Starting phenix.real_space_refine on Fri Jul 3 02:04:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ehh_48054/07_2026/9ehh_48054.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ehh_48054/07_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_48054/07_2026/9ehh_48054.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ehh_48054/07_2026/9ehh_48054.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ehh_48054/07_2026/9ehh_48054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ehh_48054/07_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): 0.00s 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: 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: 1.84, per 1000 atoms: 0.16 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: 0.82 Conformation dependent library (CDL) restraints added in 339.4 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: 1.27 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: 3.12 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 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: 15987 3.13 - 6.26: 225 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=" C1' U B 66 " pdb=" N1 U B 66 " pdb=" C6 U B 66 " ideal model delta sigma weight residual 121.20 111.64 9.56 1.40e+00 5.10e-01 4.67e+01 angle pdb=" O4' DG D 3 " pdb=" C1' DG D 3 " pdb=" N9 DG D 3 " ideal model delta sigma weight residual 108.00 112.77 -4.77 7.00e-01 2.04e+00 4.64e+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: 1455 0.065 - 0.129: 331 0.129 - 0.193: 54 0.193 - 0.258: 7 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: 5.100 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: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.480 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:5.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.800 ------------------------------------------------------------------------------- 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= 0.321 Angle : 0.997 15.657 16255 Z= 0.671 Chirality : 0.057 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 0.00526 / 0.32 (11651) covalent geometry : angle 0.99731 / 0.67 (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 : 0.373 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: 0.4378 time to fit residues: 33.0910 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 : 0.387 ------------------------------------------------------------------------------- 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: 7.9990 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 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: 1.8186 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.097873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.073606 restraints weight = 21729.144| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.47 r_work: 0.2892 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11651 Z= 0.247 Angle : 0.631 7.452 16255 Z= 0.361 Chirality : 0.045 0.274 1851 Planarity : 0.004 0.027 1656 Dihedral : 19.185 172.672 2825 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: 0.84 (0.25), residues: 1047 helix: 0.88 (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 0.010 0.001 ARG A1540 TYR 0.018 0.002 TYR A1160 PHE 0.015 0.002 PHE A1441 TRP 0.016 0.002 TRP A 79 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.25 (11651) covalent geometry : angle 0.63073 / 0.36 (16255) hydrogen bonds : bond 0.05310 / 3.53 ( 507) hydrogen bonds : angle 4.76270 / 3.38 ( 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 81 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8770 (mmm-85) cc_final: 0.8252 (mmm-85) REVERT: A 52 MET cc_start: 0.9039 (mmp) cc_final: 0.8766 (mmt) REVERT: A 344 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8526 (tmmm) REVERT: A 407 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7960 (tp-100) REVERT: A 408 ASP cc_start: 0.9261 (m-30) cc_final: 0.8923 (m-30) REVERT: A 410 LYS cc_start: 0.8771 (pttm) cc_final: 0.8405 (ptmm) REVERT: A 555 GLU cc_start: 0.9002 (tp30) cc_final: 0.8619 (tp30) REVERT: A 849 ARG cc_start: 0.9112 (mtp85) cc_final: 0.8602 (mtt90) REVERT: A 1135 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6989 (mp0) REVERT: A 1239 MET cc_start: 0.9496 (mtp) cc_final: 0.9004 (mtt) REVERT: A 1563 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8027 (mm) REVERT: A 1577 MET cc_start: 0.8805 (mmm) cc_final: 0.8599 (mmt) outliers start: 15 outliers final: 6 residues processed: 77 average time/residue: 0.4444 time to fit residues: 37.5462 Evaluate side-chains 62 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 1487 ILE 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: 5.9990 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 12 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.097975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.073590 restraints weight = 21999.552| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.48 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: 0.8824 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11651 Z= 0.179 Angle : 0.556 6.423 16255 Z= 0.323 Chirality : 0.042 0.251 1851 Planarity : 0.003 0.033 1656 Dihedral : 19.034 171.545 2823 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.57 % Allowed : 13.82 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.26), residues: 1047 helix: 1.36 (0.24), residues: 462 sheet: 0.58 (0.42), residues: 136 loop : 0.49 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1540 TYR 0.017 0.001 TYR A1160 PHE 0.015 0.002 PHE A1119 TRP 0.013 0.001 TRP A 79 HIS 0.003 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (11651) covalent geometry : angle 0.55607 / 0.32 (16255) hydrogen bonds : bond 0.04584 / 3.06 ( 507) hydrogen bonds : angle 4.46229 / 3.17 ( 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 78 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4516 (tmt) cc_final: 0.3072 (tmt) REVERT: A 32 ARG cc_start: 0.8738 (mmm-85) cc_final: 0.8282 (mmm-85) REVERT: A 43 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9085 (mp) REVERT: A 344 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8486 (tmmm) REVERT: A 407 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7848 (tp-100) REVERT: A 408 ASP cc_start: 0.9224 (m-30) cc_final: 0.8906 (m-30) REVERT: A 410 LYS cc_start: 0.8798 (pttm) cc_final: 0.8259 (ptmm) REVERT: A 555 GLU cc_start: 0.9041 (tp30) cc_final: 0.8580 (tm-30) REVERT: A 591 GLN cc_start: 0.9022 (tp40) cc_final: 0.8731 (mm-40) REVERT: A 849 ARG cc_start: 0.9093 (mtp85) cc_final: 0.8667 (mtt90) REVERT: A 890 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7980 (mm-40) REVERT: A 1135 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7117 (mp0) REVERT: A 1239 MET cc_start: 0.9463 (mtp) cc_final: 0.9075 (mtt) REVERT: A 1540 ARG cc_start: 0.9210 (mmm160) cc_final: 0.8930 (mmm160) outliers start: 15 outliers final: 5 residues processed: 76 average time/residue: 0.3805 time to fit residues: 32.2335 Evaluate side-chains 61 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU 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 1117 ILE Chi-restraints excluded: chain A residue 1133 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: 3.9990 chunk 46 optimal weight: 0.2980 chunk 105 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.097447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.073158 restraints weight = 21993.271| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.48 r_work: 0.2884 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11651 Z= 0.182 Angle : 0.538 6.242 16255 Z= 0.312 Chirality : 0.041 0.249 1851 Planarity : 0.003 0.034 1656 Dihedral : 18.976 171.691 2823 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.20 % Allowed : 13.51 % 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: 1.43 (0.26), residues: 1047 helix: 1.60 (0.24), residues: 461 sheet: 0.62 (0.43), residues: 134 loop : 0.52 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1540 TYR 0.015 0.001 TYR A1160 PHE 0.011 0.001 PHE A1398 TRP 0.012 0.001 TRP A 79 HIS 0.010 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (11651) covalent geometry : angle 0.53820 / 0.31 (16255) hydrogen bonds : bond 0.04380 / 2.94 ( 507) hydrogen bonds : angle 4.38007 / 3.10 ( 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 82 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.358 