Starting phenix.real_space_refine on Sat Aug 8 08:46:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t0f_55400/08_2026/9t0f_55400.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t0f_55400/08_2026/9t0f_55400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9t0f_55400/08_2026/9t0f_55400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t0f_55400/08_2026/9t0f_55400.map" model { file = "/net/cci-nas-00/data/ceres_data/9t0f_55400/08_2026/9t0f_55400.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t0f_55400/08_2026/9t0f_55400.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 2 5.21 5 S 93 5.16 5 C 8128 2.51 5 N 2209 2.21 5 O 2404 1.98 5 H 12979 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25817 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 25813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1604, 25813 Classifications: {'peptide': 1604} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1554} Chain breaks: 12 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1645 SG CYS A1028 20.464 44.355 28.875 1.00 60.79 S ATOM 1677 SG CYS A1031 19.824 47.868 27.840 1.00 59.88 S ATOM 2161 SG CYS A1062 17.012 46.124 29.554 1.00 64.03 S ATOM 2196 SG CYS A1065 19.886 46.939 31.642 1.00 62.85 S ATOM 5204 SG CYS A1294 31.510 59.680 79.567 1.00 41.65 S Time building chain proxies: 4.38, per 1000 atoms: 0.17 Number of scatterers: 25817 At special positions: 0 Unit cell: (107.18, 98.792, 125.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 93 16.00 Mg 2 11.99 O 2404 8.00 N 2209 7.00 C 8128 6.00 H 12979 1.00 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: 1.80 Conformation dependent library (CDL) restraints added in 656.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A4001 " pdb="ZN ZN A4001 " - pdb=" SG CYS A1031 " pdb="ZN ZN A4001 " - pdb=" SG CYS A1062 " pdb="ZN ZN A4001 " - pdb=" SG CYS A1065 " pdb="ZN ZN A4001 " - pdb=" SG CYS A1028 " pdb=" ZN A4002 " pdb="ZN ZN A4002 " - pdb=" ND1 HIS A1365 " pdb="ZN ZN A4002 " - pdb=" NE2 HIS A1090 " pdb="ZN ZN A4002 " - pdb=" SG CYS A1294 " Number of angles added : 6 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3074 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 11 sheets defined 64.0% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 930 through 947 removed outlier: 5.287A pdb=" N GLU A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N HIS A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) removed outlier: 3.549A 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 1008 through 1024 removed outlier: 3.532A pdb=" N LYS A1024 " --> pdb=" O SER A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1041 Processing helix chain 'A' and resid 1044 through 1057 removed outlier: 3.901A pdb=" N GLN A1057 " --> pdb=" O ALA A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1061 Processing helix chain 'A' and resid 1076 through 1081 Processing helix chain 'A' and resid 1084 through 1088 Processing helix chain 'A' and resid 1106 through 1112 Processing helix chain 'A' and resid 1118 through 1139 Processing helix chain 'A' and resid 1172 through 1187 Processing helix chain 'A' and resid 1188 through 1194 removed outlier: 3.689A pdb=" N ASP A1194 " --> pdb=" O SER A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1209 Processing helix chain 'A' and resid 1221 through 1232 Processing helix chain 'A' and resid 1266 through 1277 Processing helix chain 'A' and resid 1297 through 1309 removed outlier: 3.506A pdb=" N TYR A1308 " --> pdb=" O CYS A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1328 Processing helix chain 'A' and resid 1330 through 1350 Processing helix chain 'A' and resid 1401 through 1410 removed outlier: 3.927A pdb=" N LEU A1407 " --> pdb=" O ARG A1403 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A1410 " --> pdb=" O VAL A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1426 removed outlier: 3.672A pdb=" N ILE A1414 " --> pdb=" O SER A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1435 removed outlier: 4.101A pdb=" N ASN A1433 " --> pdb=" O GLU A1430 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL A1435 " --> pdb=" O ILE A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1463 removed outlier: 3.554A pdb=" N GLU A1463 " --> pdb=" O THR A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1465 through 1481 removed outlier: 3.745A 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 1513 Processing helix chain 'A' and resid 1515 through 1524 Processing helix chain 'A' and resid 1524 through 1531 Processing helix chain 'A' and resid 1532 through 1534 No H-bonds generated for 'chain 'A' and resid 1532 through 1534' Processing helix chain 'A' and resid 1538 through 1545 removed outlier: 3.667A pdb=" N LYS A1544 " --> pdb=" O ASN A1540 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS A1545 " --> pdb=" O GLU A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1572 removed outlier: 4.529A pdb=" N ASP A1572 " --> pdb=" O CYS A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1572 through 1581 removed outlier: 4.115A pdb=" N LYS A1581 " --> pdb=" O VAL A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1611 Processing