Starting phenix.real_space_refine on Sat Sep 12 00:15:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25xm_80448/09_2026/25xm_80448.cif Found real_map, /net/cci-nas-00/data/ceres_data/25xm_80448/09_2026/25xm_80448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/25xm_80448/09_2026/25xm_80448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25xm_80448/09_2026/25xm_80448.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/25xm_80448/09_2026/25xm_80448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25xm_80448/09_2026/25xm_80448.map" } resolution = 2.67 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 11 5.49 5 S 80 5.16 5 C 7490 2.51 5 N 2068 2.21 5 O 2209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11860 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 11608 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1548, 11597 Classifications: {'peptide': 1548} Incomplete info: {'truncation_to_alanine': 228} Link IDs: {'PTRANS': 45, 'TRANS': 1502} Chain breaks: 17 Unresolved non-hydrogen bonds: 806 Unresolved non-hydrogen angles: 968 Unresolved non-hydrogen dihedrals: 661 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLU:plan': 42, 'ASP:plan': 25, 'ARG:plan': 17, 'ASN:plan1': 11, 'TYR:plan': 3, 'GLN:plan1': 10, 'PHE:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 445 Conformer: "B" Number of residues, atoms: 1548, 11597 Classifications: {'peptide': 1548} Incomplete info: {'truncation_to_alanine': 228} Link IDs: {'PTRANS': 45, 'TRANS': 1502} Chain breaks: 17 Unresolved non-hydrogen bonds: 806 Unresolved non-hydrogen angles: 968 Unresolved non-hydrogen dihedrals: 661 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLU:plan': 42, 'ASP:plan': 25, 'ARG:plan': 17, 'ASN:plan1': 11, 'TYR:plan': 3, 'GLN:plan1': 10, 'PHE:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 445 bond proxies already assigned to first conformer: 11777 Chain: "B" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 250 Classifications: {'RNA': 12} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 3, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 8} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 777 SG CYS A1028 51.075 83.260 89.799 1.00116.90 S ATOM 796 SG CYS A1031 47.313 83.988 89.975 1.00131.58 S ATOM 1039 SG CYS A1062 49.566 86.523 88.466 1.00130.94 S ATOM 1059 SG CYS A1065 49.040 83.390 86.570 1.00136.59 S ATOM 2313 SG CYS A1294 44.016 69.390 39.240 1.00118.79 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A2641 " occ=0.40 ... (20 atoms not shown) pdb=" CZ BPHE A2641 " occ=0.60 Time building chain proxies: 4.43, per 1000 atoms: 0.37 Number of scatterers: 11860 At special positions: 0 Unit cell: (100.7, 99.75, 120.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 80 16.00 P 11 15.00 O 2209 8.00 N 2068 7.00 C 7490 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1766 " - pdb=" SG CYS A2558 " 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: 0.89 Conformation dependent library (CDL) restraints added in 910.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A4001 " pdb="ZN ZN A4001 " - pdb=" SG CYS A1062 " pdb="ZN ZN A4001 " - pdb=" SG CYS A1031 " pdb="ZN ZN A4001 " - pdb=" SG CYS A1065 " pdb="ZN ZN A4001 " - pdb=" SG CYS A1028 " pdb=" ZN A4002 " pdb="ZN ZN A4002 " - pdb=" ND1 HIS A1365 " pdb="ZN ZN A4002 " - pdb=" SG CYS A1294 " pdb="ZN ZN A4002 " - pdb=" NE2 HIS A1090 " Number of angles added : 6 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2972 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 11 sheets defined 64.9% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 930 through 947 removed outlier: 4.782A pdb=" N GLU A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N HIS A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 947 " --> pdb=" O GLU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 967 removed outlier: 3.603A pdb=" N ALA A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 987 Processing helix chain 'A' and resid 987 through 997 Processing helix chain 'A' and resid 1008 through 1024 removed outlier: 3.553A pdb=" N LYS A1024 " --> pdb=" O SER A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1042 removed outlier: 3.543A pdb=" N THR A1042 " --> pdb=" O THR A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1057 removed outlier: 3.541A pdb=" N GLN A1057 " --> pdb=" O ALA A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1061 removed outlier: 3.502A pdb=" N HIS A1061 " --> pdb=" O LEU A1058 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1058 through 1061' Processing helix chain 'A' and resid 1076 through 1082 Processing helix chain 'A' and resid 1104 through 1112 Processing helix chain 'A' and resid 1119 through 1140 Processing helix chain 'A' and resid 1180 through 1187 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 removed outlier: 3.705A pdb=" N VAL A1241 " --> pdb=" O ARG A1237 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A1242 " --> pdb=" O ASP A1238 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1281 removed outlier: 3.595A pdb=" N CYS A1273 " --> pdb=" O GLU A1269 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE A1279 " --> pdb=" O ASP A1275 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A1280 " --> pdb=" O VAL A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1296 removed outlier: 3.509A pdb=" N ILE A1295 " --> pdb=" O GLN A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1307 Processing helix chain 'A' and resid 1315 through 1329 removed outlier: 3.528A pdb=" N ARG A1329 " --> pdb=" O ASN A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1352 removed outlier: 3.509A pdb=" N CYS A1349 " --> pdb=" O THR A1345 " (cutoff:3.500A) Processing helix chain 'A' and resid 1401 through 1426 removed outlier: 4.138A pdb=" N LEU A1407 " --> pdb=" O ARG A1403 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU A1412 " --> pdb=" O GLY A1408 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N TYR A1413 " --> pdb=" O SER A1409 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN A1424 " --> pdb=" O ILE A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1435 removed outlier: 3.707A pdb=" N ASN A1433 " --> pdb=" O GLU A1430 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL A1435 " --> pdb=" O ILE A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1464 Processing helix chain 'A' and resid 1465 through 1481 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 1530 Processing helix chain 'A' and resid 1531 through 1534 Processing helix chain 'A' and resid 1538 through 1545 removed outlier: 3.693A pdb=" N LYS A1544 " --> pdb=" O ASN A1540 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A1545 " --> pdb=" O GLU A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1570 removed outlier: 3.561A pdb=" N ILE A1557 " --> pdb=" O ILE A1553 " (cutoff:3.500A) Processing helix chain 'A' and resid 1572 through 1581 removed outlier: 4.204A pdb=" N LYS A1578 " --> pdb=" O GLU A1574 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS A1581 " --> pdb=" O VAL A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1612 Processing helix chain 'A' and resid 1613 through 1616 Processing helix chain 'A' and resid 1629 through 1652 removed outlier: 3.818A pdb=" N SER A1652 " --> pdb=" O ASN A1648 " (cutoff:3.500A) 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 1791 Processing helix chain 'A' and resid 1792 through 1795 Processing helix chain 'A' and resid 1796 through 1805 Processing helix chain 'A' and resid 1806 through 1810 Processing helix chain 'A' and resid 1831 through 1852 removed outlier: 3.793A pdb=" N ILE A1847 " --> pdb=" O GLU A1843 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A1848 " --> pdb=" O ASN A1844 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A1852 " --> pdb=" O VAL A1848 " (cutoff:3.500A) Processing helix chain 'A' and resid 2295 through 2306 removed outlier: 3.778A 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 removed outlier: 3.641A pdb=" N PHE A2388 " --> pdb=" O ASP A2384 " (cutoff:3.500A) Processing helix chain 'A' and resid 2404 through 2422 removed outlier: 3.623A pdb=" N LEU A2415 " --> pdb=" O ILE A2411 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER A2421 " --> pdb=" O TYR A2417 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS A2422 " --> pdb=" O ARG A2418 " (cutoff:3.500A) Processing helix chain 'A' and resid 2429 through 2440 removed outlier: 3.611A pdb=" N THR A2438 " --> pdb=" O ARG A2434 " (cutoff:3.500A) Processing helix chain 'A' and resid 2441 through 2445 Processing helix chain 'A' and resid 2447 through 2457 Processing helix chain 'A' and resid 2476 through 2503 removed outlier: 3.666A pdb=" N LEU A2483 " --> pdb=" O THR A2479 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A2489 " --> pdb=" O SER A2485 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A2490 " --> pdb=" O LEU A2486 " (cutoff:3.500A) Processing helix chain 'A' and resid 2530 through 2540 removed outlier: 3.801A pdb=" N THR A2540 " --> pdb=" O GLN A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2540 through 2559 removed outlier: 3.630A pdb=" N CYS A2558 " --> pdb=" O ALA A2554 " (cutoff:3.500A) Processing helix chain 'A' and resid 2589 through 2594 Processing helix chain 'A' and resid 2595 through 2600 Processing helix chain 'A' and resid 2605 through 2623 Processing helix chain 'A' and resid 2626 through 2645 removed outlier: 3.601A pdb=" N APHE A2641 " --> pdb=" O ARG A2637 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS A2644 " --> pdb=" O ILE A2640 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A2645 " --> pdb=" O APHE A2641 " (cutoff:3.500A) Processing helix chain 'A' and resid 2645 through 2653 Processing helix chain 'A' and resid 2660 through 2664 Processing helix chain 'A' and resid 2670 through 2675 Processing helix chain 'A' and resid 2678 through 2697 Processing helix chain 'A' and resid 