Starting phenix.real_space_refine on Sat Oct 24 01:20:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wet_65915/10_2026/9wet_65915.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wet_65915/10_2026/9wet_65915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wet_65915/10_2026/9wet_65915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wet_65915/10_2026/9wet_65915.map" model { file = "/net/cci-nas-00/data/ceres_data/9wet_65915/10_2026/9wet_65915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wet_65915/10_2026/9wet_65915.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 53 5.16 5 C 7430 2.51 5 N 1903 2.21 5 O 2048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11442 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1417, 11210 Classifications: {'peptide': 1417} Link IDs: {'PTRANS': 58, 'TRANS': 1358} Chain breaks: 2 Chain: "A" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 232 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 2.59, per 1000 atoms: 0.23 Number of scatterers: 11442 At special positions: 0 Unit cell: (79.58, 89.96, 150.164, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 53 16.00 P 6 15.00 Mg 2 11.99 O 2048 8.00 N 1903 7.00 C 7430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 32 " 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: 0.80 Conformation dependent library (CDL) restraints added in 670.3 milliseconds 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2644 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 8 sheets defined 70.6% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 Processing helix chain 'A' and resid 16 through 22 Processing helix chain 'A' and resid 26 through 28 No H-bonds generated for 'chain 'A' and resid 26 through 28' Processing helix chain 'A' and resid 29 through 37 removed outlier: 3.519A pdb=" N ALA A 33 " --> pdb=" O TYR A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 59 removed outlier: 3.568A pdb=" N ILE A 54 " --> pdb=" O CYS A 50 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 56 " --> pdb=" O TYR A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 94 removed outlier: 3.827A pdb=" N ALA A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Proline residue: A 88 - end of helix removed outlier: 3.960A pdb=" N MET A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 130 removed outlier: 3.542A pdb=" N PHE A 112 " --> pdb=" O PRO A 108 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 113 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 162 removed outlier: 3.584A pdb=" N VAL A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 160 " --> pdb=" O VAL A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 169 through 191 Processing helix chain 'A' and resid 232 through 238 Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 242 through 252 Processing helix chain 'A' and resid 267 through 285 removed outlier: 3.789A pdb=" N LYS A 281 " --> pdb=" O HIS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 300 through 332 removed outlier: 3.706A pdb=" N GLY A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 337 through 385 removed outlier: 3.880A pdb=" N ILE A 341 " --> pdb=" O TRP A 337 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 394 removed outlier: 3.548A pdb=" N ARG A 392 " --> pdb=" O ASN A 388 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 413 removed outlier: 3.697A pdb=" N ASP A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 417 removed outlier: 4.053A pdb=" N LEU A 417 " --> pdb=" O CYS A 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 414 through 417' Processing helix chain 'A' and resid 418 through 438 Proline residue: A 424 - end of helix removed outlier: 3.636A pdb=" N GLN A 436 " --> pdb=" O ILE A 432 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 451 removed outlier: 3.927A pdb=" N LEU A 443 " --> pdb=" O GLY A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 487 removed outlier: 4.213A pdb=" N LEU A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 496 through 546 Proline residue: A 533 - end of helix removed outlier: 3.526A pdb=" N THR A 537 " --> pdb=" O PRO A 533 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 538 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 545 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 595 removed outlier: 3.656A pdb=" N PHE A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) Proline residue: A 569 - end of helix Proline residue: A 574 - end of helix Processing helix chain 'A' and resid 654 through 663 Processing helix chain 'A' and resid 694 through 700 Processing helix chain 'A' and resid 705 through 716 removed outlier: 3.508A pdb=" N THR A 716 " --> pdb=" O ALA A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 725 Processing helix chain 'A' and resid 727 through 730 Processing helix chain 'A' and resid 734 through 738 removed outlier: 3.604A pdb=" N VAL A 738 " --> pdb=" O GLU A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 757 removed outlier: 3.737A pdb=" N ASN A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 783 Processing helix chain 'A' and resid 801 through 805 removed outlier: 3.861A pdb=" N VAL A 805 " --> pdb=" O LEU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 828 Processing helix chain 'A' and resid 829 through 839 Processing helix chain 'A' and resid 904 through 916 removed outlier: 3.694A pdb=" N LEU A 908 " --> pdb=" O SER A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 947 removed outlier: 3.710A pdb=" N VAL A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 932 " --> pdb=" O TYR A 928 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR A 937 " --> pdb=" O VAL A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 1002 removed outlier: 3.699A pdb=" N TYR A 959 " --> pdb=" O GLY A 955 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN A 970 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 984 " --> pdb=" O TRP A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1011 removed outlier: 3.700A pdb=" N PHE A1008 " --> pdb=" O PRO A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1030 removed outlier: 3.683A pdb=" N ASP A1023 " --> pdb=" O ARG A1019 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU A1024 " --> pdb=" O PHE A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1056 Processing helix chain 'A' and resid 1058 through 1091 Proline residue: A1065 - end of helix removed outlier: 3.802A pdb=" N TYR A1071 " --> pdb=" O LEU A1067 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A1076 