helix chain 'A' and resid 1612 through 1616 Processing helix chain 'A' and resid 1623 through 1650 Processing helix chain 'A' and resid 1658 through 1666 Processing helix chain 'A' and resid 1758 through 1773 Processing helix chain 'A' and resid 1780 through 1792 Processing helix chain 'A' and resid 1793 through 1795 No H-bonds generated for 'chain 'A' and resid 1793 through 1795' Processing helix chain 'A' and resid 1796 through 1805 Processing helix chain 'A' and resid 1806 through 1811 Processing helix chain 'A' and resid 1831 through 1839 Processing helix chain 'A' and resid 2250 through 2259 Processing helix chain 'A' and resid 2286 through 2306 removed outlier: 3.805A pdb=" N THR A2306 " --> pdb=" O ASN A2302 " (cutoff:3.500A) Processing helix chain 'A' and resid 2316 through 2336 Processing helix chain 'A' and resid 2367 through 2379 Processing helix chain 'A' and resid 2382 through 2396 Processing helix chain 'A' and resid 2404 through 2423 removed outlier: 4.231A pdb=" N SER A2421 " --> pdb=" O TYR A2417 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS A2422 " --> pdb=" O ARG A2418 " (cutoff:3.500A) Processing helix chain 'A' and resid 2429 through 2440 Processing helix chain 'A' and resid 2441 through 2445 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: 3.839A pdb=" N VAL A2489 " --> pdb=" O SER A2485 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A2490 " --> pdb=" O LEU A2486 " (cutoff:3.500A) Processing helix chain 'A' and resid 2531 through 2540 removed outlier: 3.593A pdb=" N GLU A2539 " --> pdb=" O SER A2535 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR A2540 " --> pdb=" O GLN A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2540 through 2558 removed outlier: 3.568A pdb=" N CYS A2558 " --> pdb=" O ALA A2554 " (cutoff:3.500A) Processing helix chain 'A' and resid 2589 through 2594 removed outlier: 3.844A pdb=" N MET A2594 " --> pdb=" O ILE A2591 " (cutoff:3.500A) Processing helix chain 'A' and resid 2595 through 2600 removed outlier: 3.526A pdb=" N ILE A2599 " --> pdb=" O PHE A2595 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN A2600 " --> pdb=" O THR A2596 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2595 through 2600' Processing helix chain 'A' and resid 2605 through 2623 removed outlier: 3.543A pdb=" N ASN A2623 " --> pdb=" O GLN A2619 " (cutoff:3.500A) Processing helix chain 'A' and resid 2626 through 2645 removed outlier: 3.722A pdb=" N PHE A2641 " --> pdb=" O ARG A2637 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS A2644 " --> pdb=" O ILE A2640 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A2645 " --> pdb=" O PHE A2641 " (cutoff:3.500A) Processing helix chain 'A' and resid 2645 through 2657 removed outlier: 6.260A pdb=" N ILE A2654 " --> pdb=" O ARG A2650 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LEU A2655 " --> pdb=" O ARG A2651 " (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 2670 through 2675 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 2815 Processing helix chain 'A' and resid 2816 through 2836 removed outlier: 3.678A pdb=" N SER A2826 " --> pdb=" O ASN A2822 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A2827 " --> pdb=" O ARG A2823 " (cutoff:3.500A) Processing helix chain 'A' and resid 2898 through 2911 Processing helix chain 'A' and resid 2948 through 2955 Processing helix chain 'A' and resid 2993 through 3003 Processing helix chain 'A' and resid 3043 through 3060 removed outlier: 3.595A pdb=" N LYS A3047 " --> pdb=" O GLN A3043 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A3048 " --> pdb=" O SER A3044 " (cutoff:3.500A) Processing helix chain 'A' and resid 3062 through 3073 Processing helix chain 'A' and resid 3091 through 3100 removed outlier: 4.453A pdb=" N ALA A3095 " --> pdb=" O LEU A3092 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR A3096 " --> pdb=" O PHE A3093 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A3100 " --> pdb=" O GLU A3097 " (cutoff:3.500A) Processing helix chain 'A' and resid 3104 through 3114 Processing helix chain 'A' and resid 3114 through 3120 removed outlier: 4.275A pdb=" N ILE A3118 " --> pdb=" O ASP A3114 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A3119 " --> pdb=" O GLU A3115 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU A3120 " --> pdb=" O SER A3116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3114 through 3120' Processing helix chain 'A' and resid 3130 through 3142 removed outlier: 3.510A pdb=" N ARG A3135 " --> pdb=" O LEU A3131 " (cutoff:3.500A) Processing helix chain 'A' and resid 3142 through 3163 Processing helix chain 'A' and resid 3167 through 3185 removed outlier: 3.612A pdb=" N VAL A3171 " --> pdb=" O ASP A3167 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A3172 " --> pdb=" O LEU A3168 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A3175 " --> pdb=" O VAL A3171 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN A3176 " --> pdb=" O ALA A3172 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A3185 " --> pdb=" O LEU A3181 " (cutoff:3.500A) Processing helix chain 'A' and resid 3208 through 3217 removed outlier: 3.979A 