2753 through 2765 Processing helix chain 'A' and resid 2770 through 2783 removed outlier: 3.541A pdb=" N ASN A2777 " --> pdb=" O GLU A2773 " (cutoff:3.500A) Processing helix chain 'A' and resid 2801 through 2805 Processing helix chain 'A' and resid 2806 through 2816 Processing helix chain 'A' and resid 2816 through 2837 removed outlier: 3.714A pdb=" N VAL A2827 " --> pdb=" O ARG A2823 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A2837 " --> pdb=" O ALA A2833 " (cutoff:3.500A) Processing helix chain 'A' and resid 2899 through 2909 Processing helix chain 'A' and resid 2993 through 3003 Processing helix chain 'A' and resid 3043 through 3060 removed outlier: 3.501A 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 3094 through 3100 Processing helix chain 'A' and resid 3104 through 3114 removed outlier: 3.516A pdb=" N LEU A3113 " --> pdb=" O MET A3109 " (cutoff:3.500A) Processing helix chain 'A' and resid 3127 through 3142 removed outlier: 4.122A pdb=" N LEU A3132 " --> pdb=" O PHE A3128 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LYS A3133 " --> pdb=" O SER A3129 " (cutoff:3.500A) Processing helix chain 'A' and resid 3142 through 3159 Processing helix chain 'A' and resid 3167 through 3185 removed outlier: 3.842A pdb=" N LEU A3181 " --> pdb=" O HIS A3177 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A3184 " --> pdb=" O LEU A3180 " (cutoff:3.500A) Processing helix chain 'A' and resid 3208 through 3217 removed outlier: 3.539A pdb=" N ILE A3217 " --> pdb=" O VAL A3213 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 971 through 972 removed outlier: 6.472A pdb=" N VAL A 971 " --> pdb=" O TYR A1755 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1003 through 1004 Processing sheet with id=AA3, first strand: chain 'A' and resid 1144 through 1145 Processing sheet with id=AA4, first strand: chain 'A' and resid 1357 through 1362 removed outlier: 4.383A pdb=" N LEU A1383 " --> pdb=" O LYS A1373 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEU A1386 " --> pdb=" O GLY A1396 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLY A1396 " --> pdb=" O LEU A1386 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2347 through 2348 Processing sheet with id=AA6, first strand: chain 'A' and resid 2507 through 2514 Processing sheet with id=AA7, first strand: chain 'A' and resid 2399 through 2402 Processing sheet with id=AA8, first strand: chain 'A' and resid 2574 through 2576 removed outlier: 4.465A pdb=" N PHE A2580 " --> pdb=" O THR A2587 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 3005 through 3009 Processing sheet with id=AB1, first strand: chain 'A' and resid 3078 through 3081 removed outlier: 3.525A pdb=" N SER A3078 " --> pdb=" O ARG A3224 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 3086 through 3089 719 hydrogen bonds defined for protein. 2065 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: 2.35 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3834 1.34 - 1.46: 1541 1.46 - 1.57: 6573 1.57 - 1.69: 22 1.69 - 1.81: 112 Bond restraints: 12082 Sorted by residual: bond pdb=" N TYR A2577 " pdb=" CA TYR A2577 " ideal model delta sigma weight residual 1.462 1.485 -0.023 1.46e-02 4.69e+03 2.50e+00 bond pdb=" CB GLU A1392 " pdb=" CG GLU A1392 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" CB MET A2581 " pdb=" CG MET A2581 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.30e-01 bond pdb=" CB GLN A3170 " pdb=" CG GLN A3170 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.15e-01 bond pdb=" CG GLU A1392 " pdb=" CD GLU A1392 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 8.91e-01 ... (remaining 12077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 16323 2.11 - 4.21: 111 4.21 - 6.32: 11 6.32 - 8.42: 2 8.42 - 10.53: 1 Bond angle restraints: 16448 Sorted by residual: angle pdb=" CB MET A2581 " pdb=" CG MET A2581 " pdb=" SD MET A2581 " ideal model delta sigma weight residual 112.70 123.23 -10.53 3.00e+00 1.11e-01 1.23e+01 angle pdb=" O5' A B 11 " pdb=" C5' A B 11 " pdb=" C4' A B 11 " ideal model delta sigma weight residual 109.40 111.94 -2.54 8.00e-01 1.56e+00 1.00e+01 angle pdb=" O5' A B 7 " pdb=" C5' A B 7 " pdb=" C4' A B 7 " ideal model delta sigma weight residual 109.40 111.92 -2.52 8.00e-01 1.56e+00 9.95e+00 angle pdb=" O5' A B 6 " pdb=" C5' A B 6 " pdb=" C4' A B 6 " ideal model delta sigma weight residual 109.40 111.77 -2.37 8.00e-01 1.56e+00 8.76e+00 angle pdb=" O5' G B 8 " pdb=" C5' G B 8 " pdb=" C4' G B 8 " ideal model delta sigma weight residual 109.40 111.69 -2.29 8.00e-01 1.56e+00 8.18e+00 ... (remaining 16443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 6438 17.87 - 35.73: 634 35.73 - 53.60: 157 53.60 - 71.47: 45 71.47 - 89.33: 15 Dihedral angle restraints: 7289 sinusoidal: 2742 harmonic: 4547 Sorted by residual: dihedral pdb=" CB CYS A1766 " pdb=" SG CYS A1766 " pdb=" SG CYS A2558 " pdb=" CB CYS A2558 " ideal model delta sinusoidal sigma weight residual 93.00 160.43 -67.43 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CA ASN A1613 " pdb=" CB ASN A1613 " pdb=" CG ASN A1613 " pdb=" OD1 ASN A1613 " ideal model delta sinusoidal sigma weight residual 120.00 -166.58 -73.42 2 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA PHE A1505 " pdb=" C PHE A1505 " pdb=" N LEU A1506 " pdb=" CA LEU A1506 " ideal model delta harmonic sigma weight residual -180.00 -163.54 -16.46 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 7286 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1328 0.028 - 0.057: 432 0.057 - 0.085: 141 0.085 - 0.113: 59 0.113 - 0.141: 19 Chirality restraints: 1979 Sorted by residual: chirality pdb=" CG LEU A1242 " pdb=" CB LEU A1242 " pdb=" CD1 LEU A1242 " pdb=" CD2 LEU A1242 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" C2' G B 8 " pdb=" C3' G B 8 " pdb=" O2' G B 8 " pdb=" C1' G B 8 " both_signs ideal model delta sigma weight residual False -2.62 -2.75 0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" C2' U B 12 " pdb=" C3' U B 12 " pdb=" O2' U B 12 " pdb=" C1' U B 12 " both_signs ideal model delta sigma weight residual False -2.62 -2.75 0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 1976 not shown) Planarity restraints: 2041 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A3189 " -0.034 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO A3190 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A3190 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A3190 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A1234 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO A1235 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A1235 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1235 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A1286 " 0.019 5.00e-02 4.00e+02 2.95e-02 1.40e+00 pdb=" N PRO A1287 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A1287 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A1287 " 0.017 5.00e-02 4.00e+02 ... (remaining 2038 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 95 2.61 - 3.18: 10532 3.18 - 3.75: 19516 3.75 - 4.33: 27338 4.33 - 4.90: 44314 Nonbonded interactions: 101795 Sorted by model distance: nonbonded pdb=" OE2 GLU A2788 " pdb="ZN ZN A4002 " model vdw 2.037 2.230 nonbonded pdb=" O ILE A1493 " pdb=" OG SER A1497 " model vdw 2.249 3.040 nonbonded pdb=" O LEU A1533 " pdb=" OG SER A2570 " model vdw 2.323 3.040 nonbonded pdb=" OH TYR A2835 " pdb=" O VAL A3027 " model vdw 2.358 3.040 nonbonded pdb=" O ASP A2358 " pdb=" OG SER A2564 " model vdw 2.372 3.040 ... (remaining 101790 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=0.40 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: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.030 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 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 : 0.002 0.032 12090 Z= 0.084 Angle : 0.418 10.529 16456 Z= 0.220 Chirality : 0.036 0.141 1979 Planarity : 0.003 0.051 2041 Dihedral : 15.932 89.332 4314 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.08 % Allowed : 24.08 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.22), residues: 1515 helix: 1.59 (0.18), residues: 895 sheet: -0.03 (0.54), residues: 98 loop : -0.26 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1583 TYR 0.013 0.001 TYR A1413 PHE 0.010 0.001 PHE A2633 TRP 0.006 0.001 TRP A2542 HIS 0.005 0.001 HIS A1066 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.08 (12082) covalent geometry : angle 0.41517 / 0.22 (16448) SS BOND : bond 0.00105 / 0.07 ( 1) SS BOND : angle 0.54507 / 0.36 ( 2) hydrogen bonds : bond 0.23071 / 15.83 ( 719) hydrogen bonds : angle 6.66524 / 4.75 ( 2065) metal coordination : bond 0.00493 / 0.26 ( 7) metal coordination : angle 2.61070 / 1.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.475 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.4993 time to fit residues: 42.3436 Evaluate side-chains 70 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.0060 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1060 ASN A1213 GLN A1563 GLN ** A2302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.087519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.068554 restraints weight = 47650.584| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.41 r_work: 0.2665 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12090 Z= 0.147 Angle : 0.510 7.776 16456 Z= 0.269 Chirality : 0.038 0.164 1979 Planarity : 0.004 0.040 2041 Dihedral : 6.908 73.057 1813 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.67 % Allowed : 22.33 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.22), residues: 1515 helix: 1.65 (0.17), residues: 922 sheet: -0.09 (0.59), residues: 83 loop : -0.47 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3224 TYR 0.016 0.001 TYR A1413 PHE 0.016 0.001 PHE A1781 TRP 0.010 0.001 TRP A2542 HIS 0.004 0.001 HIS A1066 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (12082) covalent geometry : angle 0.50707 / 0.27 (16448) SS BOND : bond 0.00669 / 0.45 ( 1) SS BOND : angle 0.95848 / 0.51 ( 2) hydrogen bonds : bond 0.05594 / 3.82 ( 719) hydrogen bonds : angle 4.73134 / 3.42 ( 2065) metal coordination : bond 0.00553 / 0.32 ( 7) metal coordination : angle 2.90163 / 2.