) cc_final: 0.7833 (t0) REVERT: A 2493 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7244 (tp30) REVERT: A 2538 ASP cc_start: 0.8173 (t0) cc_final: 0.7919 (t0) REVERT: A 2580 PHE cc_start: 0.8637 (m-80) cc_final: 0.8329 (m-80) REVERT: A 2683 ASP cc_start: 0.7621 (m-30) cc_final: 0.7411 (m-30) REVERT: A 2744 PHE cc_start: 0.7671 (t80) cc_final: 0.7360 (m-80) REVERT: A 2747 GLU cc_start: 0.7764 (tp30) cc_final: 0.7557 (tp30) REVERT: A 2788 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6541 (mm-30) REVERT: A 2993 LYS cc_start: 0.7385 (mttt) cc_final: 0.7155 (mtmm) REVERT: A 3089 LYS cc_start: 0.8343 (ttmt) cc_final: 0.8140 (ttmt) REVERT: A 3091 LYS cc_start: 0.8077 (mmpt) cc_final: 0.7788 (mmpt) REVERT: A 3203 MET cc_start: 0.6631 (mpp) cc_final: 0.6294 (mpp) outliers start: 37 outliers final: 27 residues processed: 316 average time/residue: 0.6775 time to fit residues: 230.4403 Evaluate side-chains 323 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 293 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1320 LEU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1393 LEU Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1420 ILE Chi-restraints excluded: chain A residue 1452 GLU Chi-restraints excluded: chain A residue 1512 LEU Chi-restraints excluded: chain A residue 1534 SER Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 2391 LEU Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2463 MET Chi-restraints excluded: chain A residue 2475 ILE Chi-restraints excluded: chain A residue 2579 GLU Chi-restraints excluded: chain A residue 2677 SER Chi-restraints excluded: chain A residue 2758 GLN Chi-restraints excluded: chain A residue 2793 ARG Chi-restraints excluded: chain A residue 3006 VAL Chi-restraints excluded: chain A residue 3226 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 134 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 146 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2366 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.145476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.124623 restraints weight = 17106.171| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.86 r_work: 0.3542 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13043 Z= 0.160 Angle : 0.582 9.976 17622 Z= 0.290 Chirality : 0.041 0.163 2037 Planarity : 0.004 0.051 2189 Dihedral : 7.152 73.199 1840 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.28 % Allowed : 18.87 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.64 (0.22), residues: 1541 helix: 1.51 (0.18), residues: 887 sheet: 0.32 (0.61), residues: 77 loop : -1.30 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1348 TYR 0.014 0.001 TYR A2417 PHE 0.027 0.001 PHE A2633 TRP 0.016 0.001 TRP A2542 HIS 0.003 0.001 HIS A2794 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (13039) covalent geometry : angle 0.57554 / 0.29 (17616) hydrogen bonds : bond 0.03720 / 2.42 ( 653) hydrogen bonds : angle 4.06630 / 2.93 ( 1884) metal coordination : bond 0.01185 / 0.48 ( 4) metal coordination : angle 4.87554 / 2.46 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 293 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 968 GLU cc_start: 0.7671 (mp0) cc_final: 0.7349 (mp0) REVERT: A 1249 LEU cc_start: 0.8662 (mt) cc_final: 0.8419 (mm) REVERT: A 1277 GLN cc_start: 0.7468 (mm-40) cc_final: 0.6995 (mm110) REVERT: A 1279 PHE cc_start: 0.8481 (m-80) cc_final: 0.8143 (m-80) REVERT: A 1348 ARG cc_start: 0.8093 (ttm-80) cc_final: 0.7813 (ttm-80) REVERT: A 1434 SER cc_start: 0.8058 (p) cc_final: 0.7831 (t) REVERT: A 1442 ASP cc_start: 0.7764 (m-30) cc_final: 0.7514 (m-30) REVERT: A 1448 MET cc_start: 0.8546 (mmt) cc_final: 0.7836 (mpp) REVERT: A 1452 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: A 1634 GLU cc_start: 0.7757 (tp30) cc_final: 0.7498 (tp30) REVERT: A 1647 MET cc_start: 0.8335 (ttt) cc_final: 0.8090 (ttp) REVERT: A 1763 LEU cc_start: 0.8472 (tp) cc_final: 0.8217 (tp) REVERT: A 1789 GLU cc_start: 0.7819 (tp30) cc_final: 0.7469 (tp30) REVERT: A 1850 MET cc_start: 0.6282 (mtt) cc_final: 0.5940 (mtt) REVERT: A 2298 MET cc_start: 0.8268 (ttp) cc_final: 0.7969 (tpp) REVERT: A 2345 ASN cc_start: 0.8158 (t0) cc_final: 0.7846 (t0) REVERT: A 2538 ASP cc_start: 0.8183 (t0) cc_final: 0.7935 (t0) REVERT: A 2580 PHE cc_start: 0.8626 (m-80) cc_final: 0.8317 (m-80) REVERT: A 2744 PHE cc_start: 0.7587 (t80) cc_final: 0.7272 (m-80) REVERT: A 2747 GLU cc_start: 0.7784 (tp30) cc_final: 0.7556 (tp30) REVERT: A 2993 LYS cc_start: 0.7359 (mttt) cc_final: 0.7136 (mtmm) REVERT: A 3089 LYS cc_start: 0.8348 (ttmt) cc_final: 0.8134 (ttmt) REVERT: A 3091 LYS cc_start: 0.8091 (mmpt) cc_final: 0.7804 (mmpt) REVERT: A 3203 MET cc_start: 0.6610 (mpp) cc_final: 0.6283 (mpp) outliers start: 33 outliers final: 30 residues processed: 305 average time/residue: 0.7002 time to fit residues: 229.4163 Evaluate side-chains 317 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 286 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1320 LEU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1393 LEU Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1420 ILE Chi-restraints excluded: chain A residue 1452 GLU Chi-restraints excluded: chain A residue 1534 SER Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 2391 LEU Chi-restraints excluded: chain A residue 2449 THR Chi-restraints excluded: chain A residue 2462 LEU Chi-restraints excluded: chain A residue 2463 MET Chi-restraints excluded: chain A residue 2475 ILE Chi-restraints excluded: chain A residue 2579 GLU Chi-restraints excluded: chain A residue 2677 SER Chi-restraints excluded: chain A residue 2793 ARG Chi-restraints excluded: chain A residue 3006 VAL Chi-restraints excluded: chain A residue 3226 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 123 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 134 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 80 optimal weight: 0.0020 chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2366 HIS A2758 GLN ** A2825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.146486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.125585 restraints weight = 17153.800| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.90 r_work: 0.3556 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13043 Z= 0.129 Angle : 0.562 10.664 17622 Z= 0.280 Chirality : 0.040 0.165 2037 Planarity : 0.004 0.051 2189 Dihedral : 7.046 73.286 1840 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.00 % Allowed : 19.42 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.77 (0.22), residues: 1541 helix: 1.62 (0.18), residues: 887 sheet: 0.34 (0.62), residues: 77 loop : -1.27 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1348 TYR 0.010 0.001 TYR A2994 PHE 0.025 0.001 PHE A2633 TRP 0.016 0.001 TRP A2542 HIS 0.002 0.001 HIS A2794 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (13039) covalent geometry : angle 0.55696 / 0.28 (17616) hydrogen bonds : bond 0.03449 / 2.26 ( 653) hydrogen bonds : angle 3.99407 / 2.88 ( 1884) metal coordination : bond 0.00854 / 0.34 ( 4) metal coordination : angle 3.99048 / 2.04 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5728.51 seconds wall clock time: 98 minutes 11.72 seconds (5891.72 seconds total)