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: 6.551A 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: 4.329A pdb=" N CYS A1143 " --> pdb=" O VAL A1220 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1358 through 1362 removed outlier: 4.108A pdb=" N LEU A1383 " --> pdb=" O LYS A1373 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU A1386 " --> pdb=" O GLY A1396 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLY A1396 " --> pdb=" O LEU A1386 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2284 through 2285 removed outlier: 7.322A pdb=" N ALA A2268 " --> pdb=" O GLU A2402 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2507 through 2514 Processing sheet with id=AA7, first strand: chain 'A' and resid 2574 through 2576 removed outlier: 4.420A pdb=" N PHE A2580 " --> pdb=" O THR A2587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2958 through 2959 Processing sheet with id=AA9, first strand: chain 'A' and resid 3005 through 3009 removed outlier: 6.039A pdb=" N SER A3005 " --> pdb=" O LEU A3039 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL A3041 " --> pdb=" O SER A3005 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N SER A3007 " --> pdb=" O VAL A3041 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 3076 through 3081 removed outlier: 4.159A pdb=" N SER A3078 " --> pdb=" O ARG A3224 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 3086 through 3090 removed outlier: 4.118A pdb=" N PHE A3195 " --> pdb=" O THR A3090 " (cutoff:3.500A) 730 hydrogen bonds defined for protein. 2091 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: 6.14 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 12934 1.04 - 1.24: 1795 1.24 - 1.44: 3706 1.44 - 1.65: 7461 1.65 - 1.85: 136 Bond restraints: 26032 Sorted by residual: bond pdb=" C GLY A2789 " pdb=" N PRO A2790 " ideal model delta sigma weight residual 1.326 1.345 -0.019 1.44e-02 4.82e+03 1.66e+00 bond pdb=" CB CYS A1294 " pdb=" SG CYS A1294 " ideal model delta sigma weight residual 1.808 1.849 -0.041 3.30e-02 9.18e+02 1.52e+00 bond pdb=" N ILE A1616 " pdb=" CA ILE A1616 " ideal model delta sigma weight residual 1.474 1.458 0.016 1.57e-02 4.06e+03 1.04e+00 bond pdb=" CA ASP A1105 " pdb=" CB ASP A1105 " ideal model delta sigma weight residual 1.541 1.531 0.010 1.20e-02 6.94e+03 7.14e-01 bond pdb=" CG PRO A3022 " pdb=" CD PRO A3022 " ideal model delta sigma weight residual 1.503 1.476 0.027 3.40e-02 8.65e+02 6.43e-01 ... (remaining 26027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 46872 2.01 - 4.03: 175 4.03 - 6.04: 9 6.04 - 8.06: 0 8.06 - 10.07: 4 Bond angle restraints: 47060 Sorted by residual: angle pdb=" CA PRO A2662 " pdb=" N PRO A2662 " pdb=" CD PRO A2662 " ideal model delta sigma weight residual 112.00 106.72 5.28 1.40e+00 5.10e-01 1.42e+01 angle pdb=" N PRO A3022 " pdb=" CD PRO A3022 " pdb=" CG PRO A3022 " ideal model delta sigma weight residual 103.20 97.67 5.53 1.50e+00 4.44e-01 1.36e+01 angle pdb=" N PRO A2662 " pdb=" CD PRO A2662 " pdb=" CG PRO A2662 " ideal model delta sigma weight residual 103.20 97.68 5.52 1.50e+00 4.44e-01 1.35e+01 angle pdb=" CA PRO A3022 " pdb=" N PRO A3022 " pdb=" CD PRO A3022 " ideal model delta sigma weight residual 112.00 106.92 5.08 1.40e+00 5.10e-01 1.32e+01 angle pdb=" CB PRO A3022 " pdb=" CG PRO A3022 " pdb=" CD PRO A3022 " ideal model delta sigma weight residual 106.10 96.03 10.07 3.20e+00 9.77e-02 9.91e+00 ... (remaining 47055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 11217 17.46 - 34.92: 724 34.92 - 52.38: 169 52.38 - 69.83: 62 69.83 - 87.29: 11 Dihedral angle restraints: 12183 sinusoidal: 6720 harmonic: 5463 Sorted by residual: 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 -156.94 -23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CB GLU A2297 " pdb=" CG GLU A2297 " pdb=" CD GLU A2297 " pdb=" OE1 GLU A2297 " ideal model delta sinusoidal sigma weight residual 0.00 -87.29 87.29 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU A1789 " pdb=" CG GLU A1789 " pdb=" CD GLU A1789 " pdb=" OE1 GLU A1789 " ideal model delta sinusoidal sigma weight residual 0.00 -82.74 82.74 1 3.00e+01 1.11e-03 9.32e+00 ... (remaining 12180 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1331 0.029 - 0.057: 486 0.057 - 0.086: 125 0.086 - 0.115: 57 0.115 - 0.144: 25 Chirality restraints: 2024 Sorted by residual: chirality pdb=" CA VAL A1234 " pdb=" N VAL A1234 " pdb=" C VAL A1234 " pdb=" CB VAL A1234 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA ILE A1616 " pdb=" N ILE A1616 " pdb=" C ILE A1616 " pdb=" CB ILE A1616 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA ILE A1591 " pdb=" N ILE A1591 " pdb=" C ILE A1591 " pdb=" CB ILE A1591 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 2021 not shown) Planarity restraints: 3772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A1796 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO A1797 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A1797 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1797 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A3156 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C SER A3156 " -0.029 2.00e-02 2.50e+03 pdb=" O