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR A1080 " --> pdb=" O TYR A1076 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLU A1083 " --> pdb=" O ASN A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1105 removed outlier: 4.016A pdb=" N TYR A1096 " --> pdb=" O ARG A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1113 Processing helix chain 'A' and resid 1114 through 1167 removed outlier: 3.942A pdb=" N PHE A1132 " --> pdb=" O ASN A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1174 Processing helix chain 'A' and resid 1175 through 1187 Processing helix chain 'A' and resid 1188 through 1218 removed outlier: 3.529A pdb=" N SER A1201 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA A1209 " --> pdb=" O ASN A1205 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A1210 " --> pdb=" O SER A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1290 removed outlier: 3.632A pdb=" N LEU A1286 " --> pdb=" O LYS A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1317 Processing helix chain 'A' and resid 1333 through 1338 Processing helix chain 'A' and resid 1344 through 1355 Processing helix chain 'A' and resid 1357 through 1364 removed outlier: 4.043A pdb=" N ASN A1364 " --> pdb=" O THR A1360 " (cutoff:3.500A) Processing helix chain 'A' and resid 1373 through 1377 Processing helix chain 'A' and resid 1380 through 1396 Processing helix chain 'A' and resid 1410 through 1425 Processing helix chain 'A' and resid 1436 through 1440 Processing helix chain 'A' and resid 1459 through 1466 Processing helix chain 'A' and resid 1469 through 1478 removed outlier: 3.530A pdb=" N MET A1474 " --> pdb=" O SER A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1479 through 1491 removed outlier: 3.676A pdb=" N GLU A1484 " --> pdb=" O ALA A1480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 66 removed outlier: 4.320A pdb=" N TYR A 135 " --> pdb=" O PHE A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 638 through 639 removed outlier: 3.570A pdb=" N ILE A 614 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 619 through 621 removed outlier: 5.710A pdb=" N GLY A 619 " --> pdb=" O ASN A 634 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 680 through 683 removed outlier: 6.277A pdb=" N ALA A 681 " --> pdb=" O ILE A 762 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ASP A 764 " --> pdb=" O ALA A 681 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 683 " --> pdb=" O ASP A 764 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A 645 " --> pdb=" O LEU A 794 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE A 808 " --> pdb=" O GLU A 819 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU A 819 " --> pdb=" O ILE A 808 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU A 810 " --> pdb=" O LYS A 817 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 692 through 693 Processing sheet with id=AA6, first strand: chain 'A' and resid 1259 through 1266 removed outlier: 7.060A pdb=" N HIS A1260 " --> pdb=" O VAL A1248 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL A1248 " --> pdb=" O HIS A1260 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N VAL A1262 " --> pdb=" O ASP A1246 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A1246 " --> pdb=" O VAL A1262 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1319 through 1322 removed outlier: 6.603A pdb=" N VAL A1448 " --> pdb=" O GLN A1455 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1331 through 1332 731 hydrogen bonds defined for protein. 2133 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: 2.79 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.18: 12 1.18 - 1.36: 3711 1.36 - 1.55: 7802 1.55 - 1.73: 68 1.73 - 1.91: 116 Bond restraints: 11709 Sorted by residual: bond pdb=" C7 CLR A1709 " pdb=" C8 CLR A1709 " ideal model delta sigma weight residual 1.525 0.997 0.528 2.00e-02 2.50e+03 6.97e+02 bond pdb=" C7 CLR A1710 " pdb=" C8 CLR A1710 " ideal model delta sigma weight residual 1.525 0.999 0.526 2.00e-02 2.50e+03 6.91e+02 bond pdb=" C7 CLR A1705 " pdb=" C8 CLR A1705 " ideal model delta sigma weight residual 1.525 1.000 0.525 2.00e-02 2.50e+03 6.89e+02 bond pdb=" C7 CLR A1706 " pdb=" C8 CLR A1706 " ideal model delta sigma weight residual 1.525 1.002 0.523 2.00e-02 2.50e+03 6.85e+02 bond pdb=" C7 CLR A1707 " pdb=" C8 CLR A1707 " ideal model delta sigma weight residual 1.525 1.002 0.523 2.00e-02 2.50e+03 6.84e+02 ... (remaining 11704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.44: 15817 4.44 - 8.89: 106 8.89 - 13.33: 18 13.33 - 17.78: 2 17.78 - 22.22: 6 Bond angle restraints: 15949 Sorted by residual: angle pdb=" PB ATP A1702 " pdb=" O3B ATP A1702 " pdb=" PG ATP A1702 " ideal model delta sigma weight residual 139.87 122.59 17.28 1.00e+00 1.00e+00 2.99e+02 angle pdb=" PB ATP A1701 " pdb=" O3B ATP A1701 " pdb=" PG ATP A1701 " ideal model delta sigma weight residual 139.87 125.41 14.46 1.00e+00 1.00e+00 2.09e+02 angle pdb=" PA ATP A1702 " pdb=" O3A ATP A1702 " pdb=" PB ATP A1702 " ideal model delta sigma weight residual 136.83 124.85 11.98 1.00e+00 1.00e+00 1.43e+02 angle pdb=" PA ATP A1701 " pdb=" O3A ATP A1701 " pdb=" PB ATP A1701 " ideal model delta sigma weight residual 136.83 125.18 11.65 1.00e+00 1.00e+00 1.36e+02 angle pdb=" C5 ATP A1701 " pdb=" C4 ATP A1701 " pdb=" N3 ATP A1701 " ideal model delta sigma weight residual 126.80 119.28 7.52 1.00e+00 1.00e+00 5.65e+01 ... (remaining 15944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 6055 17.77 - 35.55: 829 35.55 - 53.32: 301 53.32 - 71.09: 77 71.09 - 88.87: 21 Dihedral angle restraints: 7283 sinusoidal: 3180 harmonic: 4103 Sorted by residual: dihedral pdb=" CA CYS A 493 " pdb=" C CYS A 493 " pdb=" N TYR A 494 " pdb=" CA TYR A 494 " ideal model delta harmonic sigma weight residual 180.00 159.09 20.91 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CB CYS A 10 " pdb=" SG CYS A 10 " pdb=" SG CYS A 32 " pdb=" CB CYS A 32 " ideal model delta sinusoidal sigma weight residual 93.00 61.61 31.39 1 1.00e+01 1.00e-02 1.41e+01 dihedral pdb=" CA ILE A 93 " pdb=" C ILE A 93 " pdb=" N MET A 94 " pdb=" CA MET A 94 " ideal model delta harmonic sigma weight residual 180.00 162.36 17.64 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 7280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.392: 1830 0.392 - 0.785: 2 0.785 - 1.177: 0 1.177 - 1.570: 6 1.570 - 1.962: 6 Chirality restraints: 1844 Sorted by residual: chirality pdb=" C10 CLR A1705 " pdb=" C1 CLR A1705 " pdb=" C5 CLR A1705 " pdb=" C9 CLR A1705 " both_signs ideal model delta sigma weight