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.468 Fit side-chains REVERT: A 2298 MET cc_start: 0.8742 (tpp) cc_final: 0.8441 (mmm) REVERT: A 2611 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8283 (mt0) REVERT: A 2797 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.9083 (mp) outliers start: 20 outliers final: 3 residues processed: 93 average time/residue: 0.4900 time to fit residues: 50.9732 Evaluate side-chains 75 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1384 CYS Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2797 ILE Chi-restraints excluded: chain A residue 3014 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 11 optimal weight: 0.0770 chunk 17 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 103 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1213 GLN A2302 ASN A2638 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.082727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.062024 restraints weight = 48151.593| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 3.39 r_work: 0.2573 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12090 Z= 0.130 Angle : 0.469 7.661 16456 Z= 0.244 Chirality : 0.038 0.148 1979 Planarity : 0.003 0.035 2041 Dihedral : 6.888 73.156 1813 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.08 % Allowed : 22.58 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.22), residues: 1515 helix: 1.70 (0.17), residues: 925 sheet: -0.02 (0.59), residues: 83 loop : -0.50 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1552 TYR 0.019 0.001 TYR A3111 PHE 0.014 0.001 PHE A2633 TRP 0.011 0.001 TRP A2542 HIS 0.004 0.001 HIS A1066 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (12082) covalent geometry : angle 0.46558 / 0.24 (16448) SS BOND : bond 0.00349 / 0.23 ( 1) SS BOND : angle 1.45208 / 0.76 ( 2) hydrogen bonds : bond 0.04387 / 2.98 ( 719) hydrogen bonds : angle 4.36102 / 3.17 ( 2065) metal coordination : bond 0.00499 / 0.28 ( 7) metal coordination : angle 2.75210 / 1.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.486 Fit side-chains REVERT: A 1227 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.9022 (ttpt) REVERT: A 1555 ASP cc_start: 0.8807 (m-30) cc_final: 0.8545 (m-30) REVERT: A 2298 MET cc_start: 0.8620 (tpp) cc_final: 0.8337 (mmm) REVERT: A 2611 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8354 (mt0) REVERT: A 2797 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.9058 (mp) outliers start: 13 outliers final: 3 residues processed: 91 average time/residue: 0.4718 time to fit residues: 48.0548 Evaluate side-chains 79 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1227 LYS Chi-restraints excluded: chain A residue 1384 CYS Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 2356 SER Chi-restraints excluded: chain A residue 2797 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 67 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.081140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.060513 restraints weight = 38719.182| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 3.06 r_work: 0.2552 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12090 Z= 0.188 Angle : 0.491 8.871 16456 Z= 0.254 Chirality : 0.039 0.165 1979 Planarity : 0.003 0.034 2041 Dihedral : 6.943 73.079 1813 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.00 % Allowed : 22.25 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.22), residues: 1515 helix: 1.76 (0.17), residues: 925 sheet: -0.20 (0.57), residues: 83 loop : -0.47 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2650 TYR 0.015 0.001 TYR A3111 PHE 0.014 0.001 PHE A2633 TRP 0.012 0.001 TRP A2542 HIS 0.004 0.001 HIS A1066 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (12082) covalent geometry : angle 0.48841 / 0.25 (16448) SS BOND : bond 0.00304 / 0.20 ( 1) SS BOND : angle 1.72434 / 0.91 ( 2) hydrogen bonds : bond 0.04113 / 2.80 ( 719) hydrogen bonds : angle 4.23302 / 3.08 ( 2065) metal coordination : bond 0.00701 / 0.41 ( 7) metal coordination : angle 2.56113 / 1.