Starting phenix.real_space_refine on Wed Aug 5 19:58:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ehh_48054/08_2026/9ehh_48054.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ehh_48054/08_2026/9ehh_48054.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ehh_48054/08_2026/9ehh_48054.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ehh_48054/08_2026/9ehh_48054.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ehh_48054/08_2026/9ehh_48054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ehh_48054/08_2026/9ehh_48054.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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 115 5.49 5 Mg 2 5.21 5 S 22 5.16 5 C 6694 2.51 5 N 1949 2.21 5 O 2410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11192 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8738 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 28, 'TRANS': 1032} Chain breaks: 6 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1814 Classifications: {'RNA': 86} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 8, 'rna3p_pur': 33, 'rna3p_pyr': 40} Link IDs: {'rna2p': 12, 'rna3p': 73} Chain: "C" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 452 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 186 Classifications: {'DNA': 9} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 8} Chain: "B" 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: 2.18, per 1000 atoms: 0.19 Number of scatterers: 11192 At special positions: 0 Unit cell: (77.4876, 112.482, 143.31, 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 22 16.00 P 115 15.00 Mg 2 11.99 O 2410 8.00 N 1949 7.00 C 6694 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: 0.70 Conformation dependent library (CDL) restraints added in 428.8 milliseconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2042 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 11 sheets defined 47.6% alpha, 13.3% beta 44 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 29 through 33 Processing helix chain 'A' and resid 52 through 82 removed outlier: 3.989A pdb=" N LYS A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 100 Processing helix chain 'A' and resid 311 through 324 Processing helix chain 'A' and resid 330 through 342 Processing helix chain 'A' and resid 349 through 362 Processing helix chain 'A' and resid 364 through 373 removed outlier: 3.844A pdb=" N LEU A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 384 through 399 Processing helix chain 'A' and resid 416 through 431 removed outlier: 3.564A pdb=" N GLN A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 466 through 474 Processing helix chain 'A' and resid 476 through 486 Processing helix chain 'A' and resid 487 through 495 Processing helix chain 'A' and resid 496 through 503 Processing helix chain 'A' and resid 529 through 543 Processing helix chain 'A' and resid 545 through 549 Processing helix chain 'A' and resid 552 through 565 Processing helix chain 'A' and resid 579 through 587 Processing helix chain 'A' and resid 606 through 623 Processing helix chain 'A' and resid 649 through 652 Processing helix chain 'A' and resid 663 through 667 Processing helix chain 'A' and resid 814 through 825 Processing helix chain 'A' and resid 860 through 887 removed outlier: 5.322A pdb=" N GLN A 879 " --> pdb=" O ASP A 875 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN A 880 " --> pdb=" O ASP A 876 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 881 " --> pdb=" O ASN A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1110 removed outlier: 3.802A pdb=" N ALA A1096 " --> pdb=" O GLN A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1115 No H-bonds generated for 'chain 'A' and resid 1113 through 1115' Processing helix chain 'A' and resid 1127 through 1131 Processing helix chain 'A' and resid 1132 through 1144 Processing helix chain 'A' and resid 1144 through 1150 Processing helix chain 'A' and resid 1159 through 1177 removed outlier: 4.011A pdb=" N LEU A1163 " --> pdb=" O SER A1159 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A1176 " --> pdb=" O ILE A1172 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS A1177 " --> pdb=" O ALA A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1213 Processing helix chain 'A' and resid 1282 through 1292 Processing helix chain 'A' and resid 1293 through 1296 removed outlier: 3.563A pdb=" N VAL A1296 " --> pdb=" O LEU A1293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1293 through 1296' Processing helix chain 'A' and resid 1308 through 1319 removed