Starting phenix.real_space_refine on Thu Jul 2 07:15:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kby_62234/07_2026/9kby_62234.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kby_62234/07_2026/9kby_62234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kby_62234/07_2026/9kby_62234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kby_62234/07_2026/9kby_62234.map" model { file = "/net/cci-nas-00/data/ceres_data/9kby_62234/07_2026/9kby_62234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kby_62234/07_2026/9kby_62234.cif" } resolution = 3.15 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= -0.063 sd= 0.354 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 65 5.49 5 Mg 2 5.21 5 S 31 5.16 5 C 4387 2.51 5 N 1246 2.21 5 O 1518 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7249 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5864 Classifications: {'peptide': 731} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 699} Chain breaks: 5 Chain: "B" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1383 Classifications: {'RNA': 65} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 32, 'rna3p_pyr': 31} Link IDs: {'rna2p': 1, 'rna3p': 63} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.33, per 1000 atoms: 0.18 Number of scatterers: 7249 At special positions: 0 Unit cell: (64.98, 83.79, 133.38, 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 31 16.00 P 65 15.00 Mg 2 11.99 O 1518 8.00 N 1246 7.00 C 4387 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 275.1 milliseconds 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1394 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 5 sheets defined 51.7% alpha, 13.8% beta 27 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 776 through 780 Processing helix chain 'A' and resid 820 through 825 removed outlier: 4.331A pdb=" N THR A 825 " --> pdb=" O VAL A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 871 removed outlier: 3.567A pdb=" N ARG A 856 " --> pdb=" O ASN A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 922 Processing helix chain 'A' and resid 923 through 927 Processing helix chain 'A' and resid 953 through 957 removed outlier: 3.705A pdb=" N LYS A 957 " --> pdb=" O ILE A 953 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 953 through 957' Processing helix chain 'A' and resid 992 through 999 removed outlier: 4.031A pdb=" N TYR A 998 " --> pdb=" O VAL A 994 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 999 " --> pdb=" O GLU A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1067 removed outlier: 4.067A pdb=" N LEU A1067 " --> pdb=" O SER A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1089 removed outlier: 3.508A pdb=" N ARG A1074 " --> pdb=" O SER A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1091 No H-bonds generated for 'chain 'A' and resid 1090 through 1091' Processing helix chain 'A' and resid 1092 through 1098 Processing helix chain 'A' and resid 1099 through 1108 removed outlier: 3.712A pdb=" N GLU A1105 " --> pdb=" O HIS A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1141 removed outlier: 4.023A pdb=" N VAL A1123 " --> pdb=" O GLU A1119 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU A1124 " --> pdb=" O ARG A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1158 removed outlier: 3.880A pdb=" N THR A1150 " --> pdb=" O GLU A1146 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A1151 " --> pdb=" O GLY A1147 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL A1156 " --> pdb=" O ARG A1152 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN A1158 " --> pdb=" O SER A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1168 removed outlier: 3.580A pdb=" N LYS A1168 " --> pdb=" O ARG A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1174 removed outlier: 5.877A pdb=" N GLN A1172 " --> pdb=" O LYS A1169 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A1173 " --> pdb=" O ASN A1170 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR A1174 " --> pdb=" O LEU A1171 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1169 through 1174' Processing helix chain 'A' and resid 1233 through 1250 removed outlier: 3.770A pdb=" N VAL A1239 " --> pdb=" O ILE A1235 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A1243 " --> pdb=" O VAL A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1263 removed outlier: 4.010A pdb=" N LYS A1257 " --> pdb=" O LYS A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1270 through 1279 removed outlier: 3.800A pdb=" N GLN A1274 " --> pdb=" O SER A1270 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A1276 " --> pdb=" O GLN A1272 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS A1277 " --> pdb=" O VAL A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1288 Proline residue: A1285 - end of helix removed outlier: 4.183A pdb=" N THR A1288 " --> pdb=" O PRO A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1300 removed outlier: 4.208A pdb=" N LEU A1295 " --> pdb=" O ASN A1291 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN A1297 " --> pdb=" O GLU A1293 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN A1298 " --> pdb=" O THR A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1312 removed outlier: 4.270A pdb=" N LEU A1309 " --> pdb=" O HIS A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1326 through 1349 removed outlier: 3.756A pdb=" N ASP A1334 " --> pdb=" O GLU A1330 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A1335 " --> pdb=" O PHE A1331 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A1342 " --> pdb=" O ASP A1338 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE A1345 " --> pdb=" O MET A1341 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A1347 " --> pdb=" O SER A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1353 through 1365 removed outlier: 3.601A pdb=" N ARG A1361 " --> pdb=" O LEU A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1378 removed outlier: 4.481A pdb=" N ASN A1372 " --> pdb=" O GLU A1368 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL A1373 " --> pdb=" O ALA A1369 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA A1374 " --> pdb=" O LEU A1370 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1382 Processing helix chain 'A' and resid 1387 through 1399 removed outlier: 3.575A pdb=" N HIS A1391 " --> pdb=" O SER A1387 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU A1395 " --> pdb=" O HIS A1391 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP A1396 " --> pdb=" O GLU A1392 " (cutoff:3.500A) Processing helix chain 'A' and resid 1417 through 1435 removed outlier: 4.510A pdb=" N GLY A1421 " --> pdb=" O PRO A1417 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A1422 " --> pdb=" O LYS A1418 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A1424 " --> pdb=" O LEU A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1450 removed outlier: 3.565A pdb=" N VAL A1442 " --> pdb=" O ASN A1438 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1475 removed outlier: 3.988A pdb=" N GLU A1466 " --> pdb=" O SER A1462 " (cutoff:3.500A) Processing helix chain 'A' and resid 1510 through 1530 removed outlier: 3.689A pdb=" N THR A1524 " --> pdb=" O GLN A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1536 through 1545 removed outlier: 4.043A pdb=" N ASP A1540 " --> pdb=" O HIS A1536 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL A1541 " --> pdb=" O PRO A1537 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A1542 " --> pdb=" O LEU A1538 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 827 through 831 removed outlier: 3.576A pdb=" N SER A 837 " --> pdb=" O HIS A 802 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 841 " --> pdb=" O MET A 798 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N SER A 794 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL A 847 " --> pdb=" O LEU A 792 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 792 " --> pdb=" O VAL A 847 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU A 849 " --> pdb=" O VAL A 790 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL A 790 " --> pdb=" O GLU A 849 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A 815 " --> pdb=" O HIS A 793 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE A 811 " --> pdb=" O ILE A 797 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 899 " --> pdb=" O GLY A 812 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 943 through 946 removed outlier: 3.643A pdb=" N GLY A 949 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1043 through 1045 removed outlier: 6.607A pdb=" N LEU A1012 " --> pdb=" O ILE A 975 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE A 975 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG A1014 " --> pdb=" O ALA A 973 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN A 968 " --> pdb=" O THR A 963 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER A 959 " --> pdb=" O VAL A 972 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU A 960 " --> pdb=" O LYS A1053 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1478 through 1479 Processing sheet with id=AA5, first strand: chain 'A' and resid 1478 through 1479 removed outlier: 3.534A pdb=" N VAL A1495 " --> pdb=" O LEU A1502 " (cutoff:3.500A) 255 hydrogen bonds defined for protein. 