Starting phenix.real_space_refine on Sat Aug 8 22:23:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t0e_55399/08_2026/9t0e_55399.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t0e_55399/08_2026/9t0e_55399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9t0e_55399/08_2026/9t0e_55399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t0e_55399/08_2026/9t0e_55399.map" model { file = "/net/cci-nas-00/data/ceres_data/9t0e_55399/08_2026/9t0e_55399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t0e_55399/08_2026/9t0e_55399.cif" } resolution = 2.3 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= 0.014 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 13 5.49 5 Mg 2 5.21 5 S 99 5.16 5 C 9144 2.51 5 N 2512 2.21 5 O 3058 1.98 5 H 14560 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s 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: 29390 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1776 Classifications: {'peptide': 118} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "R" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 414 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna2p': 4, 'rna3p': 8} Chain: "A" Number of atoms: 26903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1671, 26903 Classifications: {'peptide': 1671} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1621} 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} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 287 Classifications: {'water': 287} Link IDs: {None: 286} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3835 SG CYS A1028 63.080 35.299 94.509 1.00 50.87 S ATOM 3867 SG CYS A1031 66.572 36.585 95.257 1.00 50.92 S ATOM 4351 SG CYS A1062 66.192 33.180 93.595 1.00 52.34 S ATOM 4386 SG CYS A1065 65.354 36.326 91.686 1.00 50.40 S ATOM 7745 SG CYS A1294 68.199 53.491 44.700 1.00 36.18 S Time building chain proxies: 4.30, per 1000 atoms: 0.15 Number of scatterers: 29390 At special positions: 0 Unit cell: (99.28, 140.89, 127.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 99 16.00 P 13 15.00 Mg 2 11.99 O 3058 8.00 N 2512 7.00 C 9144 6.00 H 14560 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 611.3 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 A1065 " pdb="ZN ZN A4001 " - pdb=" SG CYS A1028 " pdb="ZN ZN A4001 " - pdb=" SG CYS A1062 " pdb=" ZN A4002 " pdb="ZN ZN A4002 " - pdb=" NE2 HIS A1090 " pdb="ZN ZN A4002 " - pdb=" ND1 HIS A1365 " pdb="ZN ZN A4002 " - pdb=" SG CYS A1294 " Number of angles added : 6 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3404 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 14 sheets defined 60.6% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'A' and resid 930 through 947 removed outlier: 4.955A pdb=" N GLU A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N HIS A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) removed outlier: 3.536A 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 1025 removed outlier: 3.629A pdb=" N LYS A1024 " --> pdb=" O SER A1020 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER A1025 " --> pdb=" O GLU A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1041 Processing helix chain 'A' and resid 1044 through 1057 removed outlier: 3.664A 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 1105 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: 3.880A 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 1237 through 1254 Processing helix chain 'A' and resid 1266 through 1281 removed outlier: 3.533A pdb=" N CYS A1273 " --> pdb=" O GLU A1269 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A1278 " --> pdb=" O PHE A1274 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE A1279 " --> pdb=" O ASP A1275 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS A1280 " --> pdb=" O VAL A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1296 removed outlier: 3.685A pdb=" N ILE A1295 " --> pdb=" O GLN A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1309 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 1426 removed outlier: 3.911A pdb=" N LEU A1407 " --> pdb=" O ARG A1403 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A1410 " --> pdb=" O VAL A1406 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU A1412 " --> pdb=" O GLY A1408 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N TYR A1413 " --> pdb=" O SER A1409 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1435 removed outlier: 3.662A pdb=" N ASN A1433 " --> pdb=" O GLU A1430 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A1435 " --> pdb=" O ILE A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1463 removed outlier: 3.614A pdb=" N GLU A1463 " --> pdb=" O THR A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1465 through 1481 removed outlier: 3.574A 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: 3.662A pdb=" N LYS A1544 " --> pdb=" O ASN A1540 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS A1545 " --> pdb=" O GLU A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1572 removed outlier: 4.581A pdb=" N ASP A1572 " --> pdb=" O CYS A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1572 through 1581 removed outlier: 4.117A 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 1854 removed outlier: 3.645A pdb=" N LYS A1854 " --> pdb=" O MET A1850 " (cutoff:3.500A) Processing helix chain 'A' and resid 1872 through 1877 Processing helix chain 'A' and resid 1883 through 1896 Processing helix chain 'A' and resid 2250 through 2259 Processing helix chain 'A' and resid 2286 through 2306 removed outlier: 3.910A 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 2397 Processing helix chain 'A' and resid 2404 through 2423 removed outlier: 3.553A pdb=" N ARG A2418 " --> pdb=" O VAL A2414 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER A2421 " --> pdb=" O TYR A2417 " (cutoff:3.500A) removed outlier: 4.044A 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: 3.800A pdb=" N VAL A2489 " --> pdb=" O SER A2485 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A2490 " --> pdb=" O LEU A2486 " (cutoff:3.500A) Processing helix chain 'A' and resid 2531 through 