residual False -2.85 -0.89 -1.96 2.00e-01 2.50e+01 9.63e+01 chirality pdb=" C10 CLR A1709 " pdb=" C1 CLR A1709 " pdb=" C5 CLR A1709 " pdb=" C9 CLR A1709 " both_signs ideal model delta sigma weight residual False -2.85 -0.89 -1.96 2.00e-01 2.50e+01 9.58e+01 chirality pdb=" C10 CLR A1706 " pdb=" C1 CLR A1706 " pdb=" C5 CLR A1706 " pdb=" C9 CLR A1706 " both_signs ideal model delta sigma weight residual False -2.85 -0.89 -1.96 2.00e-01 2.50e+01 9.56e+01 ... (remaining 1841 not shown) Planarity restraints: 1964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1487 " -0.401 9.50e-02 1.11e+02 1.80e-01 1.98e+01 pdb=" NE ARG A1487 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A1487 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A1487 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A1487 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 947 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ASP A 947 " 0.056 2.00e-02 2.50e+03 pdb=" O ASP A 947 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA A 948 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 319 " 0.040 5.00e-02 4.00e+02 6.11e-02 5.97e+00 pdb=" N PRO A 320 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " 0.034 5.00e-02 4.00e+02 ... (remaining 1961 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 35 2.53 - 3.12: 8622 3.12 - 3.71: 18955 3.71 - 4.31: 26455 4.31 - 4.90: 44186 Nonbonded interactions: 98253 Sorted by model distance: nonbonded pdb=" OG1 THR A 656 " pdb="MG MG A1703 " model vdw 1.933 2.170 nonbonded pdb=" OE1 GLN A 685 " pdb="MG MG A1703 " model vdw 1.950 2.170 nonbonded pdb=" O1G ATP A1701 " pdb="MG MG A1703 " model vdw 1.976 2.170 nonbonded pdb=" O2G ATP A1702 " pdb="MG MG A1704 " model vdw 2.205 2.170 nonbonded pdb=" OG SER A1283 " pdb="MG MG A1704 " model vdw 2.227 2.170 ... (remaining 98248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.890 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.750 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 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 : 0.029 0.528 11710 Z= 1.501 Angle : 0.980 22.222 15951 Z= 0.512 Chirality : 0.148 1.962 1844 Planarity : 0.006 0.180 1964 Dihedral : 19.176 88.866 4636 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.65 % Allowed : 28.38 % Favored : 66.97 % 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: 0.74 (0.22), residues: 1411 helix: 1.04 (0.17), residues: 931 sheet: -0.48 (0.65), residues: 69 loop : -0.42 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1354 TYR 0.019 0.001 TYR A 369 PHE 0.014 0.001 PHE A 272 TRP 0.017 0.001 TRP A 260 HIS 0.003 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.02917 / 1.50 (11709) covalent geometry : angle 0.98003 / 0.51 (15949) SS BOND : bond 0.00305 / 0.16 ( 1) SS BOND : angle 0.37996 / 0.22 ( 2) hydrogen bonds : bond 0.15190 / 9.76 ( 731) hydrogen bonds : angle 6.09176 / 4.29 ( 2133) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 130 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 71 ARG cc_start: 0.2191 (OUTLIER) cc_final: 0.1117 (ttp-170) REVERT: A 130 MET cc_start: 0.6233 (OUTLIER) cc_final: 0.5841 (ptp) REVERT: A 189 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8225 (mp) REVERT: A 192 MET cc_start: 0.4736 (mmt) cc_final: 0.3485 (ttm) REVERT: A 237 ILE cc_start: 0.8865 (mt) cc_final: 0.8623 (mm) REVERT: A 307 PHE cc_start: 0.7080 (t80) cc_final: 0.6277 (m-80) REVERT: A 338 MET cc_start: 0.6987 (tpp) cc_final: 0.6476 (mmp) REVERT: A 364 VAL cc_start: 0.7835 (OUTLIER) cc_final: 0.7534 (m) REVERT: A 365 MET cc_start: 0.8803 (mtp) cc_final: 0.8441 (mtt) REVERT: A 393 LYS cc_start: 0.8568 (mtpm) cc_final: 0.8147 (mtmm) REVERT: A 489 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7870 (p0) REVERT: A 534 VAL cc_start: 0.8163 (OUTLIER) cc_final: 0.7785 (m) REVERT: A 600 ILE cc_start: 0.8079 (mm) cc_final: 0.7856 (mm) REVERT: A 785 ARG cc_start: 0.8198 (mtm110) cc_final: 0.7899 (mpp80) REVERT: A 798 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8134 (mt0) REVERT: A 899 GLU cc_start: 0.4427 (OUTLIER) cc_final: 0.2654 (pp20) REVERT: A 919 TRP cc_start: 0.6508 (OUTLIER) cc_final: 0.5836 (t60) REVERT: A 922 MET cc_start: 0.7464 (mtp) cc_final: 0.7202 (mtt) REVERT: A 1092 ARG cc_start: 0.8033 (tpp-160) cc_final: 0.7696 (tpp-160) REVERT: A 1148 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: A 1173 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7374 (tp-100) REVERT: A 1175 PHE cc_start: 0.7747 (m-80) cc_final: 0.7509 (m-80) REVERT: A 1185 TYR cc_start: 0.8731 (m-80) cc_final: 0.8269 (m-80) REVERT: A 1297 LYS cc_start: 0.8056 (mtpp) cc_final: 0.7651 (mtmt) REVERT: A 1374 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7735 (tt0) REVERT: A 1377 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8028 (pt0) REVERT: A 1396 ARG cc_start: 0.8401 (tpp80) cc_final: 0.7696 (mmt90) outliers start: 57 outliers final: 33 residues processed: 175 average time/residue: 0.4663 time to fit residues: 89.9596 Evaluate side-chains 171 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 265 TRP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 798 GLN Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1019 ARG Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1173 GLN Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1190 THR Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain A residue 1377 GLU Chi-restraints excluded: chain A residue 1397 SER Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1459 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN A 287 GLN A 401 ASN ** A 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1482 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.154912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.117990 restraints weight = 13129.105| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.74 r_work: 0.3175 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.0690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11710 Z= 0.151 Angle : 0.572 6.826 15951 Z= 0.290 Chirality : 0.042 0.247 1844 Planarity : 0.004 0.064 1964 Dihedral : 11.673 89.956 2082 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.71 % Allowed : 26.59 % Favored : 67.70 % 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: 1.07 (0.22), residues: 1411 helix: 1.29 (0.17), residues: 938 sheet: -0.23 (0.64), residues: 69 loop : -0.33 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1354 TYR 0.020 0.001 TYR A 369 PHE 0.016 0.001 PHE A 557 TRP 0.014 0.001 TRP A 55 HIS 0.003 0.001 HIS A 