723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 1.06 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.53: 7230 1.53 - 1.88: 306 1.88 - 2.22: 0 2.22 - 2.56: 0 2.56 - 2.91: 1 Bond restraints: 7537 Sorted by residual: bond pdb=" C ASN A1458 " pdb=" N GLN A1460 " ideal model delta sigma weight residual 1.334 2.906 -1.572 1.42e-02 4.96e+03 1.23e+04 bond pdb=" C GLN A1460 " pdb=" O GLN A1460 " ideal model delta sigma weight residual 1.235 1.192 0.043 1.22e-02 6.72e+03 1.22e+01 bond pdb=" N ILE A1461 " pdb=" CA ILE A1461 " ideal model delta sigma weight residual 1.458 1.503 -0.045 1.41e-02 5.03e+03 1.03e+01 bond pdb=" N ILE A1464 " pdb=" CA ILE A1464 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.55e+00 bond pdb=" N PRO A 785 " pdb=" CD PRO A 785 " ideal model delta sigma weight residual 1.473 1.438 0.035 1.40e-02 5.10e+03 6.09e+00 ... (remaining 7532 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.99: 10506 8.99 - 17.99: 1 17.99 - 26.98: 0 26.98 - 35.97: 0 35.97 - 44.96: 2 Bond angle restraints: 10509 Sorted by residual: angle pdb=" O ASN A1458 " pdb=" C ASN A1458 " pdb=" N GLN A1460 " ideal model delta sigma weight residual 122.46 82.00 40.46 1.19e+00 7.06e-01 1.16e+03 angle pdb=" C ASN A1458 " pdb=" N GLN A1460 " pdb=" CA GLN A1460 " ideal model delta sigma weight residual 121.72 166.68 -44.96 1.54e+00 4.22e-01 8.53e+02 angle pdb=" CA ASN A1458 " pdb=" C ASN A1458 " pdb=" N GLN A1460 " ideal model delta sigma weight residual 115.10 131.32 -16.22 1.26e+00 6.30e-01 1.66e+02 angle pdb=" N ASN A1458 " pdb=" CA ASN A1458 " pdb=" C ASN A1458 " ideal model delta sigma weight residual 108.56 100.10 8.46 1.74e+00 3.30e-01 2.37e+01 angle pdb=" N VAL A1266 " pdb=" CA VAL A1266 " pdb=" C VAL A1266 " ideal model delta sigma weight residual 113.71 109.36 4.35 9.50e-01 1.11e+00 2.10e+01 ... (remaining 10504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.19: 4245 29.19 - 58.37: 299 58.37 - 87.56: 78 87.56 - 116.74: 2 116.74 - 145.93: 1 Dihedral angle restraints: 4625 sinusoidal: 2484 harmonic: 2141 Sorted by residual: dihedral pdb=" O4' C B 60 " pdb=" C1' C B 60 " pdb=" N1 C B 60 " pdb=" C2 C B 60 " ideal model delta sinusoidal sigma weight residual -160.00 -14.07 -145.93 1 1.50e+01 4.44e-03 7.80e+01 dihedral pdb=" CA HIS A1190 " pdb=" C HIS A1190 " pdb=" N PRO A1191 " pdb=" CA PRO A1191 " ideal model delta harmonic sigma weight residual -180.00 -155.07 -24.93 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA PHE A 814 " pdb=" C PHE A 814 " pdb=" N MET A 815 " pdb=" CA MET A 815 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 4622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1044 0.053 - 0.106: 175 0.106 - 0.159: 21 0.159 - 0.212: 4 0.212 - 0.265: 2 Chirality restraints: 1246 Sorted by residual: chirality pdb=" CA SER A1457 " pdb=" N SER A1457 " pdb=" C SER A1457 " pdb=" CB SER A1457 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA GLN A1460 " pdb=" N GLN A1460 " pdb=" C GLN A1460 " pdb=" CB GLN A1460 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C3' A B 62 " pdb=" C4' A B 62 " pdb=" O3' A B 62 " pdb=" C2' A B 62 " both_signs ideal model delta sigma weight residual False -2.48 -2.68 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1243 not shown) Planarity restraints: 1092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A1458 " 0.164 2.00e-02 2.50e+03 2.07e-01 4.30e+02 pdb=" C ASN A1458 " -0.353 2.00e-02 2.50e+03 pdb=" O ASN A1458 " 0.132 2.00e-02 2.50e+03 pdb=" N GLN A1460 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A1457 " 0.019 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" C SER A1457 " -0.071 2.00e-02 2.50e+03 pdb=" O SER A1457 " 0.027 2.00e-02 2.50e+03 pdb=" N ASN A1458 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A1460 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.26e+00 pdb=" C GLN A1460 " -0.053 2.00e-02 2.50e+03 pdb=" O GLN A1460 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE A1461 " 0.018 2.00e-02 2.50e+03 ... (remaining 1089 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 89 2.64 - 3.20: 6085 3.20 - 3.77: 11032 3.77 - 4.33: 15211 4.33 - 4.90: 24422 Nonbonded interactions: 56839 Sorted by model distance: nonbonded pdb=" OP1 C B 22 " pdb="MG MG A1802 " model vdw 2.069 2.170 nonbonded pdb=" OE1 GLN A1240 " pdb="MG MG A1801 " model vdw 2.143 2.170 nonbonded pdb=" OG SER A 966 " pdb=" O2' U B 69 " model vdw 2.200 3.040 nonbonded pdb=" OG SER A1535 " pdb=" OE1 GLU A1539 " model vdw 2.281 3.040 nonbonded pdb=" ND2 ASN A1510 " pdb=" OP1 C B 42 " model vdw 2.284 3.120 ... (remaining 56834 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.980 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.230 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 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 : 0.018 1.572 7537 Z= 1.294 Angle : 0.866 44.965 10509 Z= 0.606 Chirality : 0.042 0.265 1246 Planarity : 0.007 0.207 1092 Dihedral : 19.150 145.931 3231 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.04 % Favored : 95.68 % Rotamer: Outliers : 0.76 % Allowed : 17.85 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.30), residues: 717 helix: -1.27 (0.28), residues: 299 sheet: 0.31 (0.54), residues: 91 loop : -0.62 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1282 