2559 removed outlier: 3.831A pdb=" N THR A2540 " --> pdb=" O GLN A2536 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N TRP A2542 " --> pdb=" O ASP A2538 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LYS A2543 " --> pdb=" O GLU A2539 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS A2558 " --> pdb=" O ALA A2554 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS A2559 " --> pdb=" O VAL A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2589 through 2594 removed outlier: 3.614A pdb=" N MET A2594 " --> pdb=" O ILE A2591 " (cutoff:3.500A) Processing helix chain 'A' and resid 2595 through 2600 Processing helix chain 'A' and resid 2605 through 2623 removed outlier: 3.505A pdb=" N ASN A2623 " --> pdb=" O GLN A2619 " (cutoff:3.500A) Processing helix chain 'A' and resid 2626 through 2643 removed outlier: 3.728A pdb=" N PHE A2641 " --> pdb=" O ARG A2637 " (cutoff:3.500A) Processing helix chain 'A' and resid 2645 through 2657 removed outlier: 6.349A pdb=" N ILE A2654 " --> pdb=" O ARG A2650 " (cutoff:3.500A) removed outlier: 6.175A 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 2678 through 2697 Processing helix chain 'A' and resid 2698 through 2701 Processing helix chain 'A' and resid 2753 through 2765 Processing helix chain 'A' and resid 2770 through 2783 Processing helix chain 'A' and resid 2801 through 2805 Processing helix chain 'A' and resid 2806 through 2815 Processing helix chain 'A' and resid 2816 through 2836 removed outlier: 3.699A pdb=" N SER A2826 " --> pdb=" O ASN A2822 " (cutoff:3.500A) removed outlier: 3.701A 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 2953 Processing helix chain 'A' and resid 2993 through 3003 Processing helix chain 'A' and resid 3043 through 3061 removed outlier: 3.597A pdb=" N LYS A3047 " --> pdb=" O GLN A3043 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A3048 " --> pdb=" O SER A3044 " (cutoff:3.500A) Processing helix chain 'A' and resid 3062 through 3072 Processing helix chain 'A' and resid 3104 through 3114 Processing helix chain 'A' and resid 3114 through 3119 removed outlier: 4.091A pdb=" N ILE A3118 " --> pdb=" O ASP A3114 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A3119 " --> pdb=" O GLU A3115 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3114 through 3119' Processing helix chain 'A' and resid 3130 through 3142 removed outlier: 3.604A 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 3172 removed outlier: 3.629A pdb=" N VAL A3171 " --> pdb=" O ASP A3167 " (cutoff:3.500A) Processing helix chain 'A' and resid 3173 through 3184 Processing helix chain 'A' and resid 3208 through 3217 removed outlier: 3.634A pdb=" N ILE A3217 " --> pdb=" O VAL A3213 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.514A pdb=" N LEU C 20 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 78 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.574A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N MET C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N THR C 52 " --> pdb=" O ASN C 32 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASN C 32 " --> pdb=" O THR C 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.574A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N MET C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N THR C 52 " --> pdb=" O ASN C 32 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASN C 32 " --> pdb=" O THR C 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 971 through 972 removed outlier: 6.693A pdb=" N VAL A 971 " --> pdb=" O TYR A1755 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1003 through 1004 Processing sheet with id=AA6, first strand: chain 'A' and resid 1151 through 1153 removed outlier: 4.133A pdb=" N CYS A1143 " --> pdb=" O VAL A1220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1358 through 1362 removed outlier: 3.948A pdb=" N LEU A1383 " --> pdb=" O LYS A1373 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N MET A1382 " --> pdb=" O PHE A1398 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N PHE A1398 " --> pdb=" O MET A1382 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N CYS A1384 " --> pdb=" O GLY A1396 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLY A1396 " --> pdb=" O CYS A1384 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A1386 " --> pdb=" O LEU A1394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2284 through 2285 removed outlier: 7.391A pdb=" N ALA A2268 " --> pdb=" O GLU A2402 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2506 through 2514 Processing sheet with id=AB1, first strand: chain 'A' and resid 2574 through 2576 removed outlier: 4.688A pdb=" N PHE A2580 " --> pdb=" O THR A2587 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2958 through 2959 Processing sheet with id=AB3, first strand: chain 'A' and resid 3005 through 3009 removed outlier: 6.344A pdb=" N SER A3005 " --> pdb=" O LEU A3039 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL A3041 " --> pdb=" O SER A3005 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER A3007 " --> pdb=" O VAL A3041 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3076 through 3081 removed outlier: 6.643A pdb=" N ARG A3224 " --> pdb=" O GLU A3077 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU A3079 " --> pdb=" O PHE A3222 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE A3222 " --> pdb=" O GLU A3079 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3086 through 3090 removed outlier: 4.070A pdb=" N PHE A3195 " --> pdb=" O THR A3090 " (cutoff:3.500A) 817 hydrogen bonds defined for protein. 