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (11709) covalent geometry : angle 0.57184 / 0.29 (15949) SS BOND : bond 0.00651 / 0.34 ( 1) SS BOND : angle 0.71793 / 0.42 ( 2) hydrogen bonds : bond 0.05108 / 3.30 ( 731) hydrogen bonds : angle 4.68544 / 3.27 ( 2133) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 139 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6527 (pt) REVERT: A 155 MET cc_start: 0.7139 (OUTLIER) cc_final: 0.6880 (mmp) REVERT: A 157 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7433 (tp) REVERT: A 192 MET cc_start: 0.4749 (mmt) cc_final: 0.3496 (ttm) REVERT: A 235 ASP cc_start: 0.8148 (m-30) cc_final: 0.7793 (m-30) REVERT: A 237 ILE cc_start: 0.8812 (mt) cc_final: 0.8527 (mm) REVERT: A 264 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7938 (m) REVERT: A 307 PHE cc_start: 0.7085 (t80) cc_final: 0.6250 (m-80) REVERT: A 338 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6525 (mmp) REVERT: A 364 VAL cc_start: 0.7851 (OUTLIER) cc_final: 0.7526 (m) REVERT: A 365 MET cc_start: 0.8783 (mtp) cc_final: 0.8417 (mtt) REVERT: A 393 LYS cc_start: 0.8467 (mtpm) cc_final: 0.8052 (mtmm) REVERT: A 398 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7492 (tttt) REVERT: A 489 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7859 (p0) REVERT: A 534 VAL cc_start: 0.8158 (p) cc_final: 0.7822 (m) REVERT: A 600 ILE cc_start: 0.8068 (mm) cc_final: 0.7850 (mm) REVERT: A 919 TRP cc_start: 0.6417 (OUTLIER) cc_final: 0.5750 (t60) REVERT: A 1082 ARG cc_start: 0.5473 (OUTLIER) cc_final: 0.4881 (mmm160) REVERT: A 1173 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7431 (tp-100) REVERT: A 1175 PHE cc_start: 0.7695 (m-80) cc_final: 0.7479 (m-80) REVERT: A 1297 LYS cc_start: 0.7852 (mtpp) cc_final: 0.7443 (mtmt) REVERT: A 1385 GLN cc_start: 0.8264 (mt0) cc_final: 0.8027 (mt0) REVERT: A 1395 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7705 (ttt180) outliers start: 70 outliers final: 23 residues processed: 192 average time/residue: 0.4936 time to fit residues: 104.1452 Evaluate side-chains 163 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 265 TRP Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1019 ARG Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1082 ARG Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1173 GLN Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1327 VAL Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1490 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [20, 61, 73, 129, 57, 5, 106, 21, 135, 67, 25] chunk 20 optimal weight: 0.0570 chunk 61 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 GLN A 183 GLN A 224 GLN A 287 GLN A 401 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.154936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.118081 restraints weight = 13259.098| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.02 r_work: 0.3160 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11710 Z= 0.136 Angle : 0.535 9.900 15951 Z= 0.274 Chirality : 0.041 0.230 1844 Planarity : 0.004 0.064 1964 Dihedral : 10.742 89.146 2035 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 6.20 % Allowed : 27.32 % Favored : 66.48 % 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: 1.26 (0.23), residues: 1411 helix: 1.40 (0.17), residues: 946 sheet: -0.18 (0.64), residues: 69 loop : -0.20 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1354 TYR 0.020 0.001 TYR A 369 PHE 0.014 0.001 PHE A 109 TRP 0.012 0.001 TRP A1142 HIS 0.003 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (11709) covalent geometry : angle 0.53524 / 0.27 (15949) SS BOND : bond 0.00525 / 0.28 ( 1) SS BOND : angle 0.69386 / 0.41 ( 2) hydrogen bonds : bond 0.04834 / 3.11 ( 731) hydrogen bonds : angle 4.49479 / 3.15 ( 2133) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 133 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.7096 (tpt) cc_final: 0.6896 (tpt) REVERT: A 192 MET cc_start: 0.4763 (mmt) cc_final: 0.3491 (ttm) REVERT: A 235 ASP cc_start: 0.8171 (m-30) cc_final: 0.7773 (m-30) REVERT: A 237 ILE cc_start: 0.8776 (mt) cc_final: 0.8487 (mm) REVERT: A 307 PHE cc_start: 0.7063 (t80) cc_final: 0.6193 (m-80) REVERT: A 338 MET cc_start: 0.6937 (tpp) cc_final: 0.6471 (mmp) REVERT: A 364 VAL cc_start: 0.7858 (OUTLIER) cc_final: 0.7536 (m) REVERT: A 365 MET cc_start: 0.8754 (mtp) cc_final: 0.8403 (mtt) REVERT: A 393 LYS cc_start: 0.8422 (mtpm) cc_final: 0.7980 (mtmm) REVERT: A 398 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7463 (tttt) REVERT: A 489 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7853 (p0) REVERT: A 534 VAL cc_start: 0.8107 (OUTLIER) cc_final: 0.7731 (m) REVERT: A 600 ILE cc_start: 0.8051 (mm) cc_final: 0.7829 (mm) REVERT: A 785 ARG cc_start: 0.8092 (mtm110) cc_final: 0.7801 (mpp80) REVERT: A 919 TRP cc_start: 0.6464 (OUTLIER) cc_final: 0.5755 (t60) REVERT: A 991 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7141 (mtpt) REVERT: A 1019 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7559 (tpp80) REVERT: A 1082 ARG cc_start: 0.5494 (OUTLIER) cc_final: 0.4891 (mmm160) REVERT: A 1124 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.6383 (mtp180) REVERT: A 1148 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: A 1173 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7327 (tp-100) REVERT: A 1175 PHE cc_start: 0.7669 (m-80) cc_final: 0.7440 (m-80) REVERT: A 1185 TYR cc_start: 0.8746 (m-80) cc_final: 0.8286 (m-80) REVERT: A 1297 LYS cc_start: 0.7824 (mtpp) cc_final: 0.7406 (mtmt) REVERT: A 1474 MET cc_start: 0.7444 (mtt) cc_final: 0.7194 (mtt) outliers start: 76 outliers final: 39 residues processed: 192 average time/residue: 0.4960 time to fit residues: 104.5994 Evaluate side-chains 178 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 128 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 265 TRP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1019 ARG Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1082 ARG Chi-restraints excluded: chain A residue 1124 ARG Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1173 GLN Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1190 THR Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1327 VAL Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1459 SER Chi-restraints excluded: chain A residue 1490 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [28, 41, 70, 11, 22, 7, 123, 50, 76, 102, 79] chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 287 GLN A 401 ASN A 584 ASN A1009 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.153040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.114799 