outlier: 3.880A pdb=" N LEU A1312 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1346 removed outlier: 3.679A pdb=" N ASN A1346 " --> pdb=" O ILE A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1350 Processing helix chain 'A' and resid 1355 through 1364 Processing helix chain 'A' and resid 1375 through 1384 Processing helix chain 'A' and resid 1385 through 1388 Processing helix chain 'A' and resid 1398 through 1410 Processing helix chain 'A' and resid 1416 through 1425 Processing helix chain 'A' and resid 1472 through 1476 Processing helix chain 'A' and resid 1538 through 1543 Processing helix chain 'A' and resid 1569 through 1579 Processing helix chain 'A' and resid 1586 through 1594 Processing helix chain 'A' and resid 1608 through 1624 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 25 removed outlier: 6.478A pdb=" N LYS A 4 " --> pdb=" O HIS A 892 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 25 removed outlier: 6.478A pdb=" N LYS A 4 " --> pdb=" O HIS A 892 " (cutoff:3.500A) removed outlier: 9.431A pdb=" N SER A1220 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY A 38 " --> pdb=" O SER A1220 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LYS A1222 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL A 40 " --> pdb=" O LYS A1222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 465 Processing sheet with id=AA4, first strand: chain 'A' and resid 597 through 598 Processing sheet with id=AA5, first strand: chain 'A' and resid 630 through 635 removed outlier: 7.414A pdb=" N GLU A 631 " --> pdb=" O THR A 644 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1441 through 1446 removed outlier: 4.726A pdb=" N PHE A1441 " --> pdb=" O ILE A1373 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG A1370 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N ILE A1244 " --> pdb=" O ARG A1370 " (cutoff:3.500A) removed outlier: 13.580A pdb=" N LYS A1372 " --> pdb=" O ASP A1242 " (cutoff:3.500A) removed outlier: 17.907A pdb=" N ASP A1242 " --> pdb=" O LYS A1372 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLY A1243 " --> pdb=" O ASN A1469 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN A1469 " --> pdb=" O GLY A1243 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A1467 " --> pdb=" O TYR A1245 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N GLU A1247 " --> pdb=" O TYR A1465 " (cutoff:3.500A) removed outlier: 10.995A pdb=" N TYR A1465 " --> pdb=" O GLU A1247 " (cutoff:3.500A) removed outlier: 18.089A pdb=" N TYR A1249 " --> pdb=" O PHE A1463 " (cutoff:3.500A) removed outlier: 22.719A pdb=" N PHE A1463 " --> pdb=" O TYR A1249 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1270 through 1273 removed outlier: 4.801A pdb=" N VAL A1261 " --> pdb=" O ILE A1273 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1276 through 1277 Processing sheet with id=AA9, first strand: chain 'A' and resid 1390 through 1391 Processing sheet with id=AB1, first strand: chain 'A' and resid 1491 through 1496 Processing sheet with id=AB2, first strand: chain 'A' and resid 1531 through 1533 removed outlier: 4.228A pdb=" N ILE A1547 " --> pdb=" O VAL A1533 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS A1562 " --> pdb=" O ALA A1545 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ILE A1547 " --> pdb=" O ARG A1560 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ARG A1560 " --> pdb=" O ILE A1547 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR A1549 " --> pdb=" O LYS A1558 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS A1558 " --> pdb=" O TYR A1549 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1116 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 111 hydrogen bonds 210 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2061 1.33 - 1.45: 3528 1.45 - 1.58: 5800 1.58 - 1.70: 229 1.70 - 1.83: 33 Bond restraints: 11651 Sorted by residual: bond pdb=" C1' DT D 4 " pdb=" N1 DT D 4 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.23e+01 bond pdb=" N1 U B 66 " pdb=" C2 U B 66 " ideal model delta sigma weight residual 1.381 1.412 -0.031 9.00e-03 1.23e+04 1.20e+01 bond pdb=" C3' DC C 8 " pdb=" C2' DC C 8 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.60e+00 bond pdb=" C1' DC C 20 " pdb=" N1 DC C 20 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.80e+00 bond pdb=" C3' DG D 8 " pdb=" C2' DG D 8 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.50e+00 ... (remaining 11646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 15978 3.13 - 6.26: 234 6.26 - 9.39: 34 9.39 - 12.53: 5 12.53 - 15.66: 