SER A3156 " 0.011 2.00e-02 2.50e+03 pdb=" N SER A3157 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 954 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO A 955 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 955 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 955 " -0.020 5.00e-02 4.00e+02 ... (remaining 3769 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1129 2.18 - 2.79: 53133 2.79 - 3.39: 74298 3.39 - 4.00: 97473 4.00 - 4.60: 153069 Nonbonded interactions: 379102 Sorted by model distance: nonbonded pdb="HH12 ARG A1265 " pdb=" O ARG A1551 " model vdw 1.578 2.450 nonbonded pdb=" HH TYR A1419 " pdb=" OD1 ASN A1500 " model vdw 1.582 2.450 nonbonded pdb=" OD1 ASP A1171 " pdb=" H ASP A1172 " model vdw 1.602 2.450 nonbonded pdb=" HZ2 LYS A3199 " pdb=" O GLY A3200 " model vdw 1.605 2.450 nonbonded pdb=" OE1 GLU A 994 " pdb="HH21 ARG A 997 " model vdw 1.607 2.450 ... (remaining 379097 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.290 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: 0.160 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 29.560 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13060 Z= 0.129 Angle : 0.514 10.072 17608 Z= 0.290 Chirality : 0.036 0.144 2024 Planarity : 0.003 0.042 2229 Dihedral : 12.984 87.293 4926 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.41 % Favored : 97.53 % Rotamer: Outliers : 0.07 % Allowed : 0.07 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.21), residues: 1578 helix: 1.58 (0.17), residues: 914 sheet: 0.06 (0.57), residues: 92 loop : -0.53 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3221 TYR 0.011 0.001 TYR A1617 PHE 0.012 0.001 PHE A3049 TRP 0.011 0.001 TRP A2542 HIS 0.004 0.001 HIS A3011 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (13053) covalent geometry : angle 0.50739 / 0.29 (17602) hydrogen bonds : bond 0.14603 / 9.63 ( 730) hydrogen bonds : angle 5.13555 / 3.67 ( 2091) metal coordination : bond 0.01226 / 0.73 ( 7) metal coordination : angle 4.57293 / 2.56 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1072 ILE cc_start: 0.6584 (mm) cc_final: 0.6146 (tp) REVERT: A 1638 ARG cc_start: 0.6767 (ttm110) cc_final: 0.6520 (ttp-110) REVERT: A 2993 LYS cc_start: 0.7095 (mttp) cc_final: 0.6894 (mttp) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 1.2772 time to fit residues: 252.9988 Evaluate side-chains 140 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 960 GLN A1286 GLN A1514 ASN A1758 ASN A2258 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.177966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.126468 restraints weight = 38092.087| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.15 r_work: 0.3443 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13060 Z= 0.200 Angle : 0.538 6.908 17608 Z= 0.290 Chirality : 0.039 0.164 2024 Planarity : 0.004 0.043 2229 Dihedral : 3.940 24.306 1727 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.64 % Rotamer: Outliers : 1.29 % Allowed : 4.62 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.86 (0.21), residues: 1578 helix: 1.45 (0.17), residues: 916 sheet: -0.36 (0.52), residues: 97 loop : -0.66 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2837 TYR 0.015 0.002 TYR A1617 PHE 0.039 0.002 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.007 0.001 HIS A1639 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (13053) covalent geometry : angle 0.53000 / 0.29 (17602) hydrogen bonds : bond 0.05087 / 3.32 ( 730) hydrogen bonds : angle 4.29856 / 3.08 ( 2091) metal coordination : bond 0.01027 / 0.70 ( 7) metal coordination : angle 5.04147 / 2.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2400 GLN cc_start: 0.7623 (mm110) cc_final: 0.7187 (mp10) REVERT: A 2682 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6519 (tp30) REVERT: A 3183 ARG cc_start: 0.6439 (OUTLIER) cc_final: 0.6025 (mtt90) outliers start: 19 outliers final: 7 residues processed: 162 average time/residue: 1.1691 time to fit residues: 211.4509 Evaluate side-chains 146 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1350 CYS Chi-restraints excluded: chain A residue 1548 THR Chi-restraints excluded: chain A residue 1657 ASP Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2682 GLU Chi-restraints excluded: chain A residue 2757 LEU Chi-restraints excluded: chain A residue 3006 VAL Chi-restraints excluded: chain A residue 3183 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 960 GLN A1286 GLN A1514 ASN A2314 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.176909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.125077 restraints weight = 38145.338| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.17 r_work: 0.3454 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13060 Z= 0.189 Angle : 0.517 6.940 17608 Z= 0.278 Chirality : 0.039 0.162 2024 Planarity : 0.004 0.042 2229 Dihedral : 3.992 25.106 1727 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.04 % Favored : 96.89 % Rotamer: Outliers : 1.36 % Allowed : 6.59 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.79 (0.21), residues: 1578 helix: 1.41 (0.17), residues: 915 sheet: -0.20 (0.53), residues: 90 loop : -0.76 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2837 TYR 0.014 0.002 TYR A1617 PHE 0.038 0.002 PHE A2633 TRP 0.013 0.001 TRP A2542 HIS 0.007 0.001 HIS A1639 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (13053) covalent geometry : angle 0.50944 / 0.28 (17602) hydrogen bonds : bond 0.04712 / 3.06 ( 730) hydrogen bonds : angle 4.16431 / 2.98 ( 2091) metal coordination : bond 0.01089 / 0.74 ( 7) metal coordination : angle 4.64514 / 2.