restraints weight = 13363.452| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.64 r_work: 0.3138 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11710 Z= 0.198 Angle : 0.581 8.060 15951 Z= 0.298 Chirality : 0.043 0.274 1844 Planarity : 0.004 0.066 1964 Dihedral : 10.600 82.407 2032 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 7.42 % Allowed : 25.69 % Favored : 66.88 % 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: 1.08 (0.23), residues: 1411 helix: 1.26 (0.17), residues: 947 sheet: -0.32 (0.62), residues: 69 loop : -0.24 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1354 TYR 0.021 0.001 TYR A 369 PHE 0.017 0.002 PHE A 557 TRP 0.014 0.001 TRP A 265 HIS 0.003 0.001 HIS A 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (11709) covalent geometry : angle 0.58087 / 0.30 (15949) SS BOND : bond 0.00638 / 0.34 ( 1) SS BOND : angle 0.75716 / 0.44 ( 2) hydrogen bonds : bond 0.05278 / 3.42 ( 731) hydrogen bonds : angle 4.53664 / 3.19 ( 2133) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 128 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: 0.7473 (t) cc_final: 0.7103 (t) REVERT: A 71 ARG cc_start: 0.2388 (OUTLIER) cc_final: 0.1118 (ttp-170) REVERT: A 96 ILE cc_start: 0.6791 (OUTLIER) cc_final: 0.6342 (pt) REVERT: A 125 MET cc_start: 0.7290 (tpt) cc_final: 0.7033 (tpt) REVERT: A 192 MET cc_start: 0.4727 (mmt) cc_final: 0.3489 (ttm) REVERT: A 237 ILE cc_start: 0.8883 (mt) cc_final: 0.8642 (mm) REVERT: A 264 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.8031 (m) REVERT: A 307 PHE cc_start: 0.7221 (t80) cc_final: 0.6475 (m-80) REVERT: A 338 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6827 (mmp) REVERT: A 365 MET cc_start: 0.8969 (mtp) cc_final: 0.8660 (mtt) REVERT: A 393 LYS cc_start: 0.8590 (mtpm) cc_final: 0.8201 (mtmm) REVERT: A 398 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.7726 (tttt) REVERT: A 489 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7984 (p0) REVERT: A 673 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8197 (mm) REVERT: A 919 TRP cc_start: 0.6641 (OUTLIER) cc_final: 0.5912 (t60) REVERT: A 922 MET cc_start: 0.7674 (mtp) cc_final: 0.7430 (mtt) REVERT: A 991 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7597 (mtpt) REVERT: A 1082 ARG cc_start: 0.5656 (OUTLIER) cc_final: 0.5074 (mmp-170) REVERT: A 1092 ARG cc_start: 0.8122 (tpp-160) cc_final: 0.7850 (tpp-160) REVERT: A 1173 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7447 (tp-100) REVERT: A 1297 LYS cc_start: 0.7972 (mtpp) cc_final: 0.7710 (mtmt) REVERT: A 1385 GLN cc_start: 0.8459 (mt0) cc_final: 0.8234 (mt0) outliers start: 91 outliers final: 43 residues processed: 201 average time/residue: 0.4618 time to fit residues: 102.5385 Evaluate side-chains 177 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 123 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 265 TRP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1019 ARG Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1082 ARG Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1173 GLN Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1190 THR Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1459 SER Chi-restraints excluded: chain A residue 1490 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [113, 80, 37, 34, 16, 140, 133, 89, 25, 30, 6] chunk 113 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 287 GLN A 316 GLN A 401 ASN A1009 HIS A1172 GLN A1208 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.154288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.116986 restraints weight = 13217.485| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.80 r_work: 0.3168 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11710 Z= 0.148 Angle : 0.559 10.640 15951 Z= 0.284 Chirality : 0.041 0.262 1844 Planarity : 0.004 0.064 1964 Dihedral : 10.322 79.218 2032 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 6.69 % Allowed : 27.16 % Favored : 66.15 % 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: 1.18 (0.23), residues: 1411 helix: 1.36 (0.17), residues: 947 sheet: -0.33 (0.61), residues: 69 loop : -0.25 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1354 TYR 0.019 0.001 TYR A 369 PHE 0.014 0.001 PHE A 109 TRP 0.013 0.001 TRP A1142 HIS 0.003 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (11709) covalent geometry : angle 0.55862 / 0.28 (15949) SS BOND : bond 0.00500 / 0.26 ( 1) SS BOND : angle 0.60306 / 0.35 ( 2) hydrogen bonds : bond 0.04878 / 3.14 ( 731) hydrogen bonds : angle 4.46130 / 3.13 ( 2133) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 131 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: 0.7445 (t) cc_final: 0.7089 (t) REVERT: A 71 ARG cc_start: 0.2284 (OUTLIER) cc_final: 0.1034 (ttp-170) REVERT: A 96 ILE cc_start: 0.6774 (OUTLIER) cc_final: 0.6327 (pt) REVERT: A 125 MET cc_start: 0.7329 (tpt) cc_final: 0.7046 (tpt) REVERT: A 192 MET cc_start: 0.4792 (mmt) cc_final: 0.3536 (ttm) REVERT: A 237 ILE cc_start: 0.8874 (mt) cc_final: 0.8636 (mm) REVERT: A 264 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.8055 (m) REVERT: A 307 PHE cc_start: 0.7274 (t80) cc_final: 0.6553 (m-80) REVERT: A 338 MET cc_start: 0.7229 (tpp) cc_final: 0.6878 (mmp) REVERT: A 364 VAL cc_start: 0.8197 (OUTLIER) cc_final: 0.7939 (m) REVERT: A 393 LYS cc_start: 0.8605 (mtpm) cc_final: 0.8238 (mtmm) REVERT: A 398 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.7760 (tttt) REVERT: A 489 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.8041 (p0) REVERT: A 534 VAL cc_start: 0.8412 (OUTLIER) cc_final: 0.8043 (m) REVERT: A 785 ARG cc_start: 0.8149 (mtm110) cc_final: 0.7888 (mpp80) REVERT: A 919 TRP cc_start: 0.6648 (OUTLIER) cc_final: 0.5941 (t60) REVERT: A 922 MET cc_start: 0.7761 (mtp) cc_final: 0.7514 (mtt) REVERT: A 991 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7682 (mtpt) REVERT: A 1071 TYR cc_start: 0.6446 (OUTLIER) cc_final: 0.5874 (t80) REVERT: A 1082 ARG cc_start: 0.5597 (OUTLIER) cc_final: 0.5076 (mmm160) REVERT: A 1146 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8508 (mpt180) REVERT: A 1297 LYS cc_start: 0.7936 (mtpp) cc_final: 0.7689 (mtmt) REVERT: A 1385 GLN cc_start: 0.8471 (mt0) cc_final: 0.8250 (mt0) outliers start: 82 outliers final: 46 residues processed: 194 average time/residue: 0.4789 time to fit residues: 102.4240 Evaluate side-chains 186 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 128 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 265 TRP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1019 