2337 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: 6.62 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14514 1.03 - 1.23: 214 1.23 - 1.42: 5934 1.42 - 1.62: 8556 1.62 - 1.82: 145 Bond restraints: 29363 Sorted by residual: bond pdb=" N7 A R 5 " pdb=" C5 A R 5 " ideal model delta sigma weight residual 1.388 1.379 0.009 6.00e-03 2.78e+04 2.48e+00 bond pdb=" C8 A R 5 " pdb=" N7 A R 5 " ideal model delta sigma weight residual 1.311 1.300 0.011 7.00e-03 2.04e+04 2.37e+00 bond pdb=" C8 G R 8 " pdb=" N7 G R 8 " ideal model delta sigma weight residual 1.305 1.296 0.009 6.00e-03 2.78e+04 2.01e+00 bond pdb=" N7 A R 9 " pdb=" C5 A R 9 " ideal model delta sigma weight residual 1.388 1.380 0.008 6.00e-03 2.78e+04 1.85e+00 bond pdb=" CB LYS A1298 " pdb=" CG LYS A1298 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.60e+00 ... (remaining 29358 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 47403 0.94 - 1.87: 5205 1.87 - 2.81: 358 2.81 - 3.75: 77 3.75 - 4.68: 24 Bond angle restraints: 53067 Sorted by residual: angle pdb=" O5' A R 11 " pdb=" C5' A R 11 " pdb=" C4' A R 11 " ideal model delta sigma weight residual 109.40 112.60 -3.20 8.00e-01 1.56e+00 1.60e+01 angle pdb=" O4' A R 5 " pdb=" C1' A R 5 " pdb=" N9 A R 5 " ideal model delta sigma weight residual 108.50 110.93 -2.43 7.00e-01 2.04e+00 1.20e+01 angle pdb=" N VAL A1288 " pdb=" CA VAL A1288 " pdb=" C VAL A1288 " ideal model delta sigma weight residual 109.19 106.58 2.61 8.20e-01 1.49e+00 1.01e+01 angle pdb=" O5' U R 10 " pdb=" C5' U R 10 " pdb=" C4' U R 10 " ideal model delta sigma weight residual 109.40 111.79 -2.39 8.00e-01 1.56e+00 8.92e+00 angle pdb=" CA VAL A1288 " pdb=" C VAL A1288 " pdb=" N PRO A1289 " ideal model delta sigma weight residual 116.57 119.46 -2.89 9.80e-01 1.04e+00 8.67e+00 ... (remaining 53062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.94: 12527 18.94 - 37.87: 846 37.87 - 56.81: 278 56.81 - 75.74: 71 75.74 - 94.68: 9 Dihedral angle restraints: 13731 sinusoidal: 7682 harmonic: 6049 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 -156.49 -23.51 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA SER A2570 " pdb=" C SER A2570 " pdb=" N ASP A2571 " pdb=" CA ASP A2571 " ideal model delta harmonic sigma weight residual 180.00 159.70 20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLY A2514 " pdb=" C GLY A2514 " pdb=" N SER A2515 " pdb=" CA SER A2515 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 13728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1419 0.034 - 0.068: 657 0.068 - 0.102: 162 0.102 - 0.135: 64 0.135 - 0.169: 5 Chirality restraints: 2307 Sorted by residual: chirality pdb=" CB ILE A1787 " pdb=" CA ILE A1787 " pdb=" CG1 ILE A1787 " pdb=" CG2 ILE A1787 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.16e-01 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 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" C1' A R 5 " pdb=" O4' A R 5 " pdb=" C2' A R 5 " pdb=" N9 A R 5 " both_signs ideal model delta sigma weight residual False 2.47 2.32 0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 2304 not shown) Planarity restraints: 4227 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1605 " 0.164 9.50e-02 1.11e+02 5.48e-02 3.31e+00 pdb=" NE ARG A1605 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A1605 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A1605 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A1605 " 0.005 2.00e-02 2.50e+03 pdb="HH11 ARG A1605 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A1605 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A1605 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A1605 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A2659 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.83e+00 pdb=" C THR A2659 " -0.029 2.00e-02 2.50e+03 pdb=" O THR A2659 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A2660 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A2633 " 0.011 2.00e-02 2.50e+03 8.02e-03 1.93e+00 pdb=" CG PHE A2633 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A2633 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A2633 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A2633 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A2633 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A2633 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A2633 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A2633 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A2633 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A2633 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A2633 " -0.000 2.00e-02 2.50e+03 ... (remaining 4224 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1180 2.16 - 2.77: 57745 2.77 - 3.38: 85662 3.38 - 3.99: 115234 3.99 - 4.60: 178153 Nonbonded interactions: 437974 Sorted by model distance: nonbonded pdb=" HZ2 LYS A1520 " pdb=" O HOH A4101 " model vdw 1.551 2.450 nonbonded pdb=" O LEU A2966 " pdb=" HE ARG A2969 " model vdw 1.600 2.450 nonbonded pdb=" OE1 GLU A3033 " pdb=" H GLU A3033 " model vdw 1.600 2.450 nonbonded pdb=" HZ2 LYS A3199 " pdb=" O GLY A3200 " model vdw 1.605 2.450 nonbonded pdb=" O SER A3116 " pdb=" HG SER A3119 " model vdw 1.612 2.450 ... (remaining 437969 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: 4.670 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: 0.190 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 31.620 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: 0.010 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 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 : 0.005 0.054 14811 Z= 0.240 Angle : 0.579 4.684 20029 Z= 0.331 Chirality : 0.042 0.169 2307 Planarity : 0.004 0.073 2495 Dihedral : 15.848 94.681 5650 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.78 % Favored : 97.10 % Rotamer: Outliers : 1.17 % Allowed : 12.62 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.94 (0.20), residues: 1761 helix: 1.52 (0.17), residues: 977 sheet: 0.25 (0.44), residues: 145 loop : -0.65 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 963 TYR 0.015 0.002 TYR A1503 PHE 0.024 0.002 PHE A2633 TRP 0.015 0.002 TRP A2542 HIS 0.006 0.002 HIS A1639 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.24 (14803) covalent geometry : angle 0.57819 / 0.33 (20021) SS BOND : bond 0.00162 / 0.08 ( 1) SS BOND : angle 0.77379 / 0.42 ( 2) hydrogen bonds : bond 0.13134 / 8.57 ( 804) hydrogen bonds : angle 5.35574 / 4.47 ( 2337) metal coordination : bond 0.00910 / 0.59 ( 7) metal coordination : angle 1.52219 / 0.