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.491 Fit side-chains REVERT: A 1382 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8493 (mtt) REVERT: A 1555 ASP cc_start: 0.8834 (m-30) cc_final: 0.8565 (m-30) REVERT: A 2298 MET cc_start: 0.8661 (tpp) cc_final: 0.8414 (mmm) REVERT: A 2611 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8368 (mt0) REVERT: A 2797 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9065 (mp) outliers start: 24 outliers final: 5 residues processed: 95 average time/residue: 0.4680 time to fit residues: 49.9089 Evaluate side-chains 77 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1384 CYS Chi-restraints excluded: chain A residue 1784 ILE Chi-restraints excluded: chain A residue 2356 SER Chi-restraints excluded: chain A residue 2797 ILE Chi-restraints excluded: chain A residue 2859 ILE Chi-restraints excluded: chain A residue 3014 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 111 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.081683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.061251 restraints weight = 36654.885| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.99 r_work: 0.2573 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12090 Z= 0.147 Angle : 0.474 8.949 16456 Z= 0.245 Chirality : 0.038 0.152 1979 Planarity : 0.003 0.033 2041 Dihedral : 6.931 73.131 1813 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.58 % Allowed : 22.75 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.22), residues: 1515 helix: 1.84 (0.17), residues: 921 sheet: -0.20 (0.56), residues: 83 loop : -0.44 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1552 TYR 0.013 0.001 TYR A3111 PHE 0.018 0.001 PHE A2633 TRP 0.012 0.001 TRP A2542 HIS 0.004 0.001 HIS A1066 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (12082) covalent geometry : angle 0.47119 / 0.24 (16448) SS BOND : bond 0.00354 / 0.24 ( 1) SS BOND : angle 2.55826 / 1.83 ( 2) hydrogen bonds : bond 0.03816 / 2.60 ( 719) hydrogen bonds : angle 4.13445 / 3.01 ( 2065) metal coordination : bond 0.00566 / 0.33 ( 7) metal coordination : angle 2.39830 / 1.71 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.481 Fit side-chains REVERT: A 1382 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8502 (mtt) REVERT: A 1555 ASP cc_start: 0.8793 (m-30) cc_final: 0.8550 (m-30) REVERT: A 2298 MET cc_start: 0.8645 (tpp) cc_final: 0.8354 (mmm) REVERT: A 2611 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8374 (mt0) REVERT: A 2797 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9054 (mp) outliers start: 19 outliers final: 7 residues processed: 95 average time/residue: 0.4625 time to fit residues: 49.5709 Evaluate side-chains 83 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1384 CYS Chi-restraints excluded: chain A residue 1491 HIS Chi-restraints excluded: chain A residue 1784 ILE Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2356 SER Chi-restraints excluded: chain A residue 2797 ILE Chi-restraints excluded: chain A residue 2859 ILE Chi-restraints excluded: chain A residue 3014 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 22 optimal weight: 30.0000 chunk 62 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.081952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.061200 restraints weight = 40871.231| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.16 r_work: 0.2567 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12090 Z= 0.140 Angle : 0.463 9.318 16456 Z= 0.239 Chirality : 0.038 0.149 1979 Planarity : 0.003 0.032 2041 Dihedral : 6.922 73.135 1813 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.92 % Allowed : 23.25 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.22), residues: 1515 helix: 1.91 (0.17), residues: 921 sheet: -0.17 (0.56), residues: 83 loop : -0.43 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1552 TYR 0.012 0.001 TYR A3111 PHE 0.018 0.001 PHE A2633 TRP 0.012 0.001 TRP A2542 HIS 0.004 0.001 HIS A1066 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (12082) covalent geometry : angle 0.46053 / 0.24 (16448) SS BOND : bond 0.00452 / 0.30 ( 1) SS BOND : angle 1.82406 / 1.27 ( 2) hydrogen bonds : bond 0.03683 / 2.51 ( 719) hydrogen bonds : angle 4.08093 / 2.97 ( 2065) metal coordination : bond 0.00536 / 0.31 ( 7) metal coordination : angle 2.25375 / 1.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.489 Fit side-chains REVERT: A 1246 ARG cc_start: 0.9434 (ttp80) cc_final: 0.8474 (mmt90) REVERT: A 1555 ASP cc_start: 0.8810 (m-30) cc_final: 0.8564 (m-30) REVERT: A 2298 MET cc_start: 0.8662 (tpp) cc_final: 0.8359 (mmm) REVERT: A 2611 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8381 (mt0) REVERT: A 2797 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.9047 (mp) outliers start: 11 outliers final: 6 residues processed: 86 average time/residue: 0.4966 time to fit residues: 47.7087 Evaluate side-chains 82 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1384 CYS Chi-restraints excluded: chain A residue 1784 ILE Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2356 SER Chi-restraints excluded: chain A residue 2797 ILE Chi-restraints excluded: chain A residue 2859 ILE Chi-restraints excluded: chain A residue 3014 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 133 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 150 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 987 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.080833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.060269 restraints weight = 31890.228| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.87 