ARG Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1071 TYR Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1082 ARG Chi-restraints excluded: chain A residue 1146 ARG Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1190 THR Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1459 SER Chi-restraints excluded: chain A residue 1490 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [41, 129, 131, 2, 108, 115, 64, 68, 117, 45, 30] chunk 41 optimal weight: 3.9990 chunk 129 optimal weight: 0.0370 chunk 131 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 287 GLN A 316 GLN A 401 ASN A1009 HIS A1172 GLN A1208 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.155067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.117521 restraints weight = 13184.117| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.69 r_work: 0.3130 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11710 Z= 0.140 Angle : 0.555 9.834 15951 Z= 0.281 Chirality : 0.041 0.260 1844 Planarity : 0.004 0.064 1964 Dihedral : 10.024 77.413 2029 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 6.12 % Allowed : 27.41 % Favored : 66.48 % 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: 1.29 (0.23), residues: 1411 helix: 1.47 (0.17), residues: 944 sheet: -0.30 (0.60), residues: 69 loop : -0.30 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1354 TYR 0.019 0.001 TYR A 369 PHE 0.014 0.001 PHE A 109 TRP 0.015 0.001 TRP A 260 HIS 0.003 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (11709) covalent geometry : angle 0.55501 / 0.28 (15949) SS BOND : bond 0.00530 / 0.28 ( 1) SS BOND : angle 0.51239 / 0.30 ( 2) hydrogen bonds : bond 0.04711 / 3.02 ( 731) hydrogen bonds : angle 4.38688 / 3.08 ( 2133) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 134 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: 0.7378 (t) cc_final: 0.7043 (t) REVERT: A 71 ARG cc_start: 0.2430 (OUTLIER) cc_final: 0.1158 (ttp-170) REVERT: A 96 ILE cc_start: 0.6729 (OUTLIER) cc_final: 0.6260 (pt) REVERT: A 130 MET cc_start: 0.6408 (ptp) cc_final: 0.6095 (ptp) REVERT: A 192 MET cc_start: 0.4771 (mmt) cc_final: 0.3516 (ttm) REVERT: A 237 ILE cc_start: 0.8838 (mt) cc_final: 0.8586 (mm) REVERT: A 264 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.8033 (m) REVERT: A 307 PHE cc_start: 0.7208 (t80) cc_final: 0.6469 (m-80) REVERT: A 338 MET cc_start: 0.7138 (tpp) cc_final: 0.6757 (mmp) REVERT: A 364 VAL cc_start: 0.8083 (OUTLIER) cc_final: 0.7828 (m) REVERT: A 365 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8512 (mtt) REVERT: A 393 LYS cc_start: 0.8527 (mtpm) cc_final: 0.8132 (mtmm) REVERT: A 398 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.7651 (tttt) REVERT: A 534 VAL cc_start: 0.8298 (OUTLIER) cc_final: 0.7944 (m) REVERT: A 785 ARG cc_start: 0.8130 (mtm110) cc_final: 0.7851 (mpp80) REVERT: A 919 TRP cc_start: 0.6569 (OUTLIER) cc_final: 0.5913 (t60) REVERT: A 922 MET cc_start: 0.7684 (mtp) cc_final: 0.7409 (mtt) REVERT: A 991 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7547 (mtpt) REVERT: A 1019 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7856 (tpp80) REVERT: A 1082 ARG cc_start: 0.5539 (OUTLIER) cc_final: 0.5010 (mmm160) REVERT: A 1092 ARG cc_start: 0.8104 (tpp-160) cc_final: 0.7850 (tpp-160) REVERT: A 1124 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.6650 (mtp180) REVERT: A 1297 LYS cc_start: 0.7862 (mtpp) cc_final: 0.7611 (mtmt) REVERT: A 1385 GLN cc_start: 0.8405 (mt0) cc_final: 0.8183 (mt0) outliers start: 75 outliers final: 41 residues processed: 193 average time/residue: 0.4602 time to fit residues: 97.7404 Evaluate side-chains 181 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 128 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 265 TRP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1019 ARG Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1082 ARG Chi-restraints excluded: chain A residue 1124 ARG Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1459 SER Chi-restraints excluded: chain A residue 1490 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [26, 139, 40, 90, 120, 113, 89, 112, 99, 43, 124] chunk 26 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 287 GLN A 401 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.154459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.116206 restraints weight = 13199.228| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.75 r_work: 0.3122 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11710 Z= 0.154 Angle : 0.579 10.522 15951 Z= 0.289 Chirality : 0.042 0.295 1844 Planarity : 0.004 0.064 1964 Dihedral : 10.085 78.267 2027 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.87 % Allowed : 27.90 % Favored : 66.23 % 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: 1.23 (0.23), residues: 1411 helix: 1.43 (0.17), residues: 944 sheet: -0.29 (0.59), residues: 69 loop : -0.34 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1354 TYR 0.020 0.001 TYR A 369 PHE 0.014 0.001 PHE A 557 TRP 0.016 0.001 TRP A 260 HIS 0.006 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (11709) covalent geometry : angle 0.57885 / 0.29 (15949) SS BOND : bond 0.00563 / 0.30 ( 1) SS BOND : angle 0.48855 / 0.29 ( 2) hydrogen bonds : bond 0.04820 / 3.09 ( 731) hydrogen bonds : angle 4.39328 / 3.09 ( 2133) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 127 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.2453 (OUTLIER) cc_final: 0.1199 (ttp-170) REVERT: A 96 ILE cc_start: 0.6774 (OUTLIER) cc_final: 0.6335 (pt) REVERT: A 125 MET cc_start: 0.7285 (tpt) cc_final: 0.7081 (tpt) REVERT: A 192 MET cc_start: 0.4690 (mmt) cc_final: 0.3447 (ttm) REVERT: A 237 ILE cc_start: 0.8851 (mt) cc_final: 0.8595 (mm) REVERT: A 264 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.8035 (m) REVERT: A 307 PHE cc_start: 0.7231 (t80) cc_final: 0.6461 (m-80) REVERT: A 338 MET cc_start: 0.7204 (tpp) cc_final: 0.6822 (mmp) REVERT: A 364 VAL cc_start: 0.8105 (OUTLIER) cc_final: 0.7799 (m) REVERT: A 365 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8550 (mtt) REVERT: A 393 LYS cc_start: 0.8536 (mtpm) cc_final: 0.8128 (mtmm) REVERT: A 398 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.7652 (tttt) REVERT: A 534 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.8000 (m) REVERT: A 785 ARG cc_start: 0.8135 (mtm110) cc_final: 0.7866 (mpp80) REVERT: A 919 TRP cc_start: 0.6587 (OUTLIER) cc_final: 0.5858 (t60) REVERT: A 991 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7561 (mtpt) REVERT: A 1019 