4 Bond angle restraints: 16255 Sorted by residual: angle pdb=" C1' U B 66 " pdb=" N1 U B 66 " pdb=" C2 U B 66 " ideal model delta sigma weight residual 117.70 130.32 -12.62 1.20e+00 6.94e-01 1.11e+02 angle pdb=" O2 U B 66 " pdb=" C2 U B 66 " pdb=" N3 U B 66 " ideal model delta sigma weight residual 122.20 115.05 7.15 7.00e-01 2.04e+00 1.04e+02 angle pdb=" N1 U B 66 " pdb=" C2 U B 66 " pdb=" O2 U B 66 " ideal model delta sigma weight residual 122.80 129.91 -7.11 7.00e-01 2.04e+00 1.03e+02 angle pdb=" O5' G B 90 " pdb=" C5' G B 90 " pdb=" C4' G B 90 " ideal model delta sigma weight residual 109.40 115.50 -6.10 8.00e-01 1.56e+00 5.82e+01 angle pdb=" O5' U B 67 " pdb=" C5' U B 67 " pdb=" C4' U B 67 " ideal model delta sigma weight residual 109.40 115.09 -5.69 8.00e-01 1.56e+00 5.06e+01 ... (remaining 16250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 6715 35.72 - 71.43: 336 71.43 - 107.15: 35 107.15 - 142.87: 1 142.87 - 178.59: 1 Dihedral angle restraints: 7088 sinusoidal: 3936 harmonic: 3152 Sorted by residual: dihedral pdb=" CA ASP A 859 " pdb=" C ASP A 859 " pdb=" N GLY A 860 " pdb=" CA GLY A 860 " ideal model delta harmonic sigma weight residual -180.00 -145.05 -34.95 0 5.00e+00 4.00e-02 4.89e+01 dihedral pdb=" O4' U B 66 " pdb=" C1' U B 66 " pdb=" N1 U B 66 " pdb=" C2 U B 66 " ideal model delta sinusoidal sigma weight residual 232.00 130.47 101.53 1 1.70e+01 3.46e-03 3.99e+01 dihedral pdb=" CA PHE A1233 " pdb=" C PHE A1233 " pdb=" N ASN A1234 " pdb=" CA ASN A1234 " ideal model delta harmonic sigma weight residual -180.00 -153.64 -26.36 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 7085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1372 0.065 - 0.129: 369 0.129 - 0.193: 97 0.193 - 0.258: 9 0.258 - 0.322: 4 Chirality restraints: 1851 Sorted by residual: chirality pdb=" C3' U B 66 " pdb=" C4' U B 66 " pdb=" O3' U B 66 " pdb=" C2' U B 66 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C4' G B 90 " pdb=" C5' G B 90 " pdb=" O4' G B 90 " pdb=" C3' G B 90 " both_signs ideal model delta sigma weight residual False -2.50 -2.22 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA LYS A1595 " pdb=" N LYS A1595 " pdb=" C LYS A1595 " pdb=" CB LYS A1595 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 1848 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 849 " 0.449 9.50e-02 1.11e+02 2.03e-01 3.14e+01 pdb=" NE ARG A 849 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG A 849 " 0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG A 849 " -0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG A 849 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 452 " -0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C ASN A 452 " 0.061 2.00e-02 2.50e+03 pdb=" O ASN A 452 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN A 453 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1588 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C ASP A1588 " 0.059 2.00e-02 2.50e+03 pdb=" O ASP A1588 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS A1589 " -0.020 2.00e-02 2.50e+03 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.02: 5734 3.02 - 3.49: 11205 3.49 - 3.96: 20118 3.96 - 4.43: 23336 4.43 - 4.90: 33728 Nonbonded interactions: 94121 Sorted by model distance: nonbonded pdb=" O4' C B 18 " pdb=" C6 C B 18 " model vdw 2.544 2.672 nonbonded pdb=" O ASN A 452 " pdb=" OD1 ASN A 452 " model vdw 2.578 3.040 nonbonded pdb=" O4' C B 34 " pdb=" C6 C B 34 " model vdw 2.583 2.672 nonbonded pdb=" O4' U B 66 " pdb=" C6 U B 66 " model vdw 2.584 2.672 nonbonded pdb=" N1 G B 36 " pdb=" C4 G B 36 " model vdw 2.584 2.672 ... (remaining 94116 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.750 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.340 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 11651 Z= 0.333 Angle : 1.040 15.657 16255 Z= 0.721 Chirality : 0.064 0.322 1851 Planarity : 0.009 0.203 1656 Dihedral : 18.676 178.586 5046 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.31 % Allowed : 15.39 % Favored : 84.29 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.12 (0.24), residues: 1047 helix: -0.22 (0.22), residues: 457 sheet: 0.43 (0.44), residues: 122 loop : 0.15 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.044 0.004 ARG A 849 TYR 0.026 0.003 TYR A1160 PHE 0.044 0.002 PHE A1095 TRP 0.024 0.002 TRP A1459 HIS 0.005 0.001 HIS A 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.33 (11651) covalent geometry : angle 1.04033 / 0.72 (16255) hydrogen bonds : bond 0.14359 / 9.33 ( 507) hydrogen bonds : angle 5.84656 / 4.20 ( 1326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.231 Fit side-chains REVERT: A 32 ARG cc_start: 0.8731 (mmm-85) cc_final: 0.8116 (mtp85) REVERT: A 52 MET cc_start: 0.8952 (mmp) cc_final: 0.8735 (mmt) REVERT: A 407 GLN cc_start: 0.8439 (mm-40) cc_final: 0.7977 (tp-100) REVERT: A 408 ASP cc_start: 0.9357 (m-30) cc_final: 0.9089 (m-30) REVERT: A 410 LYS cc_start: 0.8728 (pttm) cc_final: 0.8269 (ptmm) REVERT: A 529 ASP cc_start: 0.8554 (t70) cc_final: 0.7768 (p0) REVERT: A 555 GLU cc_start: 0.9019 (tp30) cc_final: 0.8664 (tp30) REVERT: A 849 ARG cc_start: 0.9022 (mtp85) cc_final: 0.8792 (mtt90) REVERT: A 1239 MET cc_start: 0.9421 (mtp) cc_final: 0.9142 (mmm) REVERT: A 1572 LYS cc_start: 0.9024 (mtpt) cc_final: 0.8728 (mttm) outliers start: 3 outliers final: 1 residues processed: 68 average time/residue: 0.4347 time to fit residues: 32.7329 Evaluate side-chains 64 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1570 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 823 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.098416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.074143 restraints weight = 21704.931| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.46 r_work: 0.2902 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11651 Z= 0.225 Angle : 0.630 8.103 16255 Z= 0.355 Chirality : 0.046 0.473 1851 Planarity : 0.004 0.025 1656 Dihedral : 19.145 174.302 2825 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.47 % Allowed : 14.03 % Favored : 84.50 % 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: 0.85 (0.25), residues: 1047 helix: 0.90 (0.23), residues: 469 sheet: 0.60 (0.43), residues: 135 loop : 0.37 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1540 TYR 0.019 0.002 TYR A1160 PHE 0.015 0.002 PHE A1441 TRP 0.015 0.002 TRP A 79 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.23 (11651) covalent geometry : angle 0.62956 / 0.36 (16255) hydrogen bonds : bond 0.05149 / 3.42 ( 507) hydrogen bonds : angle 4.73032 / 3.36 ( 1326) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.289 Fit side-chains REVERT: A 32 ARG cc_start: 0.8768 (mmm-85) cc_final: 0.8251 (mmm-85) REVERT: A 52 MET cc_start: 0.9036 (mmp) cc_final: 0.8759 (mmt) REVERT: A 344 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8526 (tmmm) REVERT: A 407 GLN cc_start: 0.8382 (mm-40) cc_final: 0.7951 (tp-100) REVERT: A 408 ASP cc_start: 0.9259 (m-30) cc_final: 0.8936 (m-30) REVERT: A 410 LYS cc_start: 0.8769 (pttm) cc_final: 0.8400 (ptmm) REVERT: A 555 GLU cc_start: 0.9005 (tp30) cc_final: 0.8619 (tp30) REVERT: A 849 ARG cc_start: 0.9099 (mtp85) cc_final: 0.8589 (mtt90) REVERT: A 1135 GLU cc_start: 0.7350 (mm-30) cc_final: 0.6837 (mp0) REVERT: A 1239 MET cc_start: 0.9491 (mtp) cc_final: 0.8991 (mtt) REVERT: A 1563 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8019 (mm) REVERT: A 1577 MET cc_start: 0.8775 (mmm) cc_final: 0.8571 (mmt) outliers start: 14 outliers final: 5 residues processed: 77 average time/residue: 0.4974 time to fit residues: 41.9261 Evaluate side-chains 59 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 1164 ILE Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1563 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 79 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 823 HIS A 890 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.098597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.074204 restraints weight = 21969.973| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.48 r_work: 0.2904 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11651 Z= 0.170 Angle : 0.561 8.720 16255 Z= 0.322 Chirality : 0.043 0.433 1851 Planarity : 0.003 0.027 1656 Dihedral : 18.907 173.642 2823 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.47 % Allowed : 14.24 % Favored : 84.29 % 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: 1.22 (0.26), residues: 1047 helix: 1.34 (0.24), residues: 462 sheet: 0.59 (0.42), residues: 136 loop : 0.48 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1540 TYR 0.014 0.001 TYR A1329 PHE 0.012 0.001 PHE A1119 TRP 0.012 0.001 TRP A 79 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (11651) covalent geometry : angle 0.56085 / 0.32 (16255) hydrogen bonds : bond 0.04651 / 3.11 ( 507) hydrogen bonds : angle 4.49344 / 3.19 ( 1326) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.409 Fit side-chains REVERT: A 32 ARG cc_start: 0.8745 (mmm-85) cc_final: 0.8283 (mmm-85) REVERT: A 344 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8479 (tmmm) REVERT: A 407 GLN cc_start: 