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.830 Fit side-chains REVERT: C 19 ARG cc_start: 0.7058 (mmm160) cc_final: 0.6653 (mtp-110) REVERT: A 1139 SER cc_start: 0.6483 (OUTLIER) cc_final: 0.6278 (p) REVERT: A 1620 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6942 (pt0) outliers start: 19 outliers final: 14 residues processed: 180 average time/residue: 1.1570 time to fit residues: 231.8426 Evaluate side-chains 171 residues out of total 1625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain A residue 1139 SER Chi-restraints excluded: chain A residue 1248 SER Chi-restraints excluded: chain A residue 1356 SER Chi-restraints excluded: chain A residue 1434 SER Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2564 SER Chi-restraints excluded: chain A residue 2596 THR Chi-restraints excluded: chain A residue 2764 SER Chi-restraints excluded: chain A residue 2805 SER Chi-restraints excluded: chain A residue 2912 VAL Chi-restraints excluded: chain A residue 3094 SER Chi-restraints excluded: chain A residue 3112 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2316 HIS ** A2396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2777 ASN A2961 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.148653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.092935 restraints weight = 41876.933| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.86 r_work: 0.2960 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14811 Z= 0.151 Angle : 0.516 4.308 20029 Z= 0.283 Chirality : 0.038 0.152 2307 Planarity : 0.004 0.052 2495 Dihedral : 8.123 89.028 2129 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.73 % Favored : 97.16 % Rotamer: Outliers : 1.54 % Allowed : 11.94 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 1.03 (0.20), residues: 1761 helix: 1.64 (0.16), residues: 988 sheet: 0.10 (0.42), residues: 152 loop : -0.70 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 963 TYR 0.013 0.001 TYR A1503 PHE 0.023 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 0.00328 / 0.15 (14803) covalent geometry : angle 0.51448 / 0.28 (20021) SS BOND : bond 0.00279 / 0.13 ( 1) SS BOND : angle 0.91857 / 0.49 ( 2) hydrogen bonds : bond 0.05423 / 3.59 ( 804) hydrogen bonds : angle 4.52785 / 3.84 ( 2337) metal coordination : bond 0.00591 / 0.35 ( 7) metal coordination : angle 2.50132 / 1.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: C 19 ARG cc_start: 0.6623 (mmm160) cc_final: 0.6285 (mtp-110) REVERT: C 95 CYS cc_start: 0.7404 (t) cc_final: 0.7139 (t) REVERT: A 975 GLU cc_start: 0.7698 (tt0) cc_final: 0.7441 (tt0) REVERT: A 1448 MET cc_start: 0.9070 (mmp) cc_final: 0.8635 (mmp) REVERT: A 1620 GLU cc_start: 0.7451 (mm-30) cc_final: 0.6761 (pt0) REVERT: A 1798 GLU cc_start: 0.7913 (mp0) cc_final: 0.7575 (mp0) REVERT: A 1808 LYS cc_start: 0.7020 (OUTLIER) cc_final: 0.6559 (mppt) REVERT: A 2682 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7455 (mt-10) REVERT: A 2769 THR cc_start: 0.8344 (p) cc_final: 0.7974 (t) outliers start: 25 outliers final: 10 residues processed: 174 average time/residue: 1.2154 time to fit residues: 234.4259 Evaluate side-chains 165 residues out of total 1625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain A residue 1285 LYS Chi-restraints excluded: chain A residue 1808 LYS Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2596 THR Chi-restraints excluded: chain A residue 2610 MET Chi-restraints excluded: chain A residue 2682 GLU Chi-restraints excluded: chain A residue 2912 VAL Chi-restraints excluded: chain A residue 3026 CYS Chi-restraints excluded: chain A residue 3094 SER Chi-restraints excluded: chain A residue 3112 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 120 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 chunk 113 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2258 GLN A2261 ASN A2316 HIS ** A2396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2961 ASN A2996 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.148541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.092671 restraints weight = 41690.827| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.87 r_work: 0.2957 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.0624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14811 Z= 0.160 Angle : 0.501 5.259 20029 Z= 0.271 Chirality : 0.038 0.151 2307 Planarity : 0.004 0.055 2495 Dihedral : 7.817 88.522 2119 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.67 % Favored : 97.22 % Rotamer: Outliers : 1.23 % Allowed : 12.12 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 1.11 (0.20), residues: 1761 helix: 1.68 (0.16), residues: 988 sheet: 0.18 (0.44), residues: 147 loop : -0.61 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 963 TYR 0.011 0.001 TYR A1503 PHE 0.023 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.004 0.001 HIS A1639 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (14803) covalent geometry : angle 0.49962 / 0.27 (20021) SS BOND : bond 0.00263 / 0.13 ( 1) SS BOND : angle 0.87252 / 0.47 ( 2) hydrogen bonds : bond 0.05173 / 3.44 ( 804) hydrogen bonds : angle 4.33848 / 3.65 ( 2337) metal coordination : bond 0.00683 / 0.41 ( 7) metal coordination : angle 2.47166 / 1.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: C 19 ARG cc_start: 0.6611 (mmm160) cc_final: 0.6298 (mtp-110) REVERT: C 95 CYS cc_start: 0.7408 (t) cc_final: 0.7207 (t) REVERT: A 975 GLU cc_start: 0.7707 (tt0) cc_final: 0.7443 (tt0) REVERT: A 1001 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8565 (pttp) REVERT: A 1105 ASP cc_start: 0.5778 (OUTLIER) cc_final: 0.5466 (t70) REVERT: A 1448 MET cc_start: 0.9101 (mmp) cc_final: 0.8632 (mmp) REVERT: A 1620 GLU cc_start: 0.7464 (mm-30) cc_final: 0.6816 (pt0) REVERT: A 1760 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7229 (mp0) REVERT: A 1798 GLU cc_start: 0.7887 (mp0) cc_final: 0.7616 (mp0) REVERT: A 1808 LYS cc_start: 0.7026 (OUTLIER) cc_final: 0.6692 (mppt) REVERT: A 2682 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7484 (mt-10) REVERT: A 2769 THR cc_start: 0.8379 (p) cc_final: 0.7968 (t) REVERT: A 2861 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8140 (mm-30) outliers start: 20 outliers final: 10 residues processed: 170 average time/residue: 