Fit side-chains REVERT: A 1 MET cc_start: 0.4495 (OUTLIER) cc_final: 0.3635 (tmt) REVERT: A 32 ARG cc_start: 0.8744 (mmm-85) cc_final: 0.8359 (mmm-85) REVERT: A 43 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9100 (mp) REVERT: A 52 MET cc_start: 0.8994 (mmt) cc_final: 0.8640 (mmt) REVERT: A 344 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8460 (tmmm) REVERT: A 407 GLN cc_start: 0.8394 (mm-40) cc_final: 0.7848 (tp-100) REVERT: A 408 ASP cc_start: 0.9234 (m-30) cc_final: 0.8909 (m-30) REVERT: A 410 LYS cc_start: 0.8811 (pttm) cc_final: 0.8279 (ptmm) REVERT: A 555 GLU cc_start: 0.9053 (tp30) cc_final: 0.8571 (tp30) REVERT: A 849 ARG cc_start: 0.9138 (mtp85) cc_final: 0.8702 (mtt90) REVERT: A 1135 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7031 (mp0) REVERT: A 1239 MET cc_start: 0.9467 (mtp) cc_final: 0.9125 (mtt) REVERT: A 1540 ARG cc_start: 0.9184 (mmm160) cc_final: 0.8963 (mmm160) outliers start: 21 outliers final: 8 residues processed: 78 average time/residue: 0.4053 time to fit residues: 35.1068 Evaluate side-chains 65 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 43 LEU 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 891 LEU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1212 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: 1.9990 chunk 19 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.096790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.072576 restraints weight = 21853.996| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.46 r_work: 0.2886 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11651 Z= 0.183 Angle : 0.539 7.633 16255 Z= 0.311 Chirality : 0.041 0.247 1851 Planarity : 0.003 0.035 1656 Dihedral : 18.913 171.290 2823 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.09 % Allowed : 14.35 % 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: 1.43 (0.26), residues: 1047 helix: 1.63 (0.24), residues: 461 sheet: 0.66 (0.43), residues: 134 loop : 0.47 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 633 TYR 0.013 0.001 TYR A1329 PHE 0.011 0.001 PHE A1398 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 0.00392 / 0.18 (11651) covalent geometry : angle 0.53912 / 0.31 (16255) hydrogen bonds : bond 0.04336 / 2.91 ( 507) hydrogen bonds : angle 4.32462 / 3.06 ( 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 79 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.274 Fit side-chains REVERT: A 1 MET cc_start: 0.4605 (OUTLIER) cc_final: 0.3853 (tmt) REVERT: A 32 ARG cc_start: 0.8740 (mmm-85) cc_final: 0.8346 (mmm-85) REVERT: A 52 MET cc_start: 0.8997 (mmt) cc_final: 0.8625 (mmt) REVERT: A 344 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8462 (tmmm) REVERT: A 407 GLN cc_start: 0.8413 (mm-40) cc_final: 0.7871 (tp-100) REVERT: A 408 ASP cc_start: 0.9228 (m-30) cc_final: 0.8889 (m-30) REVERT: A 410 LYS cc_start: 0.8798 (pttm) cc_final: 0.8255 (ptmm) REVERT: A 555 GLU cc_start: 0.9052 (tp30) cc_final: 0.8555 (tp30) REVERT: A 591 GLN cc_start: 0.9001 (tp40) cc_final: 0.8766 (mm-40) REVERT: A 849 ARG cc_start: 0.9149 (mtp85) cc_final: 0.8936 (mtp85) REVERT: A 1135 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7020 (mp0) REVERT: A 1239 MET cc_start: 0.9464 (mtp) cc_final: 0.9141 (mtt) REVERT: A 1416 ASP cc_start: 0.8697 (t0) cc_final: 0.8228 (t70) REVERT: A 1577 MET cc_start: 0.8861 (tpp) cc_final: 0.8535 (mmm) outliers start: 20 outliers final: 8 residues processed: 78 average time/residue: 0.4143 time to fit residues: 35.6998 Evaluate side-chains 63 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 21 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 891 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 3 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.096813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.072569 restraints weight = 22139.803| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.47 r_work: 0.2886 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11651 Z= 0.173 Angle : 0.536 8.174 16255 Z= 0.308 Chirality : 0.041 0.244 1851 Planarity : 0.003 0.036 1656 Dihedral : 18.891 171.221 2823 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.51 % Allowed : 14.76 % Favored : 82.72 % 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: 1.47 (0.26), residues: 1047 helix: 1.71 (0.24), residues: 461 sheet: 0.66 (0.43), residues: 134 loop : 0.43 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1540 TYR 0.013 0.001 TYR A1160 PHE 0.011 0.001 PHE A1398 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 0.00372 / 0.17 (11651) covalent geometry : angle 0.53640 / 0.31 (16255) hydrogen bonds : bond 0.04254 / 2.85 ( 507) hydrogen bonds : angle 4.27768 / 3.03 ( 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 86 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4537 (OUTLIER) cc_final: 0.3679 (tmt) REVERT: A 32 ARG cc_start: 0.8730 (mmm-85) cc_final: 0.8367 (mmm-85) REVERT: A 52 MET cc_start: 0.8995 (mmt) cc_final: 0.8658 (mmt) REVERT: A 344 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8447 (tmmm) REVERT: A 408 ASP cc_start: 0.9216 (m-30) cc_final: 0.8945 (m-30) REVERT: A 555 GLU cc_start: 0.9052 (tp30) cc_final: 0.8553 (tp30) REVERT: A 849 ARG cc_start: 0.9154 (mtp85) cc_final: 0.8947 (mtp85) REVERT: A 1135 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7010 (mp0) REVERT: A 1239 MET cc_start: 0.9464 (mtp) cc_final: 0.9157 (mtt) REVERT: A 1358 MET cc_start: 0.8548 (tpt) cc_final: 0.8199 (tpp) REVERT: A 1416 ASP cc_start: 0.8703 (t0) cc_final: 0.8226 (t70) outliers start: 24 outliers final: 14 residues processed: 84 average time/residue: 0.3353 time to fit residues: 31.6250 Evaluate side-chains 70 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 21 SER 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 608 LEU Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 1117 ILE 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 1308 THR 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: 3.9990 chunk 64 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 83 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.3402 r_free = 0.3402 target = 0.096411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.072177 restraints weight = 22024.170| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.48 r_work: 0.2877 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11651 Z= 0.181 Angle : 0.543 9.539 16255 Z= 0.309 Chirality : 0.041 0.243 1851 Planarity : 0.003 0.036 1656 Dihedral : 18.864 171.027 2823 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.30 % Allowed : 15.39 % 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: 1.47 (0.26), residues: 1047 helix: 1.71 (0.24), residues: 462 sheet: 0.67 (0.43), residues: 134 loop : 0.43 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 633 TYR 0.014 0.001 TYR A1160 PHE 0.024 0.001 PHE A1209 TRP 0.011 0.001 TRP A 79 HIS 0.005 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (11651) covalent geometry : angle 0.54264 / 0.31 (16255) hydrogen bonds : bond 0.04260 / 2.88 ( 507) hydrogen bonds : angle 4.26206 / 3.02 ( 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 76 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4434 (OUTLIER) cc_final: 0.3623 (tmt) REVERT: A 32 ARG cc_start: 0.8772 (mmm-85) cc_final: 0.8399 (mmm-85) REVERT: A 52 MET cc_start: 0.8976 (mmt) cc_final: 0.8632 (mmt) REVERT: A 344 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8435 (tmmm) REVERT: A 408 ASP cc_start: 0.9215 (m-30) cc_final: 0.8953 (m-30) REVERT: A 555 GLU cc_start: 0.9044 (tp30) cc_final: 0.8532 (tp30) REVERT: A 849 ARG cc_start: 0.9151 (mtp85) cc_final: 0.8947 (mtp85) REVERT: A 1135 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7086 (mp0) REVERT: A 1239 MET cc_start: 0.9444 (mtp) cc_final: 0.9059 (mtt) REVERT: A 1416 ASP cc_start: 0.8715 (t0) cc_final: 0.8213 (t70) REVERT: A 1540 ARG cc_start: 0.9110 (mmm160) cc_final: 0.8907 (mmm160) REVERT: A 1551 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8734 (pp) outliers start: 22 outliers final: 12 residues processed: 71 average time/residue: 0.4028 time to fit residues: 31.9295 Evaluate side-chains 67 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 21 SER 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 608 LEU Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1307 