r_work: 0.2582 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12090 Z= 0.137 Angle : 0.461 9.609 16456 Z= 0.238 Chirality : 0.038 0.147 1979 Planarity : 0.003 0.031 2041 Dihedral : 6.914 73.132 1813 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.67 % Allowed : 24.17 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.22), residues: 1515 helix: 1.99 (0.17), residues: 918 sheet: -0.21 (0.56), residues: 83 loop : -0.38 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1804 TYR 0.011 0.001 TYR A3111 PHE 0.019 0.001 PHE A2633 TRP 0.012 0.001 TRP A2542 HIS 0.005 0.001 HIS A3177 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (12082) covalent geometry : angle 0.45868 / 0.24 (16448) SS BOND : bond 0.00251 / 0.17 ( 1) SS BOND : angle 1.36207 / 0.90 ( 2) hydrogen bonds : bond 0.03593 / 2.44 ( 719) hydrogen bonds : angle 4.03250 / 2.94 ( 2065) metal coordination : bond 0.00536 / 0.31 ( 7) metal coordination : angle 2.21141 / 1.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.548 Fit side-chains REVERT: A 1246 ARG cc_start: 0.9414 (ttp80) cc_final: 0.8457 (mmt90) REVERT: A 1555 ASP cc_start: 0.8803 (m-30) cc_final: 0.8557 (m-30) REVERT: A 2298 MET cc_start: 0.8622 (tpp) cc_final: 0.8316 (mmm) REVERT: A 2611 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8335 (mt0) REVERT: A 2797 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.9017 (mp) outliers start: 8 outliers final: 6 residues processed: 84 average time/residue: 0.4736 time to fit residues: 44.7888 Evaluate side-chains 83 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1384 CYS Chi-restraints excluded: chain A residue 1784 ILE Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2356 SER Chi-restraints excluded: chain A residue 2797 ILE Chi-restraints excluded: chain A residue 2859 ILE Chi-restraints excluded: chain A residue 3014 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 93 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.085832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.067362 restraints weight = 46658.096| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.26 r_work: 0.2638 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12090 Z= 0.163 Angle : 0.472 9.912 16456 Z= 0.243 Chirality : 0.038 0.157 1979 Planarity : 0.003 0.032 2041 Dihedral : 6.933 73.105 1813 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.08 % Allowed : 23.83 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.22), residues: 1515 helix: 2.00 (0.17), residues: 921 sheet: -0.28 (0.55), residues: 83 loop : -0.38 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2665 TYR 0.012 0.001 TYR A1413 PHE 0.018 0.001 PHE A2633 TRP 0.012 0.001 TRP A2542 HIS 0.005 0.001 HIS A3177 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (12082) covalent geometry : angle 0.46962 / 0.24 (16448) SS BOND : bond 0.00375 / 0.25 ( 1) SS BOND : angle 1.49908 / 0.95 ( 2) hydrogen bonds : bond 0.03636 / 2.47 ( 719) hydrogen bonds : angle 4.03030 / 2.93 ( 2065) metal coordination : bond 0.00642 / 0.38 ( 7) metal coordination : angle 2.14184 / 1.55 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.496 Fit side-chains REVERT: A 1246 ARG cc_start: 0.9435 (ttp80) cc_final: 0.8492 (mmt90) REVERT: A 1382 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8646 (mtt) REVERT: A 2298 MET cc_start: 0.8718 (tpp) cc_final: 0.8445 (mmm) REVERT: A 2797 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9076 (mp) outliers start: 13 outliers final: 5 residues processed: 87 average time/residue: 0.4776 time to fit residues: 46.3993 Evaluate side-chains 81 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1384 CYS Chi-restraints excluded: chain A residue 1491 HIS Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2356 SER Chi-restraints excluded: chain A residue 2797 ILE Chi-restraints excluded: chain A residue 3014 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 61 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 77 optimal weight: 0.4980 chunk 62 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.086355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.068247 restraints weight = 40242.492| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 3.03 r_work: 0.2662 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12090 Z= 0.140 Angle : 0.460 10.096 16456 Z= 0.238 Chirality : 0.038 0.152 1979 Planarity : 0.003 0.033 2041 Dihedral : 6.932 73.131 1813 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.75 % Allowed : 24.00 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.22), residues: 1515 helix: 2.03 (0.17), residues: 921 sheet: -0.25 (0.56), residues: 83 loop : -0.40 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1552 TYR 0.012 0.001 TYR A1413 PHE 0.019 0.001 PHE A2633 TRP 0.012 0.001 TRP A2542 HIS 0.004 0.001 HIS A3177 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (12082) covalent geometry : angle 0.45806 / 0.24 (16448) SS BOND : bond 0.00318 / 0.21 ( 1) SS BOND : angle 1.30463 / 0.82 ( 2) hydrogen bonds : bond 0.03531 / 2.40 ( 719) hydrogen bonds : angle 3.99582 / 2.91 ( 2065) metal coordination : bond 0.00549 / 0.32 ( 7) metal coordination : angle 2.12046 / 1.