Starting phenix.real_space_refine on Wed Feb 4 15:28:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ehw_48069/02_2026/9ehw_48069.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ehw_48069/02_2026/9ehw_48069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ehw_48069/02_2026/9ehw_48069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ehw_48069/02_2026/9ehw_48069.map" model { file = "/net/cci-nas-00/data/ceres_data/9ehw_48069/02_2026/9ehw_48069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ehw_48069/02_2026/9ehw_48069.cif" } resolution = 2.98 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= 0.012 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 6693 2.51 5 N 1946 2.21 5 O 2412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11190 Number of models: 1 Model: "" Number of chains: 5 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: "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: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1812 Classifications: {'RNA': 86} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 7, 'rna3p_pur': 33, 'rna3p_pyr': 42} Link IDs: {'rna2p': 10, 'rna3p': 75} 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: 2.50, per 1000 atoms: 0.22 Number of scatterers: 11190 At special positions: 0 Unit cell: (77.4876, 109.149, 144.144, 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 2412 8.00 N 1946 7.00 C 6693 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 460 " - pdb=" SG CYS A 657 " distance=2.09 Simple disulfide: pdb=" SG CYS A 460 " - pdb=" SG CYS A 814 " distance=1.99 Simple disulfide: pdb=" SG CYS A 657 " - pdb=" SG CYS A 814 " distance=2.05 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 817 " distance=2.02 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: 0.88 Conformation dependent library (CDL) restraints added in 454.5 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: 45 helices and 12 sheets defined 46.7% alpha, 13.2% beta 45 base pairs and 82 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: 4.034A 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: 3.839A pdb=" N LEU A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 4.155A pdb=" N LYS A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 393 Processing helix chain 'A' and resid 416 through 431 removed outlier: 3.554A pdb=" N GLN A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) removed outlier: 3.849A 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 530 through 543 Processing helix chain 'A' and resid 552 through 565 Processing helix chain 'A' and resid 579 through 587 removed outlier: 4.044A pdb=" N ALA A 585 " --> pdb=" O ASP A 581 " (cutoff:3.500A) 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: 5.341A pdb=" N GLN A 879 " --> pdb=" O ASP A 875 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN A 880 " --> pdb=" O ASP A 876 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 881 " --> pdb=" O ASN A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1110 removed outlier: 4.099A 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: 4.110A pdb=" N LEU A1163 " --> pdb=" O SER A1159 " (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: 3.540A 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: 3.734A pdb=" N LEU A1312 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1346 removed outlier: 3.776A 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 1536 through 1543 Processing helix chain 'A' and resid 1569 through 1579 Processing helix chain 'A' and resid 1586 through 1594 removed outlier: 3.946A pdb=" N GLU A1592 " --> pdb=" O ASP A1588 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1624 removed outlier: 3.736A pdb=" N MET A1614 " --> pdb=" O THR A1610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 25 removed outlier: 6.693A 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: 6.693A pdb=" N LYS A 4 " --> pdb=" O HIS A 892 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A 18 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N SER A1220 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY A 38 " --> pdb=" O SER A1220 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LYS A1222 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL A 40 " --> pdb=" O LYS A1222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 464 through 465 Processing sheet with