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 53 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 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: 9.9990 chunk 4 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.095721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.071396 restraints weight = 22154.414| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.50 r_work: 0.2855 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11651 Z= 0.208 Angle : 0.557 9.367 16255 Z= 0.316 Chirality : 0.042 0.250 1851 Planarity : 0.004 0.036 1656 Dihedral : 18.841 170.756 2823 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.30 % Allowed : 16.34 % Favored : 81.36 % 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: 1.43 (0.26), residues: 1047 helix: 1.70 (0.24), residues: 460 sheet: 0.71 (0.44), residues: 134 loop : 0.36 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 633 TYR 0.015 0.001 TYR A1160 PHE 0.013 0.001 PHE A1398 TRP 0.011 0.001 TRP A 79 HIS 0.005 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 (11651) covalent geometry : angle 0.55672 / 0.32 (16255) hydrogen bonds : bond 0.04435 / 2.99 ( 507) hydrogen bonds : angle 4.29310 / 3.04 ( 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 80 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.384 Fit side-chains REVERT: A 1 MET cc_start: 0.4700 (OUTLIER) cc_final: 0.3793 (tmt) REVERT: A 32 ARG cc_start: 0.8822 (mmm-85) cc_final: 0.8369 (mtp85) REVERT: A 52 MET cc_start: 0.8957 (mmt) cc_final: 0.8617 (mmt) REVERT: A 407 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8119 (mm110) REVERT: A 408 ASP cc_start: 0.9214 (m-30) cc_final: 0.8943 (m-30) REVERT: A 410 LYS cc_start: 0.8776 (pttm) cc_final: 0.8527 (pttm) REVERT: A 555 GLU cc_start: 0.9039 (tp30) cc_final: 0.8518 (tp30) REVERT: A 849 ARG cc_start: 0.9151 (mtp85) cc_final: 0.8942 (mtp85) REVERT: A 863 LYS cc_start: 0.8277 (tttp) cc_final: 0.7871 (tptm) REVERT: A 1135 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7147 (mp0) REVERT: A 1239 MET cc_start: 0.9445 (mtp) cc_final: 0.9068 (mtt) REVERT: A 1416 ASP cc_start: 0.8743 (t0) cc_final: 0.8188 (t70) REVERT: A 1551 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8693 (pp) outliers start: 22 outliers final: 11 residues processed: 73 average time/residue: 0.4136 time to fit residues: 33.6354 Evaluate side-chains 68 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1307 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 9 optimal weight: 0.2980 chunk 78 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 21 optimal weight: 0.0570 overall best weight: 0.6100 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.097530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.073158 restraints weight = 21764.307| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.49 r_work: 0.2894 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2159 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= 0.128 Angle : 0.523 10.282 16255 Z= 0.296 Chirality : 0.039 0.225 1851 Planarity : 0.003 0.034 1656 Dihedral : 18.844 170.515 2823 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.57 % Allowed : 17.17 % 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: 1.54 (0.26), residues: 1047 helix: 1.82 (0.24), residues: 462 sheet: 0.69 (0.44), residues: 134 loop : 0.40 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1540 TYR 0.015 0.001 TYR A1160 PHE 0.013 0.001 PHE A1209 TRP 0.013 0.001 TRP A 79 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (11651) covalent geometry : angle 0.52288 / 0.30 (16255) hydrogen bonds : bond 0.03966 / 2.68 ( 507) hydrogen bonds : angle 4.11508 / 2.91 ( 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 72 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4559 (OUTLIER) cc_final: 0.4205 (tmt) REVERT: A 32 ARG cc_start: 0.8791 (mmm-85) cc_final: 0.8350 (mtp85) REVERT: A 52 MET cc_start: 0.8959 (mmt) cc_final: 0.8626 (mmt) REVERT: A 408 ASP cc_start: 0.9193 (m-30) cc_final: 0.8918 (m-30) REVERT: A 410 LYS cc_start: 0.8779 (pttm) cc_final: 0.8547 (pttt) REVERT: A 555 GLU cc_start: 0.9053 (tp30) cc_final: 0.8530 (tp30) REVERT: A 863 LYS cc_start: 0.8231 (tttp) cc_final: 0.7898 (tptm) REVERT: A 1239 MET cc_start: 0.9437 (mtp) cc_final: 0.9059 (mtt) REVERT: A 1416 ASP cc_start: 0.8709 (t0) cc_final: 0.8199 (t70) REVERT: A 1551 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8669 (pp) outliers start: 15 outliers final: 10 residues processed: 69 average time/residue: 0.4389 time to fit residues: 33.4634 Evaluate side-chains 68 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1458 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 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 ASN A1129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.097250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.072758 restraints weight = 22078.854| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.51 r_work: 0.2892 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11651 Z= 0.145 Angle : 0.526 9.442 16255 Z= 0.298 Chirality : 0.040 0.229 1851 Planarity : 0.003 0.035 1656 Dihedral : 18.777 170.486 2823 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.57 % Allowed : 17.17 % 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: 1.55 (0.26), residues: 1047 helix: 1.88 (0.24), residues: 461 sheet: 0.66 (0.44), residues: 134 loop : 0.36 (0.30), 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 0.011 0.001 TRP A 79 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (11651) covalent geometry : angle 0.52594 / 0.30 (16255) hydrogen bonds : bond 0.03980 / 2.70 ( 507) hydrogen bonds : angle 4.07926 / 2.89 ( 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 76 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.394 Fit side-chains REVERT: A 1 MET cc_start: 0.4701 (tmt) cc_final: 0.4235 (tmt) REVERT: A 32 ARG cc_start: 0.8813 (mmm-85) cc_final: 0.8366 (mtp85) REVERT: A 52 MET cc_start: 0.8951 (mmt) cc_final: 0.8598 (mmt) REVERT: A 407 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8021 (mm110) REVERT: A 408 ASP cc_start: 0.9188 (m-30) cc_final: 0.8901 (m-30) REVERT: A 410 LYS cc_start: 0.8781 (pttm) cc_final: 0.8530 (pttm) REVERT: A 555 GLU cc_start: 0.9050 (tp30) cc_final: 0.8524 (tp30) REVERT: A 1135 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7239 (mp0) REVERT: A 1239 MET cc_start: 0.9445 (mtp) cc_final: 0.9057 (mtt) REVERT: A 1416 ASP cc_start: 0.8700 (t0) cc_final: 0.8179 (t70) REVERT: A 1542 ILE cc_start: 0.8889 (mm) cc_final: 0.8657 (mp) REVERT: A 1551 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8662 (pp) outliers start: 15 outliers final: 11 residues processed: 72 average time/residue: 0.3907 time to fit residues: 31.0854 Evaluate side-chains 70 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 44 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 891 LEU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1458 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: 0.5980 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 0.0870 chunk 79 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 41 optimal weight: 0.0980 chunk 70 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.4960 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.098686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.074283 restraints weight = 22024.934| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.51 r_work: 0.2916 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11651 Z= 0.117 Angle : 0.527 11.970 16255 Z= 0.295 Chirality : 0.039 0.216 1851 Planarity : 0.003 0.034 1656 Dihedral : 18.759 170.354 2823 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.36 % Allowed : 17.91 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.26), residues: 1047 helix: 1.97 (0.24), residues: 461 sheet: 0.66 (0.44), residues: 134 loop : 0.36 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1540 TYR 0.016 0.001 TYR A1160 PHE 0.019 0.001 PHE A1095 TRP 0.012 0.001 TRP A 79 HIS 0.002 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (11651) covalent geometry : angle 0.52706 / 0.30 (16255) hydrogen bonds : bond 0.03774 / 2.56 ( 507) hydrogen bonds : angle 4.00441 / 2.84 ( 1326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2297.76 seconds wall clock time: 40 minutes 16.81 seconds (2416.81 seconds total)