0.8375 (mm-40) cc_final: 0.7853 (tp-100) REVERT: A 408 ASP cc_start: 0.9228 (m-30) cc_final: 0.8917 (m-30) REVERT: A 410 LYS cc_start: 0.8788 (pttm) cc_final: 0.8250 (ptmm) REVERT: A 555 GLU cc_start: 0.9016 (tp30) cc_final: 0.8563 (tp30) REVERT: A 591 GLN cc_start: 0.9021 (tp40) cc_final: 0.8721 (mm-40) REVERT: A 849 ARG cc_start: 0.9085 (mtp85) cc_final: 0.8661 (mtt90) REVERT: A 890 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7946 (mm-40) REVERT: A 1135 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7064 (mp0) REVERT: A 1239 MET cc_start: 0.9476 (mtp) cc_final: 0.9063 (mtt) outliers start: 14 outliers final: 7 residues processed: 72 average time/residue: 0.4219 time to fit residues: 34.1297 Evaluate side-chains 60 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1164 ILE Chi-restraints excluded: chain A residue 1307 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 105 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.1980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 823 HIS A 889 HIS A 890 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.099232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.074965 restraints weight = 21899.062| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.48 r_work: 0.2921 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11651 Z= 0.131 Angle : 0.520 8.361 16255 Z= 0.300 Chirality : 0.041 0.420 1851 Planarity : 0.003 0.030 1656 Dihedral : 18.855 173.636 2823 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.57 % Allowed : 14.14 % Favored : 84.29 % 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: 1.50 (0.26), residues: 1047 helix: 1.64 (0.24), residues: 461 sheet: 0.72 (0.43), residues: 134 loop : 0.56 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1540 TYR 0.012 0.001 TYR A1160 PHE 0.012 0.001 PHE A1209 TRP 0.012 0.001 TRP A 79 HIS 0.012 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (11651) covalent geometry : angle 0.51959 / 0.30 (16255) hydrogen bonds : bond 0.04210 / 2.82 ( 507) hydrogen bonds : angle 4.30073 / 3.05 ( 1326) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.405 Fit side-chains REVERT: A 1 MET cc_start: 0.4222 (tmt) cc_final: 0.3945 (tmt) REVERT: A 32 ARG cc_start: 0.8726 (mmm-85) cc_final: 0.8348 (mmm-85) REVERT: A 52 MET cc_start: 0.8948 (mmt) cc_final: 0.8603 (mmt) REVERT: A 344 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8481 (tmmm) REVERT: A 407 GLN cc_start: 0.8374 (mm-40) cc_final: 0.7824 (tp-100) REVERT: A 408 ASP cc_start: 0.9217 (m-30) cc_final: 0.8914 (m-30) REVERT: A 410 LYS cc_start: 0.8791 (pttm) cc_final: 0.8232 (ptmm) REVERT: A 555 GLU cc_start: 0.9026 (tp30) cc_final: 0.8571 (tp30) REVERT: A 591 GLN cc_start: 0.8998 (tp40) cc_final: 0.8675 (mm-40) REVERT: A 849 ARG cc_start: 0.9097 (mtp85) cc_final: 0.8670 (mtt90) REVERT: A 890 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8589 (mt0) REVERT: A 1135 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7050 (mp0) REVERT: A 1239 MET cc_start: 0.9464 (mtp) cc_final: 0.9090 (mtt) outliers start: 15 outliers final: 5 residues processed: 76 average time/residue: 0.5054 time to fit residues: 42.3775 Evaluate side-chains 61 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1307 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 36 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 823 HIS A 890 GLN A1157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.094958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.070661 restraints weight = 21969.259| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.47 r_work: 0.2841 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 11651 Z= 0.296 Angle : 0.649 9.802 16255 Z= 0.357 Chirality : 0.047 0.461 1851 Planarity : 0.004 0.037 1656 Dihedral : 18.819 173.772 2823 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.30 % Allowed : 14.14 % Favored : 83.56 % 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: 1.28 (0.26), residues: 1047 helix: 1.51 (0.24), residues: 460 sheet: 0.67 (0.43), residues: 134 loop : 0.36 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1540 TYR 0.015 0.002 TYR A1329 PHE 0.018 0.002 PHE A1398 TRP 0.011 0.002 TRP A 87 HIS 0.007 0.002 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00652 / 0.30 (11651) covalent geometry : angle 0.64911 / 0.36 (16255) hydrogen bonds : bond 0.05053 / 3.39 ( 507) hydrogen bonds : angle 4.51303 / 3.19 ( 1326) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4490 (tmt) cc_final: 0.4084 (tmt) REVERT: A 32 ARG cc_start: 0.8812 (mmm-85) cc_final: 0.8445 (mmm-85) REVERT: A 43 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9063 (mp) REVERT: A 52 MET cc_start: 0.8988 (mmt) cc_final: 0.8645 (mmt) REVERT: A 408 ASP cc_start: 0.9234 (m-30) cc_final: 0.8989 (m-30) REVERT: A 555 GLU cc_start: 0.9035 (tp30) cc_final: 0.8537 (tp30) REVERT: A 591 GLN cc_start: 0.9066 (tp40) cc_final: 0.8461 (tp40) REVERT: A 849 ARG cc_start: 0.9153 (mtp85) cc_final: 0.8690 (mtt90) REVERT: A 1135 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7116 (mp0) REVERT: A 1239 MET cc_start: 0.9460 (mtp) cc_final: 0.9132 (mtt) REVERT: A 1308 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.8830 (p) REVERT: A 1416 ASP cc_start: 0.8739 (t0) cc_final: 0.8240 (t70) outliers start: 22 outliers final: 11 residues processed: 74 average time/residue: 0.4905 time to fit residues: 40.3928 Evaluate side-chains 64 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1487 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 3 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 ASN A 407 GLN A 823 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.097080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.072844 restraints weight = 22143.513| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.47 r_work: 0.2878 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11651 Z= 0.148 Angle : 0.540 8.314 16255 Z= 0.308 Chirality : 0.041 0.420 1851 Planarity : 0.003 0.034 1656 Dihedral : 18.824 172.881 2823 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.68 % Allowed : 15.50 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.26), residues: 1047 helix: 1.69 (0.24), residues: 459 sheet: 0.69 (0.43), residues: 134 loop : 0.40 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1540 TYR 0.015 0.001 TYR A1160 PHE 0.010 0.001 PHE A1576 TRP 0.012 0.001 TRP A 79 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (11651) covalent geometry : angle 0.54008 / 0.31 (16255) hydrogen bonds : bond 0.04347 / 2.93 ( 507) hydrogen bonds : angle 4.31826 / 3.05 ( 1326) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.403 Fit side-chains REVERT: A 1 MET cc_start: 0.4389 (tmt) cc_final: 0.3337 (tmt) REVERT: A 32 ARG cc_start: 0.8756 (mmm-85) cc_final: 0.8379 (mmm-85) REVERT: A 52 MET cc_start: 0.8986 (mmt) cc_final: 0.8614 (mmt) REVERT: A 407 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8161 (mm110) REVERT: A 408 ASP cc_start: 0.9224 (m-30) cc_final: 0.8946 (m-30) REVERT: A 410 LYS cc_start: 0.8792 (pttm) cc_final: 0.8590 (pttt) REVERT: A 555 GLU cc_start: 0.9048 (tp30) cc_final: 0.8550 (tp30) REVERT: A 591 GLN cc_start: 0.9026 (tp40) cc_final: 0.8407 (tp40) REVERT: A 849 ARG cc_start: 0.9151 (mtp85) cc_final: 0.8934 (mtp85) REVERT: A 1135 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7093 (mp0) REVERT: A 1239 MET cc_start: 0.9447 (mtp) cc_final: 0.9133 (mtt) REVERT: A 1358 MET cc_start: 0.8519 (tpt) cc_final: 0.8212 (tpp) REVERT: A 1416 ASP cc_start: 0.8715 (t0) cc_final: 0.8227 (t70) REVERT: A 1540 ARG cc_start: 0.9163 (mmm160) cc_final: 0.8947 (mmm160) outliers start: 16 outliers final: 9 residues processed: 73 average time/residue: 0.4718 time to fit residues: 38.4363 Evaluate side-chains 65 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1622 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 1 optimal weight: 0.2980 chunk 64 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 ASN A 823 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.097628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.073470 restraints weight = 21948.882| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.47 r_work: 0.2895 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11651 Z= 0.139 Angle : 0.540 13.401 16255 Z= 0.302 Chirality : 0.041 0.409 1851 Planarity : 0.003 0.036 1656 Dihedral : 18.753 172.834 2823 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.68 % Allowed : 16.02 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.26), residues: 1047 helix: 1.76 (0.24), residues: 462 sheet: 0.74 (0.43), residues: 134 loop : 0.42 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1540 TYR 0.016 0.001 TYR A1160 PHE 0.024 0.001 PHE A1209 TRP 0.012 0.001 TRP A 79 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (11651) covalent geometry : angle 0.53997 / 0.30 (16255) hydrogen bonds : bond 0.04156 / 2.81 ( 507) hydrogen bonds : angle 4.22333 / 2.99 ( 1326) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4580 (tmt) cc_final: 0.3582 (tmt) REVERT: A 32 ARG cc_start: 0.8749 (mmm-85) cc_final: 0.8312 (mtp85) REVERT: A 52 MET cc_start: 0.8978 (mmt) cc_final: 