TYR 0.017 0.001 TYR A 965 PHE 0.012 0.001 PHE A 971 TRP 0.013 0.001 TRP A1476 HIS 0.003 0.001 HIS A1086 Details of bonding type rmsd/Z covalent geometry : bond 0.01845 / 1.29 ( 7537) covalent geometry : angle 0.86607 / 0.61 (10509) hydrogen bonds : bond 0.28299 / 17.95 ( 322) hydrogen bonds : angle 8.30982 / 5.58 ( 861) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 956 VAL cc_start: 0.8703 (t) cc_final: 0.8473 (p) outliers start: 5 outliers final: 1 residues processed: 138 average time/residue: 0.0815 time to fit residues: 14.2091 Evaluate side-chains 105 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1457 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 968 GLN ** A1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 HIS A1190 HIS A1399 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.088092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.077860 restraints weight = 19125.549| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.99 r_work: 0.3137 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7537 Z= 0.167 Angle : 0.620 8.914 10509 Z= 0.335 Chirality : 0.039 0.159 1246 Planarity : 0.005 0.045 1092 Dihedral : 18.255 145.597 1795 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.17 % Favored : 95.69 % Rotamer: Outliers : 3.03 % Allowed : 17.25 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.69 (0.29), residues: 719 helix: -0.29 (0.27), residues: 321 sheet: 0.76 (0.52), residues: 100 loop : -0.95 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1512 TYR 0.015 0.002 TYR A 965 PHE 0.023 0.002 PHE A1432 TRP 0.012 0.001 TRP A1476 HIS 0.005 0.001 HIS A1007 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 ( 7537) covalent geometry : angle 0.62021 / 0.33 (10509) hydrogen bonds : bond 0.07181 / 4.55 ( 322) hydrogen bonds : angle 5.03591 / 3.25 ( 861) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 956 VAL cc_start: 0.8795 (t) cc_final: 0.8576 (p) REVERT: A 1171 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8470 (tt) outliers start: 20 outliers final: 4 residues processed: 114 average time/residue: 0.0744 time to fit residues: 11.1722 Evaluate side-chains 96 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1270 SER Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1462 SER Chi-restraints excluded: chain A residue 1493 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 19 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 968 GLN A1007 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.084351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.073607 restraints weight = 18693.240| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.02 r_work: 0.3044 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7537 Z= 0.167 Angle : 0.618 8.919 10509 Z= 0.328 Chirality : 0.040 0.185 1246 Planarity : 0.005 0.057 1092 Dihedral : 18.188 145.541 1794 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.06 % Favored : 96.80 % Rotamer: Outliers : 3.78 % Allowed : 17.10 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.52 (0.29), residues: 719 helix: -0.03 (0.27), residues: 316 sheet: 0.76 (0.52), residues: 100 loop : -0.96 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1135 TYR 0.015 0.002 TYR A 965 PHE 0.030 0.003 PHE A 813 TRP 0.032 0.003 TRP A1476 HIS 0.008 0.002 HIS A1007 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 ( 7537) covalent geometry : angle 0.61786 / 0.33 (10509) hydrogen bonds : bond 0.06084 / 3.88 ( 322) hydrogen bonds : angle 4.68505 / 3.01 ( 861) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1249 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7307 (m-30) REVERT: A 1502 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8429 (pp) outliers start: 25 outliers final: 18 residues processed: 112 average time/residue: 0.0769 time to fit residues: 11.4036 Evaluate side-chains 109 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 967 LYS Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1126 ASP Chi-restraints excluded: chain A residue 1249 ASP Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1395 GLU Chi-restraints excluded: chain A residue 1401 LEU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1462 SER Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1502 LEU Chi-restraints excluded: chain A residue 1504 VAL Chi-restraints excluded: chain A residue 1539 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 0.0870 chunk 62 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1529 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.083268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.072777 restraints weight = 18919.917| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.99 r_work: 0.3030 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7537 Z= 0.142 Angle : 0.557 10.151 10509 Z= 0.301 Chirality : 0.038 0.168 1246 Planarity : 0.005 0.080 1092 Dihedral : 18.172 145.916 1794 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.17 % Favored : 95.69 % Rotamer: Outliers : 3.63 % Allowed : 18.31 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.45 (0.29), residues: 719 helix: 0.20 (0.28), residues: 319 sheet: 0.57 (0.51), residues: 100 loop : -1.08 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1512 TYR 0.014 0.002 TYR A 965 PHE 0.040 0.002 PHE A 813 TRP 0.019 0.002 TRP A1476 HIS 0.003 0.001 HIS A1536 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 7537) covalent geometry : angle 0.55729 / 0.30 (10509) hydrogen bonds : bond 0.05066 / 3.22 ( 322) hydrogen bonds : angle 4.49790 / 2.91 ( 861) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 1139 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7670 (mm) outliers start: 24 outliers final: 15 residues processed: 111 average time/residue: 0.0736 time to fit residues: 10.8149 Evaluate side-chains 105 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1229 TRP Chi-restraints excluded: chain A residue 1270 SER Chi-restraints excluded: chain A residue 1273 VAL Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1401 LEU Chi-restraints excluded: chain A residue 1462 SER Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1526 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 20 optimal weight: 0.0970 chunk 12 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.081661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.071134 restraints weight = 18918.282| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.99 r_work: 0.2995 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7537 Z= 0.157 Angle : 0.574 7.460 10509 Z= 0.310 Chirality : 0.039 0.170 1246 Planarity : 0.005 0.039 1092 Dihedral : 18.241 150.350 1794 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.89 % Favored : 95.97 % Rotamer: Outliers : 3.33 % Allowed : 18.91 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.45 (0.29), residues: 719 helix: 0.14 (0.27), residues: 318 sheet: 0.71 (0.53), residues: 97 loop : -1.03 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1282 TYR 0.012 0.002 TYR A1326 PHE 0.035 0.002 PHE A 813 TRP 0.023 0.002 TRP A1476 HIS 0.007 0.001 HIS A1007 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 7537) covalent geometry : angle 0.57436 / 0.31 (10509) hydrogen bonds : bond 0.05422 / 3.44 ( 322) hydrogen bonds : angle 4.51285 / 2.93 ( 861) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 1075 MET cc_start: 0.8801 (tpp) cc_final: 0.8090 (ttp) REVERT: A 1139 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8016 (mt) REVERT: A 1465 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7832 (tttm) outliers start: 22 outliers final: 18 residues processed: 105 average time/residue: 0.0804 time to fit residues: 11.1017 Evaluate side-chains 104 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 950 CYS Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1112 CYS Chi-restraints excluded: chain A residue 1126 ASP Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1270 SER Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1401 LEU Chi-restraints excluded: chain A residue 1462 SER Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1526 LEU Chi-restraints excluded: chain A residue 1539 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 64 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 0.0060 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 63 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1007 HIS ** A1184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.082592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.072020 restraints weight = 18781.573| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.01 r_work: 0.3015 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7537 Z= 0.122 Angle : 0.527 8.244 10509 Z= 0.285 Chirality : 0.038 0.160 1246 Planarity : 0.004 0.035 1092 Dihedral : 18.253 150.198 1794 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.45 % Favored : 95.41 % Rotamer: Outliers : 3.33 % Allowed : 19.82 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.30 (0.30), residues: 719 helix: 0.41 (0.28), residues: 318 sheet: 0.65 (0.53), residues: 98 loop : -1.08 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1282 TYR 0.015 0.001 TYR A 965 PHE 0.027 0.002 PHE A 813 TRP 0.024 0.002 TRP A1476 HIS 0.004 0.001 HIS A1190 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 7537) covalent geometry : angle 0.52724 / 0.28 (10509) hydrogen bonds : bond 0.04680 / 2.97 ( 322) hydrogen bonds : angle 4.37493 / 2.84 ( 861) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 1075 MET cc_start: 0.8828 (tpp) cc_final: 0.7985 (ttp) REVERT: A 1139 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8037 (mt) REVERT: A 1465 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7843 (tttm) outliers start: 22 outliers final: 17 residues processed: 106 average time/residue: 0.0791 time to fit residues: 11.0938 Evaluate side-chains 102 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1126 ASP Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1229 TRP Chi-restraints excluded: chain A residue 1270 SER Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1401 LEU Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1493 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 0.0970 chunk 72 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.081854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.071245 restraints weight = 18754.130| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.01 r_work: 0.2998 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7537 Z= 0.133 Angle : 0.539 8.115 10509 Z= 0.292 Chirality : 0.039 0.163 1246 Planarity : 0.004 0.038 1092 Dihedral : 18.270 152.142 1794 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.59 % Favored : 95.27 % Rotamer: Outliers : 3.93 % Allowed : 19.52 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.44 (0.29), residues: 719 helix: 0.26 (0.27), residues: 323 sheet: 0.62 (0.52), residues: 98 loop : -1.15 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1282 TYR 0.013 0.001 TYR A 965 PHE 0.025 0.002 PHE A1131 TRP 0.028 0.002 TRP A1476 HIS 0.008 0.001 HIS A1007 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 7537) covalent geometry : angle 0.53900 / 0.29 (10509) hydrogen bonds : bond 0.04872 / 3.10 ( 322) hydrogen bonds : angle 4.40600 / 2.87 ( 861) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.181 Fit side-chains REVERT: A 1075 MET cc_start: 0.8836 (tpp) cc_final: 0.7975 (ttp) REVERT: A 1139 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8067 (mt) REVERT: A 1465 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7936 (tttm) outliers start: 26 outliers final: 20 residues processed: 102 average time/residue: 0.0797 time to fit residues: 10.6148 Evaluate side-chains 105 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1112 CYS Chi-restraints excluded: chain A residue 1126 ASP Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1229 TRP Chi-restraints excluded: chain A residue 1270 SER Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1401 LEU Chi-restraints excluded: chain A residue 1462 SER Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain A residue 1493 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 46 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 62 optimal weight: 0.0030 chunk 9 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 0.0980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.081868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.071233 restraints weight = 19126.116| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.99 r_work: 0.3001 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7537 Z= 0.134 Angle : 0.551 8.190 10509 Z= 0.296 Chirality : 0.038 0.162 1246 Planarity : 0.004 0.050 1092 Dihedral : 18.295 153.904 1794 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.59 % Favored : 95.27 % Rotamer: Outliers : 3.78 % Allowed : 19.67 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.40 (0.29), residues: 719 helix: 0.31 (0.27), residues: 322 sheet: 0.64 (0.52), residues: 97 loop : -1.15 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1281 TYR 0.014 0.001 TYR A 965 PHE 0.032 0.002 PHE A1131 TRP 0.043 0.002 TRP A1476 HIS 0.009 0.001 HIS A1007 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 7537) covalent geometry : angle 0.55133 / 0.30 (10509) hydrogen bonds : bond 0.04731 / 3.01 ( 322) hydrogen bonds : angle 4.36852 / 2.85 ( 861) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 1075 MET cc_start: 0.8844 (tpp) cc_final: 0.8037 (ttm) REVERT: A 1139 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8064 (mt) REVERT: A 1281 ARG cc_start: 0.7090 (mmp-170) cc_final: 0.6733 (mpt-90) REVERT: A 1465 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7971 (tttm) outliers start: 25 outliers final: 20 residues processed: 101 average time/residue: 0.0827 time to fit residues: 10.9336 Evaluate side-chains 104 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1112 CYS Chi-restraints excluded: chain A residue 1126 ASP Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1229 TRP Chi-restraints excluded: chain A residue 1270 SER Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1401 LEU Chi-restraints excluded: chain A residue 1462 SER Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1526 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 31 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 19 optimal weight: 9.9990 chunk 23 optimal weight: 0.0970 chunk 1 optimal weight: 0.0170 chunk 39 optimal weight: 0.9980 chunk 48 optimal weight: 0.0870 