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 943 GLU cc_start: 0.7125 (mp0) cc_final: 0.6688 (mp0) REVERT: A 1072 ILE cc_start: 0.6907 (OUTLIER) cc_final: 0.6450 (mp) REVERT: A 2400 GLN cc_start: 0.7698 (mm110) cc_final: 0.7260 (mp10) REVERT: A 2579 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6825 (mm-30) REVERT: A 2682 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6425 (tp30) REVERT: A 2993 LYS cc_start: 0.6779 (mttp) cc_final: 0.6528 (mttt) outliers start: 20 outliers final: 8 residues processed: 157 average time/residue: 1.1711 time to fit residues: 205.4985 Evaluate side-chains 152 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1350 CYS Chi-restraints excluded: chain A residue 1548 THR Chi-restraints excluded: chain A residue 1634 GLU Chi-restraints excluded: chain A residue 1657 ASP Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2579 GLU Chi-restraints excluded: chain A residue 2682 GLU Chi-restraints excluded: chain A residue 2757 LEU Chi-restraints excluded: chain A residue 3107 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 156 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 960 GLN A1286 GLN A1514 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.176626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125276 restraints weight = 38019.892| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.16 r_work: 0.3446 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13060 Z= 0.189 Angle : 0.508 6.468 17608 Z= 0.274 Chirality : 0.039 0.169 2024 Planarity : 0.004 0.040 2229 Dihedral : 3.997 25.537 1727 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.64 % Rotamer: Outliers : 1.43 % Allowed : 7.54 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.75 (0.21), residues: 1578 helix: 1.38 (0.17), residues: 916 sheet: -0.30 (0.52), residues: 90 loop : -0.78 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1348 TYR 0.014 0.001 TYR A1617 PHE 0.034 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.006 0.001 HIS A1639 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (13053) covalent geometry : angle 0.50227 / 0.27 (17602) hydrogen bonds : bond 0.04566 / 2.97 ( 730) hydrogen bonds : angle 4.12733 / 2.96 ( 2091) metal coordination : bond 0.00620 / 0.36 ( 7) metal coordination : angle 4.24180 / 2.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 943 GLU cc_start: 0.7192 (mp0) cc_final: 0.6727 (mp0) REVERT: A 1072 ILE cc_start: 0.6991 (OUTLIER) cc_final: 0.6429 (mp) REVERT: A 1085 ILE cc_start: 0.7374 (tp) cc_final: 0.6703 (mp) REVERT: A 2400 GLN cc_start: 0.7671 (mm110) cc_final: 0.7328 (mp10) REVERT: A 2682 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6564 (tp30) REVERT: A 3009 ASN cc_start: 0.7768 (t0) cc_final: 0.7451 (t0) REVERT: A 3183 ARG cc_start: 0.6555 (mtt90) cc_final: 0.6197 (mtt90) outliers start: 21 outliers final: 8 residues processed: 157 average time/residue: 1.1895 time to fit residues: 208.1196 Evaluate side-chains 151 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1273 CYS Chi-restraints excluded: chain A residue 1350 CYS Chi-restraints excluded: chain A residue 1548 THR Chi-restraints excluded: chain A residue 1634 GLU Chi-restraints excluded: chain A residue 1657 ASP Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2682 GLU Chi-restraints excluded: chain A residue 2757 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 150 optimal weight: 9.9990 chunk 11 optimal weight: 0.0870 chunk 138 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 96 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 960 GLN A1286 GLN A1514 ASN A2314 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.178588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.127547 restraints weight = 37815.490| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.15 r_work: 0.3475 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13060 Z= 0.120 Angle : 0.463 5.335 17608 Z= 0.249 Chirality : 0.037 0.147 2024 Planarity : 0.003 0.039 2229 Dihedral : 3.826 24.521 1727 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.79 % Favored : 97.15 % Rotamer: Outliers : 1.09 % Allowed : 8.96 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.21), residues: 1578 helix: 1.70 (0.17), residues: 917 sheet: -0.33 (0.51), residues: 90 loop : -0.69 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2837 TYR 0.013 0.001 TYR A1617 PHE 0.027 0.001 PHE A2633 TRP 0.012 0.001 TRP A2542 HIS 0.003 0.001 HIS A1639 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (13053) covalent geometry : angle 0.45828 / 0.25 (17602) hydrogen bonds : bond 0.03958 / 2.57 ( 730) hydrogen bonds : angle 3.97015 / 2.84 ( 2091) metal coordination : bond 0.00489 / 0.32 ( 7) metal coordination : angle 3.73864 / 2.