1.2187 time to fit residues: 229.3610 Evaluate side-chains 169 residues out of total 1625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain A residue 1001 LYS Chi-restraints excluded: chain A residue 1105 ASP Chi-restraints excluded: chain A residue 1808 LYS Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2596 THR Chi-restraints excluded: chain A residue 2610 MET Chi-restraints excluded: chain A residue 2682 GLU Chi-restraints excluded: chain A residue 2698 SER Chi-restraints excluded: chain A residue 2764 SER Chi-restraints excluded: chain A residue 2912 VAL Chi-restraints excluded: chain A residue 3026 CYS Chi-restraints excluded: chain A residue 3112 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 30 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2316 HIS ** A2396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2961 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.148527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.092611 restraints weight = 41614.340| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.88 r_work: 0.2954 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14811 Z= 0.165 Angle : 0.498 4.339 20029 Z= 0.270 Chirality : 0.038 0.152 2307 Planarity : 0.004 0.054 2495 Dihedral : 7.762 88.860 2118 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.73 % Favored : 97.16 % Rotamer: Outliers : 1.60 % Allowed : 12.00 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 1.13 (0.20), residues: 1761 helix: 1.70 (0.16), residues: 989 sheet: 0.16 (0.44), residues: 147 loop : -0.61 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 963 TYR 0.012 0.001 TYR A1503 PHE 0.023 0.001 PHE A2633 TRP 0.015 0.001 TRP A2542 HIS 0.005 0.001 HIS A1639 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (14803) covalent geometry : angle 0.49586 / 0.27 (20021) SS BOND : bond 0.00116 / 0.06 ( 1) SS BOND : angle 0.80971 / 0.46 ( 2) hydrogen bonds : bond 0.04983 / 3.33 ( 804) hydrogen bonds : angle 4.24929 / 3.55 ( 2337) metal coordination : bond 0.00727 / 0.44 ( 7) metal coordination : angle 2.39567 / 1.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.845 Fit side-chains REVERT: C 19 ARG cc_start: 0.6560 (mmm160) cc_final: 0.6230 (mtp-110) REVERT: A 975 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7443 (tt0) REVERT: A 1001 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8567 (pttp) REVERT: A 1105 ASP cc_start: 0.5769 (OUTLIER) cc_final: 0.5511 (t70) REVERT: A 1448 MET cc_start: 0.9108 (mmp) cc_final: 0.8613 (mmp) REVERT: A 1620 GLU cc_start: 0.7453 (mm-30) cc_final: 0.6825 (pt0) REVERT: A 1760 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7223 (mp0) REVERT: A 1798 GLU cc_start: 0.7902 (mp0) cc_final: 0.7618 (mp0) REVERT: A 2439 ASP cc_start: 0.7569 (m-30) cc_final: 0.7035 (m-30) REVERT: A 2682 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: A 2769 THR cc_start: 0.8352 (p) cc_final: 0.7951 (t) REVERT: A 3211 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7629 (mp0) outliers start: 26 outliers final: 12 residues processed: 170 average time/residue: 1.3061 time to fit residues: 246.6504 Evaluate side-chains 170 residues out of total 1625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain A residue 975 GLU Chi-restraints excluded: chain A residue 1001 LYS Chi-restraints excluded: chain A residue 1105 ASP Chi-restraints excluded: chain A residue 1285 LYS Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2596 THR Chi-restraints excluded: chain A residue 2610 MET Chi-restraints excluded: chain A residue 2682 GLU Chi-restraints excluded: chain A residue 2698 SER Chi-restraints excluded: chain A residue 2764 SER Chi-restraints excluded: chain A residue 2912 VAL Chi-restraints excluded: chain A residue 3026 CYS Chi-restraints excluded: chain A residue 3112 LEU Chi-restraints excluded: chain A residue 3151 MET Chi-restraints excluded: chain A residue 3211 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 178 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1150 GLN ** A2396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2785 ASN A2961 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.091803 restraints weight = 42093.941| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.87 r_work: 0.2940 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14811 Z= 0.209 Angle : 0.527 5.106 20029 Z= 0.286 Chirality : 0.040 0.159 2307 Planarity : 0.004 0.061 2495 Dihedral : 7.811 90.441 2118 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.07 % Favored : 96.82 % Rotamer: Outliers : 1.54 % Allowed : 12.49 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 1.06 (0.20), residues: 1761 helix: 1.63 (0.16), residues: 989 sheet: 0.18 (0.44), residues: 147 loop : -0.62 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 963 TYR 0.012 0.002 TYR A1503 PHE 0.024 0.002 PHE A2633 TRP 0.016 0.001 TRP A2542 HIS 0.006 0.001 HIS A1639 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (14803) covalent geometry : angle 0.52544 / 0.29 (20021) SS BOND : bond 0.00422 / 0.20 ( 1) SS BOND : angle 0.96985 / 0.53 ( 2) hydrogen bonds : bond 0.05317 / 3.54 ( 804) hydrogen bonds : angle 4.28824 / 3.58 ( 2337) metal coordination : bond 0.00893 / 0.55 ( 7) metal coordination : angle 2.26573 / 1.