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.083105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.072533 restraints weight = 18609.226| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.96 r_work: 0.3030 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7537 Z= 0.113 Angle : 0.523 8.256 10509 Z= 0.283 Chirality : 0.037 0.153 1246 Planarity : 0.004 0.034 1092 Dihedral : 18.311 153.298 1794 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.31 % Favored : 95.55 % Rotamer: Outliers : 3.18 % Allowed : 20.27 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.26 (0.30), residues: 719 helix: 0.54 (0.28), residues: 323 sheet: 0.54 (0.51), residues: 98 loop : -1.17 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1281 TYR 0.013 0.001 TYR A 965 PHE 0.038 0.002 PHE A1131 TRP 0.055 0.003 TRP A1476 HIS 0.012 0.001 HIS A1007 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 7537) covalent geometry : angle 0.52266 / 0.28 (10509) hydrogen bonds : bond 0.04289 / 2.73 ( 322) hydrogen bonds : angle 4.21972 / 2.75 ( 861) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 1075 MET cc_start: 0.8841 (tpp) cc_final: 0.7995 (ttm) REVERT: A 1465 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7933 (tttm) outliers start: 21 outliers final: 16 residues processed: 96 average time/residue: 0.0829 time to fit residues: 10.4196 Evaluate side-chains 99 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1126 ASP Chi-restraints excluded: chain A residue 1229 TRP Chi-restraints excluded: chain A residue 1270 SER Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1462 SER Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain A residue 1493 LEU Chi-restraints excluded: chain A residue 1496 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 64 optimal weight: 0.0370 chunk 68 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.081926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.071265 restraints weight = 18763.447| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.97 r_work: 0.3002 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7537 Z= 0.135 Angle : 0.554 8.686 10509 Z= 0.298 Chirality : 0.039 0.161 1246 Planarity : 0.004 0.037 1092 Dihedral : 18.303 155.366 1794 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.59 % Favored : 95.27 % Rotamer: Outliers : 3.03 % Allowed : 20.73 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.26 (0.30), residues: 719 helix: 0.47 (0.28), residues: 316 sheet: 0.56 (0.51), residues: 97 loop : -1.04 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1512 TYR 0.013 0.001 TYR A 965 PHE 0.038 0.002 PHE A1131 TRP 0.063 0.003 TRP A1476 HIS 0.014 0.001 HIS A1007 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 7537) covalent geometry : angle 0.55443 / 0.30 (10509) hydrogen bonds : bond 0.04685 / 2.98 ( 322) hydrogen bonds : angle 4.26320 / 2.78 ( 861) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 1139 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8165 (mt) REVERT: A 1465 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7986 (tttm) outliers start: 20 outliers final: 17 residues processed: 96 average time/residue: 0.0949 time to fit residues: 11.8007 Evaluate side-chains 100 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 950 CYS Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1126 ASP Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1229 TRP Chi-restraints excluded: chain A residue 1270 SER Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1462 SER Chi-restraints excluded: chain A residue 1465 LYS Chi-restraints excluded: chain A residue 1480 ILE Chi-restraints excluded: chain A residue 1493 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 69 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.081193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.070500 restraints weight = 18647.446| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.01 r_work: 0.2983 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7537 Z= 0.150 Angle : 0.571 9.281 10509 Z= 0.307 Chirality : 0.040 0.165 1246 Planarity : 0.004 0.037 1092 Dihedral : 18.343 159.390 1794 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.73 % Favored : 95.13 % Rotamer: Outliers : 3.33 % Allowed : 20.73 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.39 (0.29), residues: 719 helix: 0.30 (0.27), residues: 316 sheet: 0.58 (0.52), residues: 97 loop : -1.07 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1512 TYR 0.015 0.002 TYR A 965 PHE 0.040 0.002 PHE A1131 TRP 0.074 0.004 TRP A1476 HIS 0.013 0.001 HIS A1007 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 7537) covalent geometry : angle 0.57127 / 0.31 (10509) hydrogen bonds : bond 0.04906 / 3.12 ( 322) hydrogen bonds : angle 4.32446 / 2.83 ( 861) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1465.81 seconds wall clock time: 25 minutes 50.29 seconds (1550.29 seconds total)