0.8606 (mmt) REVERT: A 408 ASP cc_start: 0.9207 (m-30) cc_final: 0.8928 (m-30) REVERT: A 555 GLU cc_start: 0.9054 (tp30) cc_final: 0.8543 (tp30) REVERT: A 591 GLN cc_start: 0.9034 (tp40) cc_final: 0.8428 (tp40) REVERT: A 849 ARG cc_start: 0.9154 (mtp85) cc_final: 0.8952 (mtp85) REVERT: A 1135 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7116 (mp0) REVERT: A 1239 MET cc_start: 0.9450 (mtp) cc_final: 0.9061 (mtt) REVERT: A 1358 MET cc_start: 0.8518 (tpt) cc_final: 0.8187 (tpp) REVERT: A 1416 ASP cc_start: 0.8706 (t0) cc_final: 0.8203 (t70) REVERT: A 1540 ARG cc_start: 0.9138 (mmm160) cc_final: 0.8936 (mmm160) REVERT: A 1551 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8669 (pp) outliers start: 16 outliers final: 8 residues processed: 76 average time/residue: 0.4983 time to fit residues: 41.9829 Evaluate side-chains 67 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1551 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 53 optimal weight: 0.1980 chunk 101 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 4 optimal weight: 0.0980 chunk 90 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 ASN A 407 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.098129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.073975 restraints weight = 21987.798| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.48 r_work: 0.2909 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11651 Z= 0.133 Angle : 0.522 10.062 16255 Z= 0.294 Chirality : 0.040 0.401 1851 Planarity : 0.003 0.035 1656 Dihedral : 18.709 172.604 2823 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.47 % Allowed : 16.86 % Favored : 81.68 % 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: 1.56 (0.26), residues: 1047 helix: 1.87 (0.24), residues: 462 sheet: 0.71 (0.43), residues: 134 loop : 0.38 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 633 TYR 0.015 0.001 TYR A1160 PHE 0.015 0.001 PHE A1209 TRP 0.012 0.001 TRP A 79 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (11651) covalent geometry : angle 0.52232 / 0.29 (16255) hydrogen bonds : bond 0.04027 / 2.74 ( 507) hydrogen bonds : angle 4.12190 / 2.92 ( 1326) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.403 Fit side-chains REVERT: A 1 MET cc_start: 0.4585 (tmt) cc_final: 0.3507 (tmt) REVERT: A 32 ARG cc_start: 0.8751 (mmm-85) cc_final: 0.8341 (mtp85) REVERT: A 52 MET cc_start: 0.8960 (mmt) cc_final: 0.8630 (mmt) REVERT: A 407 GLN cc_start: 0.8371 (mm-40) cc_final: 0.8166 (mm110) REVERT: A 408 ASP cc_start: 0.9198 (m-30) cc_final: 0.8900 (m-30) REVERT: A 555 GLU cc_start: 0.9060 (tp30) cc_final: 0.8552 (tp30) REVERT: A 591 GLN cc_start: 0.9021 (tp40) cc_final: 0.8415 (tp40) REVERT: A 863 LYS cc_start: 0.8253 (tttp) cc_final: 0.8044 (tptm) REVERT: A 1135 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7078 (mp0) REVERT: A 1239 MET cc_start: 0.9451 (mtp) cc_final: 0.9053 (mtt) REVERT: A 1358 MET cc_start: 0.8526 (tpt) cc_final: 0.8181 (tpp) REVERT: A 1416 ASP cc_start: 0.8693 (t0) cc_final: 0.8213 (t70) REVERT: A 1551 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8679 (pp) outliers start: 14 outliers final: 7 residues processed: 71 average time/residue: 0.5395 time to fit residues: 42.1485 Evaluate side-chains 64 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1622 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 9 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 36 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 ASN A 823 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.097680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.073099 restraints weight = 21631.600| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.51 r_work: 0.2893 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11651 Z= 0.151 Angle : 0.538 10.536 16255 Z= 0.301 Chirality : 0.041 0.404 1851 Planarity : 0.003 0.036 1656 Dihedral : 18.684 172.359 2823 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.05 % Allowed : 17.38 % Favored : 81.57 % 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: 1.55 (0.26), residues: 1047 helix: 1.90 (0.24), residues: 462 sheet: 0.72 (0.43), residues: 134 loop : 0.32 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1540 TYR 0.016 0.001 TYR A1160 PHE 0.014 0.001 PHE A1209 TRP 0.011 0.001 TRP A 79 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (11651) covalent geometry : angle 0.53841 / 0.30 (16255) hydrogen bonds : bond 0.04076 / 2.76 ( 507) hydrogen bonds : angle 4.10501 / 2.90 ( 1326) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.396 Fit side-chains