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 943 GLU cc_start: 0.7239 (mp0) cc_final: 0.6770 (mp0) REVERT: A 1072 ILE cc_start: 0.6809 (OUTLIER) cc_final: 0.6277 (mp) REVERT: A 1830 MET cc_start: 0.4558 (ttt) cc_final: 0.3646 (pp-130) REVERT: A 2400 GLN cc_start: 0.7587 (mm110) cc_final: 0.7318 (mp10) REVERT: A 2579 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6777 (mm-30) REVERT: A 2993 LYS cc_start: 0.6678 (mttp) cc_final: 0.6420 (mttt) REVERT: A 3009 ASN cc_start: 0.7725 (t0) cc_final: 0.7492 (t0) REVERT: A 3183 ARG cc_start: 0.6478 (mtt90) cc_final: 0.6087 (mtt90) outliers start: 16 outliers final: 8 residues processed: 156 average time/residue: 1.1849 time to fit residues: 206.7425 Evaluate side-chains 150 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1273 CYS Chi-restraints excluded: chain A residue 1350 CYS Chi-restraints excluded: chain A residue 1548 THR Chi-restraints excluded: chain A residue 1634 GLU Chi-restraints excluded: chain A residue 1657 ASP Chi-restraints excluded: chain A residue 2394 ILE Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2579 GLU Chi-restraints excluded: chain A residue 2757 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 144 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 960 GLN A1286 GLN A1514 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.176874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.125108 restraints weight = 37950.852| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.19 r_work: 0.3454 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13060 Z= 0.159 Angle : 0.482 5.714 17608 Z= 0.259 Chirality : 0.038 0.160 2024 Planarity : 0.003 0.037 2229 Dihedral : 3.862 24.594 1727 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.42 % Favored : 96.51 % Rotamer: Outliers : 1.22 % Allowed : 9.57 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.21), residues: 1578 helix: 1.65 (0.17), residues: 918 sheet: -0.40 (0.51), residues: 90 loop : -0.73 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1526 TYR 0.013 0.001 TYR A1617 PHE 0.031 0.001 PHE A2633 TRP 0.013 0.001 TRP A2542 HIS 0.005 0.001 HIS A1639 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (13053) covalent geometry : angle 0.47752 / 0.26 (17602) hydrogen bonds : bond 0.04188 / 2.73 ( 730) hydrogen bonds : angle 3.97789 / 2.85 ( 2091) metal coordination : bond 0.00870 / 0.57 ( 7) metal coordination : angle 3.61065 / 2.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 943 GLU cc_start: 0.7250 (mp0) cc_final: 0.6780 (mp0) REVERT: A 1006 GLN cc_start: 0.7989 (tt0) cc_final: 0.7114 (mt0) REVERT: A 1072 ILE cc_start: 0.6832 (OUTLIER) cc_final: 0.6313 (mp) REVERT: A 1135 MET cc_start: 0.4925 (OUTLIER) cc_final: 0.3420 (tpt) REVERT: A 1830 MET cc_start: 0.4659 (ttt) cc_final: 0.3706 (pp-130) REVERT: A 2400 GLN cc_start: 0.7692 (mm110) cc_final: 0.7367 (mp10) REVERT: A 2579 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6733 (mm-30) REVERT: A 2993 LYS cc_start: 0.6719 (mttp) cc_final: 0.6440 (mttt) REVERT: A 3009 ASN cc_start: 0.7685 (t0) cc_final: 0.7436 (t0) REVERT: A 3135 ARG cc_start: 0.7502 (ttt90) cc_final: 0.7276 (ttp80) REVERT: A 3183 ARG cc_start: 0.6466 (mtt90) cc_final: 0.6051 (mtt90) outliers start: 18 outliers final: 10 residues processed: 152 average time/residue: 1.2180 time to fit residues: 206.3817 Evaluate side-chains 157 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1135 MET Chi-restraints excluded: chain A residue 1273 CYS Chi-restraints excluded: chain A residue 1350 CYS Chi-restraints excluded: chain A residue 1529 MET Chi-restraints excluded: chain A residue 1548 THR Chi-restraints excluded: chain A residue 1634 GLU Chi-restraints excluded: chain A residue 1657 ASP Chi-restraints excluded: chain A residue 2394 ILE Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2579 GLU Chi-restraints excluded: chain A residue 2757 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 88 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 960 GLN A1286 GLN A1514 ASN A2314 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.175462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.123368 restraints weight = 37969.594| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.20 r_work: 0.3425 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13060 Z= 0.188 Angle : 0.509 6.048 17608 Z= 0.273 Chirality : 0.039 0.170 2024 Planarity : 0.004 0.037 2229 Dihedral : 3.950 25.121 1727 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.49 % Favored : 96.45 % Rotamer: Outliers : 1.43 % Allowed : 9.84 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.88 (0.21), residues: 1578 helix: 1.53 (0.17), residues: 916 sheet: -0.51 (0.51), residues: 90 loop : -0.75 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1526 TYR 0.014 0.001 TYR A1617 PHE 0.032 0.002 PHE A2633 TRP 0.013 0.001 TRP A2542 HIS 0.006 0.001 HIS A1639 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (13053) covalent geometry : angle 0.50365 / 0.27 (17602) hydrogen bonds : bond 0.04426 / 2.88 ( 730) hydrogen bonds : angle 4.03006 / 2.89 ( 2091) metal coordination : bond 0.01098 / 0.72 ( 7) metal coordination : angle 3.84352 / 2.