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: C 18 LEU cc_start: 0.5748 (OUTLIER) cc_final: 0.5147 (mp) REVERT: C 19 ARG cc_start: 0.6513 (mmm160) cc_final: 0.6144 (mtp-110) REVERT: A 1001 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8572 (pttp) REVERT: A 1105 ASP cc_start: 0.5836 (OUTLIER) cc_final: 0.5574 (t70) REVERT: A 1448 MET cc_start: 0.9109 (mmp) cc_final: 0.8596 (mmp) REVERT: A 1620 GLU cc_start: 0.7492 (mm-30) cc_final: 0.6840 (pt0) REVERT: A 1760 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7246 (mp0) REVERT: A 1798 GLU cc_start: 0.7891 (mp0) cc_final: 0.7592 (mp0) REVERT: A 2439 ASP cc_start: 0.7618 (m-30) cc_final: 0.7030 (m-30) REVERT: A 2682 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7560 (mt-10) REVERT: A 2769 THR cc_start: 0.8342 (p) cc_final: 0.7933 (t) REVERT: A 3211 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7652 (mp0) outliers start: 25 outliers final: 12 residues processed: 172 average time/residue: 1.2258 time to fit residues: 234.0341 Evaluate side-chains 174 residues out of total 1625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain A residue 1001 LYS Chi-restraints excluded: chain A residue 1105 ASP Chi-restraints excluded: chain A residue 1285 LYS Chi-restraints excluded: chain A residue 1830 MET Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2596 THR Chi-restraints excluded: chain A residue 2610 MET Chi-restraints excluded: chain A residue 2682 GLU Chi-restraints excluded: chain A residue 2698 SER Chi-restraints excluded: chain A residue 2764 SER Chi-restraints excluded: chain A residue 2912 VAL Chi-restraints excluded: chain A residue 3026 CYS Chi-restraints excluded: chain A residue 3094 SER Chi-restraints excluded: chain A residue 3112 LEU Chi-restraints excluded: chain A residue 3211 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 24 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2961 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.148577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.093014 restraints weight = 41918.604| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.87 r_work: 0.2959 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14811 Z= 0.145 Angle : 0.487 4.768 20029 Z= 0.264 Chirality : 0.038 0.148 2307 Planarity : 0.004 0.055 2495 Dihedral : 7.705 88.508 2117 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.67 % Favored : 97.22 % Rotamer: Outliers : 1.35 % Allowed : 12.86 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 1.18 (0.20), residues: 1761 helix: 1.76 (0.16), residues: 989 sheet: 0.08 (0.44), residues: 147 loop : -0.59 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 963 TYR 0.011 0.001 TYR A1503 PHE 0.023 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.004 0.001 HIS A1639 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (14803) covalent geometry : angle 0.48491 / 0.26 (20021) SS BOND : bond 0.00140 / 0.07 ( 1) SS BOND : angle 1.24951 / 0.68 ( 2) hydrogen bonds : bond 0.04752 / 3.18 ( 804) hydrogen bonds : angle 4.18276 / 3.49 ( 2337) metal coordination : bond 0.00627 / 0.37 ( 7) metal coordination : angle 2.36501 / 1.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 18 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5148 (mp) REVERT: C 19 ARG cc_start: 0.6508 (mmm160) cc_final: 0.6149 (mtp-110) REVERT: A 975 GLU cc_start: 0.7703 (tt0) cc_final: 0.7450 (tt0) REVERT: A 1001 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8565 (pttp) REVERT: A 1105 ASP cc_start: 0.5793 (OUTLIER) cc_final: 0.5529 (t70) REVERT: A 1272 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7449 (mtmt) REVERT: A 1448 MET cc_start: 0.9103 (mmp) cc_final: 0.8595 (mmp) REVERT: A 1620 GLU cc_start: 0.7458 (mm-30) cc_final: 0.6836 (pt0) REVERT: A 1760 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7253 (mp0) REVERT: A 1798 GLU cc_start: 0.7895 (mp0) cc_final: 0.7592 (mp0) REVERT: A 2682 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7474 (mt-10) REVERT: A 2769 THR cc_start: 0.8336 (p) cc_final: 0.7964 (t) REVERT: A 3211 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7662 (mp0) outliers start: 22 outliers final: 11 residues processed: 171 average time/residue: 1.2815 time to fit residues: 242.9590 Evaluate side-chains 172 residues out of total 1625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain A residue 1001 LYS Chi-restraints excluded: chain A residue 1105 ASP Chi-restraints excluded: chain A residue 1272 LYS Chi-restraints excluded: chain A residue 1285 LYS Chi-restraints excluded: chain A residue 1356 SER Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2564 SER Chi-restraints excluded: chain A residue 2596 THR Chi-restraints excluded: chain A residue 2610 MET Chi-restraints excluded: chain A residue 2682 GLU Chi-restraints excluded: chain A residue 2764 SER Chi-restraints excluded: chain A residue 2912 VAL Chi-restraints excluded: chain A residue 3026 CYS Chi-restraints excluded: chain A residue 3112 LEU Chi-restraints excluded: chain A residue 3211 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 120 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2961 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.148186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.092561 restraints weight = 41986.285| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.86 r_work: 0.2953 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14811 Z= 0.165 Angle : 0.494 4.410 20029 Z= 0.268 Chirality : 0.038 0.152 2307 Planarity : 0.004 0.057 2495 Dihedral : 7.701 88.571 2117 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.01 % Favored : 96.88 % Rotamer: Outliers : 1.23 % Allowed : 13.17 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 1.17 (0.20), residues: 1761 helix: 1.74 (0.16), residues: 989 sheet: 0.10 (0.44), residues: 147 loop : -0.59 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 963 TYR 0.012 0.001 TYR A1503 PHE 0.023 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.005 0.001 HIS A1639 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (14803) covalent geometry : angle 0.49263 / 0.27 (20021) SS BOND : bond 0.00405 / 0.19 ( 1) SS BOND : angle 0.82335 / 0.48 ( 2) hydrogen bonds : bond 0.04861 / 3.25 ( 804) hydrogen bonds : angle 4.16986 / 3.48 ( 2337) metal coordination : bond 0.00716 / 0.43 ( 7) metal coordination : angle 2.29244 / 1.