REVERT: A 1 MET cc_start: 0.4604 (tmt) cc_final: 0.3589 (tmt) REVERT: A 32 ARG cc_start: 0.8768 (mmm-85) cc_final: 0.8377 (mtp85) REVERT: A 52 MET cc_start: 0.8959 (mmt) cc_final: 0.8624 (mmt) REVERT: A 410 LYS cc_start: 0.8764 (pttm) cc_final: 0.8441 (pttm) REVERT: A 426 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7465 (mp10) REVERT: A 555 GLU cc_start: 0.9057 (tp30) cc_final: 0.8539 (tp30) REVERT: A 591 GLN cc_start: 0.9029 (tp40) cc_final: 0.8416 (tp40) REVERT: A 863 LYS cc_start: 0.8276 (tttp) cc_final: 0.8009 (tptm) REVERT: A 1135 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7068 (mp0) REVERT: A 1239 MET cc_start: 0.9451 (mtp) cc_final: 0.9055 (mtt) REVERT: A 1358 MET cc_start: 0.8541 (tpt) cc_final: 0.8188 (tpp) REVERT: A 1416 ASP cc_start: 0.8709 (t0) cc_final: 0.8216 (t70) REVERT: A 1551 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8681 (pp) outliers start: 10 outliers final: 7 residues processed: 63 average time/residue: 0.4909 time to fit residues: 34.3858 Evaluate side-chains 65 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 426 GLN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1622 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 1 optimal weight: 0.0470 chunk 79 optimal weight: 0.5980 chunk 111 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.097906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.073889 restraints weight = 21951.262| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.45 r_work: 0.2903 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11651 Z= 0.139 Angle : 0.529 10.105 16255 Z= 0.296 Chirality : 0.040 0.397 1851 Planarity : 0.003 0.036 1656 Dihedral : 18.660 171.914 2823 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.94 % Allowed : 17.80 % Favored : 81.26 % 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: 1.57 (0.26), residues: 1047 helix: 1.93 (0.24), residues: 462 sheet: 0.71 (0.44), residues: 134 loop : 0.31 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 849 TYR 0.017 0.001 TYR A1160 PHE 0.014 0.001 PHE A1209 TRP 0.011 0.001 TRP A 79 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (11651) covalent geometry : angle 0.52865 / 0.30 (16255) hydrogen bonds : bond 0.03979 / 2.70 ( 507) hydrogen bonds : angle 4.05212 / 2.87 ( 1326) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.393 Fit side-chains REVERT: A 1 MET cc_start: 0.4757 (tmt) cc_final: 0.3848 (tmt) REVERT: A 32 ARG cc_start: 0.8791 (mmm-85) cc_final: 0.8386 (mtp85) REVERT: A 52 MET cc_start: 0.8940 (mmt) cc_final: 0.8599 (mmt) REVERT: A 555 GLU cc_start: 0.9051 (tp30) cc_final: 0.8524 (tp30) REVERT: A 591 GLN cc_start: 0.9031 (tp40) cc_final: 0.8414 (tp40) REVERT: A 863 LYS cc_start: 0.8248 (tttp) cc_final: 0.7860 (tptm) REVERT: A 1135 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7114 (mp0) REVERT: A 1239 MET cc_start: 0.9438 (mtp) cc_final: 0.9044 (mtt) REVERT: A 1416 ASP cc_start: 0.8697 (t0) cc_final: 0.8196 (t70) REVERT: A 1551 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8663 (pp) REVERT: A 1577 MET cc_start: 0.8767 (tpp) cc_final: 0.8502 (mmt) outliers start: 9 outliers final: 7 residues processed: 61 average time/residue: 0.4825 time to fit residues: 32.8662 Evaluate side-chains 63 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1551 ILE Chi-restraints excluded: chain A residue 1622 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 0.0570 chunk 79 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.098696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.074658 restraints weight = 21958.604| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.46 r_work: 0.2929 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11651 Z= 0.126 Angle : 0.515 10.052 16255 Z= 0.289 Chirality : 0.039 0.386 1851 Planarity : 0.003 0.036 1656 Dihedral : 18.617 171.482 2823 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.05 % Allowed : 17.70 % Favored : 81.26 % 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: 1.63 (0.26), residues: 1047 helix: 2.01 (0.24), residues: 461 sheet: 0.71 (0.44), residues: 134 loop : 0.33 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1540 TYR 0.016 0.001 TYR A1160 PHE 0.013 0.001 PHE A1209 TRP 0.012 0.001 TRP A 79 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (11651) covalent geometry : angle 0.51463 / 0.29 (16255) hydrogen bonds : bond 0.03843 / 2.62 ( 507) hydrogen bonds : angle 3.97256 / 2.81 ( 1326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2698.01 seconds wall clock time: 47 minutes 11.51 seconds (2831.51 seconds total)