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 943 GLU cc_start: 0.7287 (mp0) cc_final: 0.6887 (mp0) REVERT: A 1006 GLN cc_start: 0.8009 (tt0) cc_final: 0.7156 (mt0) REVERT: A 1072 ILE cc_start: 0.6872 (OUTLIER) cc_final: 0.6354 (mp) REVERT: A 1135 MET cc_start: 0.5107 (OUTLIER) cc_final: 0.3582 (tpt) REVERT: A 1830 MET cc_start: 0.4661 (ttt) cc_final: 0.3743 (pp-130) REVERT: A 2579 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6771 (mm-30) REVERT: A 2993 LYS cc_start: 0.6779 (mttp) cc_final: 0.6527 (mttt) REVERT: A 3009 ASN cc_start: 0.7699 (t0) cc_final: 0.7457 (t0) REVERT: A 3183 ARG cc_start: 0.6467 (mtt90) cc_final: 0.6016 (mtt90) outliers start: 21 outliers final: 11 residues processed: 157 average time/residue: 1.1933 time to fit residues: 209.3930 Evaluate side-chains 155 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1135 MET Chi-restraints excluded: chain A residue 1273 CYS Chi-restraints excluded: chain A residue 1350 CYS Chi-restraints excluded: chain A residue 1529 MET Chi-restraints excluded: chain A residue 1548 THR Chi-restraints excluded: chain A residue 1634 GLU Chi-restraints excluded: chain A residue 1657 ASP Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2579 GLU Chi-restraints excluded: chain A residue 2757 LEU Chi-restraints excluded: chain A residue 3107 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 960 GLN A1286 GLN A1514 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.177239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.125341 restraints weight = 38056.027| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.20 r_work: 0.3460 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13060 Z= 0.128 Angle : 0.467 5.230 17608 Z= 0.251 Chirality : 0.037 0.150 2024 Planarity : 0.004 0.088 2229 Dihedral : 3.815 24.323 1727 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.66 % Favored : 97.28 % Rotamer: Outliers : 1.36 % Allowed : 10.59 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.21), residues: 1578 helix: 1.72 (0.17), residues: 919 sheet: -0.48 (0.50), residues: 90 loop : -0.71 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2750 TYR 0.013 0.001 TYR A1617 PHE 0.027 0.001 PHE A2633 TRP 0.013 0.001 TRP A2542 HIS 0.003 0.001 HIS A3011 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (13053) covalent geometry : angle 0.46316 / 0.25 (17602) hydrogen bonds : bond 0.03918 / 2.55 ( 730) hydrogen bonds : angle 3.92493 / 2.81 ( 2091) metal coordination : bond 0.00672 / 0.44 ( 7) metal coordination : angle 3.27148 / 1.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 943 GLU cc_start: 0.7285 (mp0) cc_final: 0.6842 (mp0) REVERT: A 1006 GLN cc_start: 0.7945 (tt0) cc_final: 0.7052 (mt0) REVERT: A 1072 ILE cc_start: 0.6727 (OUTLIER) cc_final: 0.6198 (mp) REVERT: A 1830 MET cc_start: 0.4661 (ttt) cc_final: 0.3768 (pp-130) REVERT: A 2579 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6744 (mm-30) REVERT: A 2993 LYS cc_start: 0.6828 (mttp) cc_final: 0.6545 (mttt) REVERT: A 3009 ASN cc_start: 0.7655 (t0) cc_final: 0.7392 (t0) REVERT: A 3183 ARG cc_start: 0.6504 (mtt90) cc_final: 0.6076 (mtt90) outliers start: 20 outliers final: 12 residues processed: 156 average time/residue: 1.1515 time to fit residues: 201.4390 Evaluate side-chains 160 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1273 CYS Chi-restraints excluded: chain A residue 1350 CYS Chi-restraints excluded: chain A residue 1529 MET Chi-restraints excluded: chain A residue 1548 THR Chi-restraints excluded: chain A residue 1634 GLU Chi-restraints excluded: chain A residue 1657 ASP Chi-restraints excluded: chain A residue 2394 ILE Chi-restraints excluded: chain A residue 2400 GLN Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2579 GLU Chi-restraints excluded: chain A residue 2757 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 64 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 68 optimal weight: 0.0020 chunk 140 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 960 GLN A1286 GLN A1514 ASN A2314 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.177631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.125881 restraints weight = 38034.329| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.19 r_work: 0.3468 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13060 Z= 0.119 Angle : 0.464 5.924 17608 Z= 0.248 Chirality : 0.037 0.146 2024 Planarity : 0.003 0.036 2229 Dihedral : 3.748 23.901 1727 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.72 % Favored : 97.21 % Rotamer: Outliers : 1.09 % Allowed : 10.93 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.21), residues: 1578 helix: 1.87 (0.17), residues: 918 sheet: -0.44 (0.50), residues: 90 loop : -0.66 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1526 TYR 0.017 0.001 TYR A2994 PHE 0.027 0.001 PHE A2633 TRP 0.013 0.001 TRP A2542 HIS 0.003 0.001 HIS A1639 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (13053) covalent geometry : angle 0.45980 / 0.25 (17602) hydrogen bonds : bond 0.03799 / 2.48 ( 730) hydrogen bonds : angle 3.85703 / 2.76 ( 2091) metal coordination : bond 0.00508 / 0.34 ( 7) metal coordination : angle 3.20667 / 1.