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 19 ARG cc_start: 0.6482 (mmm160) cc_final: 0.6118 (mtp-110) REVERT: A 975 GLU cc_start: 0.7708 (tt0) cc_final: 0.7454 (tt0) REVERT: A 1001 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8570 (pttp) REVERT: A 1105 ASP cc_start: 0.5793 (OUTLIER) cc_final: 0.5540 (t70) REVERT: A 1272 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7454 (mtmt) REVERT: A 1448 MET cc_start: 0.9103 (mmp) cc_final: 0.8592 (mmp) REVERT: A 1760 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7250 (mp0) REVERT: A 1798 GLU cc_start: 0.7860 (mp0) cc_final: 0.7540 (mp0) REVERT: A 1845 LYS cc_start: 0.6708 (mmpt) cc_final: 0.6407 (UNCLASSIFIED) REVERT: A 2682 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7476 (mt-10) REVERT: A 2769 THR cc_start: 0.8300 (p) cc_final: 0.7918 (t) REVERT: A 3211 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7642 (mp0) outliers start: 20 outliers final: 10 residues processed: 170 average time/residue: 1.2539 time to fit residues: 236.3161 Evaluate side-chains 172 residues out of total 1625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain A residue 1001 LYS Chi-restraints excluded: chain A residue 1105 ASP Chi-restraints excluded: chain A residue 1272 LYS Chi-restraints excluded: chain A residue 1285 LYS Chi-restraints excluded: chain A residue 1356 SER Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2564 SER Chi-restraints excluded: chain A residue 2596 THR Chi-restraints excluded: chain A residue 2610 MET Chi-restraints excluded: chain A residue 2682 GLU Chi-restraints excluded: chain A residue 2764 SER Chi-restraints excluded: chain A residue 2912 VAL Chi-restraints excluded: chain A residue 3026 CYS Chi-restraints excluded: chain A residue 3211 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 125 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2396 ASN A2961 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.148241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.092611 restraints weight = 42030.592| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.87 r_work: 0.2953 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14811 Z= 0.163 Angle : 0.495 4.422 20029 Z= 0.268 Chirality : 0.038 0.151 2307 Planarity : 0.004 0.056 2495 Dihedral : 7.637 88.625 2115 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.90 % Favored : 96.99 % Rotamer: Outliers : 1.29 % Allowed : 13.23 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 1.18 (0.20), residues: 1761 helix: 1.75 (0.16), residues: 989 sheet: 0.10 (0.44), residues: 147 loop : -0.59 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 963 TYR 0.011 0.001 TYR A1503 PHE 0.023 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.005 0.001 HIS A1639 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (14803) covalent geometry : angle 0.49299 / 0.27 (20021) SS BOND : bond 0.00022 / 0.01 ( 1) SS BOND : angle 0.78273 / 0.44 ( 2) hydrogen bonds : bond 0.04821 / 3.22 ( 804) hydrogen bonds : angle 4.15796 / 3.46 ( 2337) metal coordination : bond 0.00706 / 0.43 ( 7) metal coordination : angle 2.25915 / 1.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: C 18 LEU cc_start: 0.5733 (OUTLIER) cc_final: 0.5140 (mp) REVERT: C 19 ARG cc_start: 0.6505 (mmm160) cc_final: 0.6136 (mtp-110) REVERT: A 1001 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8571 (pttp) REVERT: A 1105 ASP cc_start: 0.5744 (OUTLIER) cc_final: 0.5477 (t70) REVERT: A 1272 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7442 (mtmt) REVERT: A 1448 MET cc_start: 0.9104 (mmp) cc_final: 0.8594 (mmp) REVERT: A 1760 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7261 (mp0) REVERT: A 1798 GLU cc_start: 0.7832 (mp0) cc_final: 0.7515 (mp0) REVERT: A 2682 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7480 (mt-10) REVERT: A 2769 THR cc_start: 0.8293 (p) cc_final: 0.7914 (t) REVERT: A 3211 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7660 (mp0) outliers start: 21 outliers final: 11 residues processed: 173 average time/residue: 1.1902 time to fit residues: 228.5212 Evaluate side-chains 172 residues out of total 1625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain A residue 1001 LYS Chi-restraints excluded: chain A residue 1105 ASP Chi-restraints excluded: chain A residue 1272 LYS Chi-restraints excluded: chain A residue 1285 LYS Chi-restraints excluded: chain A residue 1356 SER Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2564 SER Chi-restraints excluded: chain A residue 2596 THR Chi-restraints excluded: chain A residue 2610 MET Chi-restraints excluded: chain A residue 2682 GLU Chi-restraints excluded: chain A residue 2764 SER Chi-restraints excluded: chain A residue 2912 VAL Chi-restraints excluded: chain A residue 3026 CYS Chi-restraints excluded: chain A residue 3094 SER Chi-restraints excluded: chain A residue 3211 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 154 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2396 ASN A2961 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.148298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.092703 restraints weight = 41871.814| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.86 r_work: 0.2955 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14811 Z= 0.161 Angle : 0.491 4.419 20029 Z= 0.267 Chirality : 0.038 0.150 2307 Planarity : 0.004 0.056 2495 Dihedral : 7.627 88.472 2115 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.90 % Favored : 96.99 % Rotamer: Outliers : 1.11 % Allowed : 13.42 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 1.19 (0.20), residues: 1761 helix: 1.76 (0.16), residues: 989 sheet: 0.08 (0.44), residues: 147 loop : -0.58 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 963 TYR 0.011 0.001 TYR A1503 PHE 0.023 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.005 0.001 HIS A1639 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (14803) covalent geometry : angle 0.48960 / 0.27 (20021) SS BOND : bond 0.00177 / 0.08 ( 1) SS BOND : angle 0.78834 / 0.45 ( 2) hydrogen bonds : bond 0.04782 / 3.20 ( 804) hydrogen bonds : angle 4.13182 / 3.45 ( 2337) metal coordination : bond 0.00691 / 0.42 ( 7) metal coordination : angle 2.25749 / 1.