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.488 Fit side-chains REVERT: A 1246 ARG cc_start: 0.9425 (ttp80) cc_final: 0.8485 (mmt90) REVERT: A 1555 ASP cc_start: 0.8777 (m-30) cc_final: 0.8457 (m-30) REVERT: A 2298 MET cc_start: 0.8707 (tpp) cc_final: 0.8422 (mmm) REVERT: A 2611 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8306 (mt0) REVERT: A 2797 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.9066 (mp) outliers start: 9 outliers final: 7 residues processed: 82 average time/residue: 0.5073 time to fit residues: 46.3741 Evaluate side-chains 81 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1384 CYS Chi-restraints excluded: chain A residue 1491 HIS Chi-restraints excluded: chain A residue 1784 ILE Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2356 SER Chi-restraints excluded: chain A residue 2797 ILE Chi-restraints excluded: chain A residue 2859 ILE Chi-restraints excluded: chain A residue 3014 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 111 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 89 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.087916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.069001 restraints weight = 38115.486| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 3.00 r_work: 0.2673 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12090 Z= 0.126 Angle : 0.452 10.274 16456 Z= 0.234 Chirality : 0.037 0.153 1979 Planarity : 0.003 0.032 2041 Dihedral : 6.911 73.136 1813 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.67 % Allowed : 24.17 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.22), residues: 1515 helix: 2.07 (0.17), residues: 920 sheet: -0.31 (0.55), residues: 83 loop : -0.35 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1552 TYR 0.013 0.001 TYR A1413 PHE 0.019 0.001 PHE A2633 TRP 0.012 0.001 TRP A2542 HIS 0.004 0.001 HIS A3177 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (12082) covalent geometry : angle 0.45015 / 0.23 (16448) SS BOND : bond 0.00339 / 0.23 ( 1) SS BOND : angle 1.23086 / 0.77 ( 2) hydrogen bonds : bond 0.03440 / 2.34 ( 719) hydrogen bonds : angle 3.96179 / 2.88 ( 2065) metal coordination : bond 0.00504 / 0.29 ( 7) metal coordination : angle 2.11800 / 1.53 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.481 Fit side-chains REVERT: A 1246 ARG cc_start: 0.9423 (ttp80) cc_final: 0.8483 (mmt90) REVERT: A 1555 ASP cc_start: 0.8753 (m-30) cc_final: 0.8475 (m-30) REVERT: A 2298 MET cc_start: 0.8706 (tpp) cc_final: 0.8420 (mmm) REVERT: A 2797 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9065 (mp) outliers start: 8 outliers final: 7 residues processed: 84 average time/residue: 0.4866 time to fit residues: 45.7347 Evaluate side-chains 82 residues out of total 1426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1384 CYS Chi-restraints excluded: chain A residue 1491 HIS Chi-restraints excluded: chain A residue 1784 ILE Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2356 SER Chi-restraints excluded: chain A residue 2797 ILE Chi-restraints excluded: chain A residue 2859 ILE Chi-restraints excluded: chain A residue 3014 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 63 optimal weight: 0.0370 chunk 80 optimal weight: 0.0170 chunk 123 optimal weight: 1.9990 chunk 34 optimal weight: 0.0670 chunk 77 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.2834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1365 HIS A1521 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.088060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.070357 restraints weight = 32785.291| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.74 r_work: 0.2728 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.679 12090 Z= 0.518 Angle : 0.436 10.306 16456 Z= 0.226 Chirality : 0.036 0.149 1979 Planarity : 0.003 0.034 2041 Dihedral : 6.850 73.169 1813 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.75 % Allowed : 24.08 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.22), residues: 1515 helix: 2.11 (0.17), residues: 920 sheet: -0.29 (0.55), residues: 83 loop : -0.35 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1552 TYR 0.012 0.001 TYR A3111 PHE 0.020 0.001 PHE A2633 TRP 0.011 0.001 TRP A2542 HIS 0.004 0.001 HIS A1066 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 (12082) covalent geometry : angle 0.43441 / 0.23 (16448) SS BOND : bond 0.00273 / 0.18 ( 1) SS BOND : angle 0.92844 / 0.58 ( 2) hydrogen bonds : bond 0.03203 / 2.18 ( 719) hydrogen bonds : angle 3.89399 / 2.83 ( 2065) metal coordination : bond 0.63445 / 12.69 ( 7) metal coordination : angle 2.11460 / 1.50 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3894.04 seconds wall clock time: 67 minutes 32.49 seconds (4052.49 seconds total)