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 943 GLU cc_start: 0.7282 (mp0) cc_final: 0.6835 (mp0) REVERT: A 1072 ILE cc_start: 0.6738 (OUTLIER) cc_final: 0.6202 (mp) REVERT: A 1830 MET cc_start: 0.4779 (ttt) cc_final: 0.3877 (pp-130) REVERT: A 2579 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6758 (mm-30) REVERT: A 2682 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6643 (tp30) REVERT: A 3009 ASN cc_start: 0.7639 (t0) cc_final: 0.7372 (t0) outliers start: 16 outliers final: 10 residues processed: 153 average time/residue: 1.1692 time to fit residues: 199.8643 Evaluate side-chains 153 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1273 CYS Chi-restraints excluded: chain A residue 1350 CYS Chi-restraints excluded: chain A residue 1529 MET Chi-restraints excluded: chain A residue 1548 THR Chi-restraints excluded: chain A residue 1634 GLU Chi-restraints excluded: chain A residue 1657 ASP Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2579 GLU Chi-restraints excluded: chain A residue 2682 GLU Chi-restraints excluded: chain A residue 2757 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 60 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 960 GLN A1286 GLN A1514 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.176691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.125023 restraints weight = 37928.581| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.18 r_work: 0.3456 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13060 Z= 0.146 Angle : 0.482 5.993 17608 Z= 0.258 Chirality : 0.037 0.156 2024 Planarity : 0.004 0.089 2229 Dihedral : 3.811 23.967 1727 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.17 % Favored : 96.77 % Rotamer: Outliers : 1.22 % Allowed : 10.86 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.21), residues: 1578 helix: 1.83 (0.17), residues: 919 sheet: -0.70 (0.49), residues: 95 loop : -0.72 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A2750 TYR 0.012 0.001 TYR A1617 PHE 0.029 0.001 PHE A2633 TRP 0.013 0.001 TRP A2542 HIS 0.004 0.001 HIS A1639 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (13053) covalent geometry : angle 0.47873 / 0.26 (17602) hydrogen bonds : bond 0.03977 / 2.59 ( 730) hydrogen bonds : angle 3.87601 / 2.77 ( 2091) metal coordination : bond 0.00673 / 0.44 ( 7) metal coordination : angle 3.25134 / 1.83 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 943 GLU cc_start: 0.7311 (mp0) cc_final: 0.6903 (mp0) REVERT: A 1072 ILE cc_start: 0.6740 (OUTLIER) cc_final: 0.6211 (mp) REVERT: A 1830 MET cc_start: 0.4841 (ttt) cc_final: 0.3952 (pp-130) REVERT: A 2579 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6742 (mm-30) REVERT: A 2682 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6668 (tp30) REVERT: A 3009 ASN cc_start: 0.7589 (t0) cc_final: 0.7312 (t0) REVERT: A 3183 ARG cc_start: 0.6446 (mtt90) cc_final: 0.6147 (mtt90) outliers start: 18 outliers final: 11 residues processed: 149 average time/residue: 1.1546 time to fit residues: 192.4393 Evaluate side-chains 154 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 1070 VAL Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1273 CYS Chi-restraints excluded: chain A residue 1350 CYS Chi-restraints excluded: chain A residue 1529 MET Chi-restraints excluded: chain A residue 1548 THR Chi-restraints excluded: chain A residue 1634 GLU Chi-restraints excluded: chain A residue 1657 ASP Chi-restraints excluded: chain A residue 2394 ILE Chi-restraints excluded: chain A residue 2526 THR Chi-restraints excluded: chain A residue 2579 GLU Chi-restraints excluded: chain A residue 2682 GLU Chi-restraints excluded: chain A residue 2757 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 100 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 114 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1286 GLN A1514 ASN A2314 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.175824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.124315 restraints weight = 38015.740| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.18 r_work: 0.3445 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13060 Z= 0.179 Angle : 0.505 6.077 17608 Z= 0.271 Chirality : 0.039 0.167 2024 Planarity : 0.004 0.034 2229 Dihedral : 3.906 24.452 1727 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.58 % Rotamer: Outliers : 1.09 % Allowed : 11.00 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.21), residues: 1578 helix: 1.70 (0.17), residues: 918 sheet: -0.74 (0.49), residues: 95 loop : -0.75 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1526 TYR 0.019 0.002 TYR A2994 PHE 0.032 0.001 PHE A2633 TRP 0.013 0.001 TRP A2542 HIS 0.005 0.001 HIS A1639 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (13053) covalent geometry : angle 0.50152 / 0.27 (17602) hydrogen bonds : bond 0.04267 / 2.79 ( 730) hydrogen bonds : angle 3.94606 / 2.82 ( 2091) metal coordination : bond 0.00854 / 0.56 ( 7) metal coordination : angle 3.36767 / 1.91 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9125.36 seconds wall clock time: 155 minutes 13.27 seconds (9313.27 seconds total)