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: C 18 LEU cc_start: 0.5671 (OUTLIER) cc_final: 0.5084 (mp) REVERT: C 19 ARG cc_start: 0.6481 (mmm160) cc_final: 0.6105 (mtp-110) REVERT: A 1001 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8565 (pttp) REVERT: A 1105 ASP cc_start: 0.5719 (OUTLIER) cc_final: 0.5461 (t70) REVERT: A 1272 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7431 (mtmt) REVERT: A 1448 MET cc_start: 0.9100 (mmp) cc_final: 0.8589 (mmp) REVERT: A 1760 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7260 (mp0) REVERT: A 1798 GLU cc_start: 0.7838 (mp0) cc_final: 0.7518 (mp0) REVERT: A 1845 LYS cc_start: 0.6721 (mmpt) cc_final: 0.6474 (mmtp) REVERT: A 2682 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: A 2769 THR cc_start: 0.8304 (p) cc_final: 0.7931 (t) REVERT: A 3211 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7652 (mp0) outliers start: 18 outliers final: 11 residues processed: 171 average time/residue: 1.2326 time to fit residues: 233.9313 Evaluate side-chains 175 residues out of total 1625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain A residue 1001 LYS Chi-restraints excluded: chain A residue 1105 ASP Chi-restraints excluded: chain A residue 1272 LYS Chi-restraints excluded: chain A residue 1285 LYS Chi-restraints excluded: chain A residue 1356 SER Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2564 SER Chi-restraints excluded: chain A residue 2596 THR Chi-restraints excluded: chain A residue 2610 MET Chi-restraints excluded: chain A residue 2682 GLU Chi-restraints excluded: chain A residue 2764 SER Chi-restraints excluded: chain A residue 2912 VAL Chi-restraints excluded: chain A residue 3026 CYS Chi-restraints excluded: chain A residue 3094 SER Chi-restraints excluded: chain A residue 3211 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 40 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2961 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.148443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.092907 restraints weight = 41842.015| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.86 r_work: 0.2956 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14811 Z= 0.152 Angle : 0.486 4.417 20029 Z= 0.264 Chirality : 0.038 0.149 2307 Planarity : 0.004 0.054 2495 Dihedral : 7.611 88.129 2115 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.78 % Favored : 97.10 % Rotamer: Outliers : 1.17 % Allowed : 13.54 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 1.22 (0.20), residues: 1761 helix: 1.78 (0.16), residues: 989 sheet: 0.14 (0.44), residues: 147 loop : -0.57 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 963 TYR 0.011 0.001 TYR A1503 PHE 0.023 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.005 0.001 HIS A1639 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (14803) covalent geometry : angle 0.48485 / 0.26 (20021) SS BOND : bond 0.00091 / 0.04 ( 1) SS BOND : angle 0.62719 / 0.37 ( 2) hydrogen bonds : bond 0.04698 / 3.14 ( 804) hydrogen bonds : angle 4.11523 / 3.44 ( 2337) metal coordination : bond 0.00656 / 0.39 ( 7) metal coordination : angle 2.27425 / 1.32 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3522 Ramachandran restraints generated. 1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 18 LEU cc_start: 0.5653 (OUTLIER) cc_final: 0.5071 (mp) REVERT: C 19 ARG cc_start: 0.6473 (mmm160) cc_final: 0.6106 (mtp-110) REVERT: C 58 ASP cc_start: 0.8409 (t0) cc_final: 0.8129 (t0) REVERT: A 1001 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8564 (pttp) REVERT: A 1105 ASP cc_start: 0.5726 (OUTLIER) cc_final: 0.5469 (t70) REVERT: A 1272 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7418 (mtmt) REVERT: A 1448 MET cc_start: 0.9093 (mmp) cc_final: 0.8583 (mmp) REVERT: A 1760 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7249 (mp0) REVERT: A 1798 GLU cc_start: 0.7833 (mp0) cc_final: 0.7514 (mp0) REVERT: A 1845 LYS cc_start: 0.6691 (mmpt) cc_final: 0.6451 (mmtp) REVERT: A 2682 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7461 (mt-10) REVERT: A 2769 THR cc_start: 0.8295 (p) cc_final: 0.7923 (t) REVERT: A 3211 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7658 (mp0) outliers start: 19 outliers final: 11 residues processed: 172 average time/residue: 1.2371 time to fit residues: 235.9504 Evaluate side-chains 175 residues out of total 1625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain A residue 1001 LYS Chi-restraints excluded: chain A residue 1105 ASP Chi-restraints excluded: chain A residue 1272 LYS Chi-restraints excluded: chain A residue 1285 LYS Chi-restraints excluded: chain A residue 1356 SER Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2564 SER Chi-restraints excluded: chain A residue 2596 THR Chi-restraints excluded: chain A residue 2610 MET Chi-restraints excluded: chain A residue 2682 GLU Chi-restraints excluded: chain A residue 2764 SER Chi-restraints excluded: chain A residue 2912 VAL Chi-restraints excluded: chain A residue 3026 CYS Chi-restraints excluded: chain A residue 3094 SER Chi-restraints excluded: chain A residue 3211 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 80 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 167 optimal weight: 0.0980 chunk 100 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2961 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.150263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.094858 restraints weight = 41943.158| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.87 r_work: 0.2986 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14811 Z= 0.100 Angle : 0.452 4.412 20029 Z= 0.245 Chirality : 0.037 0.142 2307 Planarity : 0.003 0.043 2495 Dihedral : 7.482 84.795 2115 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.21 % Favored : 97.67 % Rotamer: Outliers : 0.92 % Allowed : 13.91 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 1.42 (0.21), residues: 1761 helix: 2.00 (0.17), residues: 984 sheet: 0.15 (0.44), residues: 147 loop : -0.54 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 963 TYR 0.011 0.001 TYR C 94 PHE 0.022 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.003 0.001 HIS A3011 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (14803) covalent geometry : angle 0.45003 / 0.24 (20021) SS BOND : bond 0.00820 / 0.39 ( 1) SS BOND : angle 1.32541 / 0.71 ( 2) hydrogen bonds : bond 0.04053 / 2.72 ( 804) hydrogen bonds : angle 3.98583 / 3.33 ( 2337) metal coordination : bond 0.00415 / 0.21 ( 7) metal coordination : angle 2.66578 / 1.63 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10869.86 seconds wall clock time: 184 minutes 4.49 seconds (11044.49 seconds total)