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7812 (tpp80) REVERT: A 1082 ARG cc_start: 0.5640 (OUTLIER) cc_final: 0.5087 (mmm160) REVERT: A 1297 LYS cc_start: 0.7881 (mtpp) cc_final: 0.7619 (mtmt) REVERT: A 1385 GLN cc_start: 0.8437 (mt0) cc_final: 0.8200 (mt0) outliers start: 72 outliers final: 43 residues processed: 185 average time/residue: 0.4961 time to fit residues: 100.7405 Evaluate side-chains 180 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 126 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 265 TRP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1019 ARG Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1082 ARG Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1190 THR Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1459 SER Chi-restraints excluded: chain A residue 1490 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [48, 34, 13, 109, 67, 32, 56, 33, 58, 133, 60] chunk 48 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 58 optimal weight: 0.0020 chunk 133 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 287 GLN A 401 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.154851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.116486 restraints weight = 13165.530| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.72 r_work: 0.3140 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11710 Z= 0.147 Angle : 0.569 10.494 15951 Z= 0.286 Chirality : 0.042 0.286 1844 Planarity : 0.004 0.064 1964 Dihedral : 10.010 79.783 2027 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.95 % Allowed : 28.30 % Favored : 65.74 % 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: 1.26 (0.23), residues: 1411 helix: 1.46 (0.17), residues: 945 sheet: -0.25 (0.59), residues: 69 loop : -0.37 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1354 TYR 0.019 0.001 TYR A 369 PHE 0.014 0.001 PHE A 109 TRP 0.017 0.001 TRP A 260 HIS 0.003 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (11709) covalent geometry : angle 0.56915 / 0.29 (15949) SS BOND : bond 0.00503 / 0.26 ( 1) SS BOND : angle 0.43658 / 0.25 ( 2) hydrogen bonds : bond 0.04727 / 3.03 ( 731) hydrogen bonds : angle 4.38014 / 3.08 ( 2133) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 130 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 CYS cc_start: 0.6933 (OUTLIER) cc_final: 0.6013 (p) REVERT: A 71 ARG cc_start: 0.2548 (OUTLIER) cc_final: 0.1263 (ttp-170) REVERT: A 96 ILE cc_start: 0.6726 (OUTLIER) cc_final: 0.6261 (pt) REVERT: A 192 MET cc_start: 0.4659 (mmt) cc_final: 0.3348 (ttm) REVERT: A 237 ILE cc_start: 0.8895 (mt) cc_final: 0.8647 (mm) REVERT: A 264 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.8036 (m) REVERT: A 307 PHE cc_start: 0.7242 (t80) cc_final: 0.6529 (m-80) REVERT: A 338 MET cc_start: 0.7227 (tpp) cc_final: 0.6874 (mmp) REVERT: A 364 VAL cc_start: 0.8167 (OUTLIER) cc_final: 0.7885 (m) REVERT: A 365 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8576 (mtt) REVERT: A 393 LYS cc_start: 0.8567 (mtpm) cc_final: 0.8187 (mtmm) REVERT: A 398 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.7720 (tttt) REVERT: A 534 VAL cc_start: 0.8361 (OUTLIER) cc_final: 0.8017 (m) REVERT: A 919 TRP cc_start: 0.6613 (OUTLIER) cc_final: 0.5928 (t60) REVERT: A 991 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7690 (mtpt) REVERT: A 1019 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7905 (tpp80) REVERT: A 1029 ARG cc_start: 0.8276 (mtm110) cc_final: 0.7943 (mtp85) REVERT: A 1071 TYR cc_start: 0.6452 (OUTLIER) cc_final: 0.5910 (t80) REVERT: A 1082 ARG cc_start: 0.5585 (OUTLIER) cc_final: 0.5076 (mmm160) REVERT: A 1173 GLN cc_start: 0.8546 (pp30) cc_final: 0.8268 (tt0) REVERT: A 1297 LYS cc_start: 0.7887 (mtpp) cc_final: 0.7642 (mtmt) REVERT: A 1385 GLN cc_start: 0.8471 (mt0) cc_final: 0.8231 (mt0) outliers start: 73 outliers final: 46 residues processed: 186 average time/residue: 0.4852 time to fit residues: 99.3172 Evaluate side-chains 187 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 128 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 265 TRP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1019 ARG Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1071 TYR Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1082 ARG Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1190 THR Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1459 SER Chi-restraints excluded: chain A residue 1490 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [64, 100, 2, 95, 4, 130, 124, 78, 86, 104, 74] chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 287 GLN A 401 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.151387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.112810 restraints weight = 13166.093| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.86 r_work: 0.3049 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11710 Z= 0.254 Angle : 0.654 10.038 15951 Z= 0.330 Chirality : 0.046 0.365 1844 Planarity : 0.004 0.066 1964 Dihedral : 10.446 82.220 2026 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 5.71 % Allowed : 28.22 % Favored : 66.07 % 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: 0.89 (0.22), residues: 1411 helix: 1.15 (0.17), residues: 943 sheet: -0.44 (0.58), residues: 70 loop : -0.41 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1354 TYR 0.024 0.002 TYR A 369 PHE 0.020 0.002 PHE A 272 TRP 0.018 0.002 TRP A 260 HIS 0.004 0.001 HIS A1260 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.25 (11709) covalent geometry : angle 0.65419 / 0.33 (15949) SS BOND : bond 0.00730 / 0.38 ( 1) SS BOND : angle 0.48144 / 0.28 ( 2) hydrogen bonds : bond 0.05652 / 3.66 ( 731) hydrogen bonds : angle 4.55092 / 3.20 ( 2133) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 127 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.5311 (OUTLIER) cc_final: 0.3960 (tm-30) REVERT: A 45 VAL cc_start: 0.7409 (t) cc_final: 0.7043 (t) REVERT: A 71 ARG cc_start: 0.2509 (OUTLIER) cc_final: 0.1255 (ttp-170) REVERT: A 96 ILE cc_start: 0.6819 (OUTLIER) cc_final: 0.6403 (pt) REVERT: A 127 MET cc_start: 0.6629 (mmm) cc_final: 0.6418 (tmm) REVERT: A 192 MET cc_start: 0.4680 (mmt) cc_final: 0.3344 (ttm) REVERT: A 237 ILE cc_start: 0.8867 (mt) cc_final: 0.8655 (mm) REVERT: A 264 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8033 (m) REVERT: A 307 PHE cc_start: 0.7315 (t80) cc_final: 0.6509 (m-80) REVERT: A 338 MET cc_start: 0.7306 (tpp) cc_final: 0.6907 (mmp) REVERT: A 365 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8653 (mtt) REVERT: A 393 LYS cc_start: 0.8574 (mtpm) cc_final: 0.8150 (mtmm) REVERT: A 785 ARG cc_start: 0.8579 (mtt90) cc_final: 0.7868 (mpp80) REVERT: A 906 ARG cc_start: 0.6827 (ptp-110) cc_final: 0.6059 (tpm170) REVERT: A 919 TRP cc_start: 0.6610 (OUTLIER) cc_final: 0.5924 (t60) REVERT: A 991 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7585 (mtpt) REVERT: A 1071 TYR cc_start: 0.6360 (OUTLIER) cc_final: 0.5860 (t80) REVERT: A 1082 ARG cc_start: 0.5765 (OUTLIER) cc_final: 0.5187 (mmp-170) REVERT: A 1173 GLN cc_start: 0.8557 (pp30) cc_final: 0.8234 (tt0) REVERT: A 1297 LYS cc_start: 0.8023 (mtpp) cc_final: 0.7752 (mtmt) REVERT: A 1385 GLN cc_start: 0.8505 (mt0) cc_final: 0.8288 (mt0) outliers start: 70 outliers final: 45 residues processed: 180 average time/residue: 0.4803 time to fit residues: 94.8914 Evaluate side-chains 179 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 125 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 265 TRP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 909 LYS Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1019 ARG Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1071 TYR Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1082 ARG Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1190 THR Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1397 SER Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1490 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [97, 19, 112, 66, 33, 17, 110, 60, 61, 0, 18] chunk 97 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 chunk 60 optimal weight: 0.0870 chunk 61 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 287 GLN A 316 GLN A 401 ASN A1208 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.154473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.115884 restraints weight = 13153.072| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.76 r_work: 0.3129 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11710 Z= 0.142 Angle : 0.572 10.303 15951 Z= 0.289 Chirality : 0.042 0.313 1844 Planarity : 0.004 0.063 1964 Dihedral : 10.111 80.384 2026 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.32 % Allowed : 29.53 % Favored : 66.15 % 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: 1.18 (0.22), residues: 1411 helix: 1.39 (0.17), residues: 939 sheet: -0.36 (0.59), residues: 69 loop : -0.33 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1354 TYR 0.018 0.001 TYR A 369 PHE 0.014 0.001 PHE A 109 TRP 0.018 0.001 TRP A 260 HIS 0.004 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (11709) covalent geometry : angle 0.57206 / 0.29 (15949) SS BOND : bond 0.00471 / 0.25 ( 1) SS BOND : angle 0.36750 / 0.20 ( 2) hydrogen bonds : bond 0.04784 / 3.06 ( 731) hydrogen bonds : angle 4.43325 / 3.12 ( 2133) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 129 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.5525 (OUTLIER) cc_final: 0.4016 (tm-30) REVERT: A 45 VAL cc_start: 0.7467 (t) cc_final: 0.7118 (t) REVERT: A 71 ARG cc_start: 0.2654 (OUTLIER) cc_final: 0.1302 (ttp-170) REVERT: A 94 MET cc_start: 0.7324 (mmt) cc_final: 0.5894 (ptt) REVERT: A 96 ILE cc_start: 0.6715 (OUTLIER) cc_final: 0.6211 (pt) REVERT: A 127 MET cc_start: 0.6688 (mmm) cc_final: 0.6306 (tmm) REVERT: A 130 MET cc_start: 0.6573 (ptp) cc_final: 0.5916 (ptp) REVERT: A 192 MET cc_start: 0.4605 (mmt) cc_final: 0.3277 (ttm) REVERT: A 237 ILE cc_start: 0.8890 (mt) cc_final: 0.8647 (mm) REVERT: A 307 PHE cc_start: 0.7307 (t80) cc_final: 0.6595 (m-80) REVERT: A 338 MET cc_start: 0.7306 (tpp) cc_final: 0.6960 (mmp) REVERT: A 364 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7963 (m) REVERT: A 365 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8581 (mtt) REVERT: A 393 LYS cc_start: 0.8618 (mtpm) cc_final: 0.8248 (mtmm) REVERT: A 534 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8066 (m) REVERT: A 785 ARG cc_start: 0.8626 (mtt90) cc_final: 0.7949 (mpp80) REVERT: A 919 TRP cc_start: 0.6669 (OUTLIER) cc_final: 0.5973 (t60) REVERT: A 991 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7726 (mtpt) REVERT: A 1019 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7913 (tpp80) REVERT: A 1082 ARG cc_start: 0.5724 (OUTLIER) cc_final: 0.5212 (mmm160) REVERT: A 1173 GLN cc_start: 0.8578 (pp30) cc_final: 0.8267 (tt0) REVERT: A 1297 LYS cc_start: 0.7991 (mtpp) cc_final: 0.7743 (mtmt) REVERT: A 1385 GLN cc_start: 0.8495 (mt0) cc_final: 0.8264 (mt0) outliers start: 53 outliers final: 35 residues processed: 168 average time/residue: 0.5267 time to fit residues: 96.5788 Evaluate side-chains 171 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 265 TRP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1019 ARG Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 ARG Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1164 MET Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1190 THR Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1397 SER Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1490 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [23, 39, 61, 44, 36, 54, 25, 8, 11, 77, 47] chunk 23 optimal weight: 0.0670 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 44 optimal weight: 0.1980 chunk 36 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 287 GLN A 316 GLN A 401 ASN A1208 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.157689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.120832 restraints weight = 13214.286| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.57 r_work: 0.3205 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 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 : 0.002 0.038 11710 Z= 0.118 Angle : 0.550 10.331 15951 Z= 0.277 Chirality : 0.041 0.294 1844 Planarity : 0.004 0.063 1964 Dihedral : 9.616 84.037 2026 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.51 % Allowed : 30.42 % Favored : 66.07 % 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: 1.45 (0.23), residues: 1411 helix: 1.64 (0.17), residues: 940 sheet: -0.22 (0.59), residues: 68 loop : -0.37 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 785 TYR 0.017 0.001 TYR A 369 PHE 0.013 0.001 PHE A 109 TRP 0.016 0.001 TRP A 260 HIS 0.004 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (11709) covalent geometry : angle 0.54955 / 0.28 (15949) SS BOND : bond 0.00263 / 0.14 ( 1) SS BOND : angle 0.45850 / 0.24 ( 2) hydrogen bonds : bond 0.04316 / 2.74 ( 731) hydrogen bonds : angle 4.29381 / 3.02 ( 2133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4059.90 seconds wall clock time: 69 minutes 55.91 seconds (4195.91 seconds total)