id=AA4, first strand: chain 'A' and resid 513 through 514 Processing sheet with id=AA5, first strand: chain 'A' and resid 597 through 598 Processing sheet with id=AA6, first strand: chain 'A' and resid 630 through 635 removed outlier: 7.518A pdb=" N GLU A 631 " --> pdb=" O THR A 644 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1441 through 1446 removed outlier: 4.621A pdb=" N PHE A1441 " --> pdb=" O ILE A1373 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A1443 " --> pdb=" O VAL A1371 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG A1370 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N ILE A1244 " --> pdb=" O ARG A1370 " (cutoff:3.500A) removed outlier: 13.821A pdb=" N LYS A1372 " --> pdb=" O ASP A1242 " (cutoff:3.500A) removed outlier: 17.970A pdb=" N ASP A1242 " --> pdb=" O LYS A1372 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY A1243 " --> pdb=" O ASN A1469 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN A1469 " --> pdb=" O GLY A1243 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE A1467 " --> pdb=" O TYR A1245 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLU A1247 " --> pdb=" O TYR A1465 " (cutoff:3.500A) removed outlier: 10.970A pdb=" N TYR A1465 " --> pdb=" O GLU A1247 " (cutoff:3.500A) removed outlier: 18.114A pdb=" N TYR A1249 " --> pdb=" O PHE A1463 " (cutoff:3.500A) removed outlier: 22.716A pdb=" N PHE A1463 " --> pdb=" O TYR A1249 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1270 through 1272 Processing sheet with id=AA9, first strand: chain 'A' and resid 1276 through 1277 Processing sheet with id=AB1, first strand: chain 'A' and resid 1390 through 1391 Processing sheet with id=AB2, first strand: chain 'A' and resid 1491 through 1496 Processing sheet with id=AB3, first strand: chain 'A' and resid 1531 through 1533 removed outlier: 4.217A pdb=" N ILE A1547 " --> pdb=" O VAL A1533 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LYS A1562 " --> pdb=" O ALA A1545 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE A1547 " --> pdb=" O ARG A1560 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARG A1560 " --> pdb=" O ILE A1547 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR A1549 " --> pdb=" O LYS A1558 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS A1558 " --> pdb=" O TYR A1549 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1089 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 113 hydrogen bonds 210 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 3.05 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2999 1.34 - 1.46: 3469 1.46 - 1.59: 4941 1.59 - 1.71: 206 1.71 - 1.84: 33 Bond restraints: 11648 Sorted by residual: bond pdb=" CA ASP A 495 " pdb=" CB ASP A 495 " ideal model delta sigma weight residual 1.530 1.563 -0.033 1.69e-02 3.50e+03 3.88e+00 bond pdb=" CA ASP A 495 " pdb=" C ASP A 495 " ideal model delta sigma weight residual 1.523 1.548 -0.025 1.34e-02 5.57e+03 3.44e+00 bond pdb=" CB GLN A 591 " pdb=" CG GLN A 591 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.15e+00 bond pdb=" CG ARG A 665 " pdb=" CD ARG A 665 " ideal model delta sigma weight residual 1.520 1.572 -0.052 3.00e-02 1.11e+03 2.99e+00 bond pdb=" C4' U B 66 " pdb=" O4' U B 66 " ideal model delta sigma weight residual 1.451 1.425 0.026 1.50e-02 4.44e+03 2.98e+00 ... (remaining 11643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 15986 3.25 - 6.50: 219 6.50 - 9.74: 36 9.74 - 12.99: 7 12.99 - 16.24: 2 Bond angle restraints: 16250 Sorted by residual: angle pdb=" CA GLN A 591 " pdb=" CB GLN A 591 " pdb=" CG GLN A 591 " ideal model delta sigma weight residual 114.10 127.76 -13.66 2.00e+00 2.50e-01 4.67e+01 angle pdb=" CB MET A 629 " pdb=" CG MET A 629 " pdb=" SD MET A 629 " ideal model delta sigma weight residual 112.70 128.94 -16.24 3.00e+00 1.11e-01 2.93e+01 angle pdb=" CA GLN A1596 " pdb=" CB GLN A1596 " pdb=" CG GLN A1596 " ideal model delta sigma weight residual 114.10 124.42 -10.32 2.00e+00 2.50e-01 2.66e+01 angle pdb=" C2' C B 76 " pdb=" C1' C B 76 " pdb=" N1 C B 76 " ideal model delta sigma weight residual 112.00 119.66 -7.66 1.50e+00 4.44e-01 2.61e+01 angle pdb=" C ASP A 495 " pdb=" CA ASP A 495 " pdb=" CB ASP A 495 " ideal model delta sigma weight residual 110.42 120.36 -9.94 1.99e+00 2.53e-01 2.49e+01 ... (remaining 16245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.71: 6570 28.71 - 57.42: 404 57.42 - 86.12: 123 86.12 - 114.83: 4 114.83 - 143.54: 3 Dihedral angle restraints: 7104 sinusoidal: 3952 harmonic: 3152 Sorted by residual: dihedral pdb=" CB CYS A 460 " pdb=" SG CYS A 460 " pdb=" SG CYS A 814 " pdb=" CB CYS A 814 " ideal model delta sinusoidal sigma weight residual -86.00 -6.79 -79.21 1 1.00e+01 1.00e-02 7.80e+01 dihedral pdb=" O4' U B 57 " pdb=" C1' U B 57 " pdb=" N1 U B 57 " pdb=" C2 U B 57 " ideal model delta sinusoidal sigma weight residual 200.00 56.46 143.54 1 1.50e+01 4.44e-03 7.70e+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 200.00 66.65 133.35 1 1.50e+01 4.44e-03 7.20e+01 ... (remaining 7101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1494 0.070 - 0.141: 297 0.141 - 0.211: 51 0.211 - 0.282: 7 0.282 - 0.352: 2 Chirality restraints: 1851 Sorted by residual: 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 -2.14 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" C1' C B 76 " pdb=" O4' C B 76 " pdb=" C2' C B 76 " pdb=" N1 C B 76 " both_signs ideal model delta sigma weight residual False 2.47 2.12 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" C1' DT D 4 " pdb=" O4' DT D 4 " pdb=" C2' DT D 4 " pdb=" N1 DT D 4 " both_signs ideal model delta sigma weight residual False 2.47 2.21 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1848 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC C 8 " -0.043 2.00e-02 2.50e+03 2.34e-02 1.24e+01 pdb=" N1 DC C 8 " 0.052 2.00e-02 2.50e+03 pdb=" C2 DC C 8 " -0.005 2.00e-02 2.50e+03 pdb=" O2 DC C 8 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DC C 8 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DC C 8 " -0.006 2.00e-02 2.50e+03 pdb=" N4 DC C 8 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DC C 8 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DC C 8 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 591 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C GLN A 591 " 0.059 2.00e-02 2.50e+03 pdb=" O GLN A 591 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE A 592 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 46 " -0.038 2.00e-02 2.50e+03 2.27e-02 1.16e+01 pdb=" N1 C B 46 " 0.036 2.00e-02 2.50e+03 pdb=" C2 C B 46 " -0.002 2.00e-02 2.50e+03 pdb=" O2 C B 46 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C B 46 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C B 46 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C B 46 " -0.005 2.00e-02 2.50e+03 pdb=" C5 C B 46 " -0.026 2.00e-02 2.50e+03 pdb=" C6 C B 46 " 0.034 2.00e-02 2.50e+03 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 6462 3.05 - 3.51: 11421 3.51 - 3.97: 19699 3.97 - 4.44: 22979 4.44 - 4.90: 32947 Nonbonded interactions: 93508 Sorted by model distance: nonbonded pdb=" N LYS A 578 " pdb=" N LYS A 579 " model vdw 2.585 2.560 nonbonded pdb=" N1 G B 36 " pdb=" C4 G B 36 " model vdw 2.586 2.672 nonbonded pdb=" N1 G B 62 " pdb=" C4 G B 62 " model vdw 2.590 2.672 nonbonded pdb=" N1 G B 31 " pdb=" C4 G B 31 " model vdw 2.590 2.672 nonbonded pdb=" N1 G B 48 " pdb=" C4 G B 48 " model vdw 2.593 2.672 ... (remaining 93503 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.140 Find NCS groups from input model: 0.030 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:9.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 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 0.056 11652 Z= 0.229 Angle : 1.059 21.992 16258 Z= 0.583 Chirality : 0.060 0.352 1851 Planarity : 0.010 0.101 1656 Dihedral : 18.444 143.540 5050 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.94 % Allowed : 13.51 % Favored : 85.55 % Cbeta Deviations : 0.10 % 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: -0.39 (0.24), residues: 1047 helix: -0.57 (0.21), residues: 463 sheet: -0.06 (0.42), residues: 135 loop : 0.30 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.004 ARG A1474 TYR 0.024 0.003 TYR A1329 PHE 0.046 0.002 PHE A1095 TRP 0.022 0.002 TRP A1459 HIS 0.014 0.002 HIS A1177 Details of bonding type rmsd covalent geometry : bond 0.00470 (11648) covalent geometry : angle 1.03083 (16250) SS BOND : bond 0.03716 ( 4) SS BOND : angle 11.06728 ( 8) hydrogen bonds : bond 0.13581 ( 499) hydrogen bonds : angle 5.64048 ( 1299) *********************** 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 94 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.325 Fit side-chains REVERT: A 370 LYS cc_start: 0.8771 (tppt) cc_final: 0.8290 (mtpp) REVERT: A 407 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8196 (tp-100) REVERT: A 452 ASN cc_start: 0.8351 (p0) cc_final: 0.8133 (p0) REVERT: A 515 GLU cc_start: 0.8908 (tt0) cc_final: 0.8500 (tt0) REVERT: A 516 TYR cc_start: 0.8679 (m-80) cc_final: 0.7762 (m-80) REVERT: A 521 GLN cc_start: 0.8882 (tp40) cc_final: 0.8525 (tp40) REVERT: A 522 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.7573 (tm-30) REVERT: A 849 ARG cc_start: 0.9184 (mtp85) cc_final: 0.8750 (mtt90) REVERT: A 1167 MET cc_start: 0.8308 (mtm) cc_final: 0.8003 (mtp) REVERT: A 1171 CYS cc_start: 0.9116 (m) cc_final: 0.8888 (m) REVERT: A 1260 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8486 (mp0) REVERT: A 1274 LYS cc_start: 0.8545 (tmtt) cc_final: 0.8301 (tmtt) REVERT: A 1416 ASP cc_start: 0.8326 (t0) cc_final: 0.7967 (t0) REVERT: A 1442 SER cc_start: 0.9031 (p) cc_final: 0.8689 (t) REVERT: A 1491 GLU cc_start: 0.8355 (tt0) cc_final: 0.7957 (mt-10) REVERT: A 1539 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8641 (mm) REVERT: A 1540 ARG cc_start: 0.9018 (mmm160) cc_final: 0.8780 (tpp80) REVERT: A 1544 ILE cc_start: 0.9358 (mt) cc_final: 0.8997 (pp) outliers start: 9 outliers final: 3 residues processed: 94 average time/residue: 0.5172 time to fit residues: 52.8166 Evaluate side-chains 84 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1539 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.084249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.064255 restraints weight = 24804.492| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.77 r_work: 0.2770 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 11652 Z= 0.286 Angle : 0.677 13.515 16258 Z= 0.364 Chirality : 0.045 0.219 1851 Planarity : 0.004 0.044 1656 Dihedral : 19.118 147.445 2837 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.30 % Allowed : 11.62 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.25), residues: 1047 helix: 0.71 (0.24), residues: 465 sheet: 0.54 (0.41), residues: 138 loop : 0.55 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 662 TYR 0.012 0.002 TYR A1265 PHE 0.016 0.002 PHE A1398 TRP 0.017 0.002 TRP A 477 HIS 0.007 0.001 HIS A1579 Details of bonding type rmsd covalent geometry : bond 0.00638 (11648) covalent geometry : angle 0.65524 (16250) SS BOND : bond 0.02435 ( 4) SS BOND : angle 7.68134 ( 8) hydrogen bonds : bond 0.04915 ( 499) hydrogen bonds : angle 4.42613 ( 1299) *********************** 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 99 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.252 Fit side-chains REVERT: A 370 LYS cc_start: 0.8907 (tppt) cc_final: 0.8445 (mtpp) REVERT: A 407 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8414 (tp-100) REVERT: A 515 GLU cc_start: 0.8854 (tt0) cc_final: 0.8493 (tt0) REVERT: A 516 TYR cc_start: 0.8737 (m-80) cc_final: 0.8208 (m-80) REVERT: A 1115 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8258 (m-30) REVERT: A 1135 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7580 (mm-30) REVERT: A 1167 MET cc_start: 0.8379 (mtm) cc_final: 0.7966 (mtp) REVERT: A 1260 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8494 (mp0) REVERT: A 1416 ASP cc_start: 0.8247 (t0) cc_final: 0.7926 (t0) REVERT: A 1442 SER cc_start: 0.9086 (p) cc_final: 0.8719 (t) REVERT: A 1491 GLU cc_start: 0.7889 (tt0) cc_final: 0.7595 (mt-10) REVERT: A 1540 ARG cc_start: 0.9004 (mmm160) cc_final: 0.8760 (tpp80) REVERT: A 1544 ILE cc_start: 0.9412 (mt) cc_final: 0.9060 (pp) REVERT: A 1570 ASP cc_start: 0.8874 (p0) cc_final: 0.8610 (t70) outliers start: 22 outliers final: 9 residues processed: 92 average time/residue: 0.4960 time to fit residues: 49.9061 Evaluate side-chains 75 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1115 ASP Chi-restraints excluded: chain A residue 1164 ILE Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1567 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 49 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN A1157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.086343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.066392 restraints weight = 25042.334| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.76 r_work: 0.2829 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11652 Z= 0.133 Angle : 0.559 9.635 16258 Z= 0.302 Chirality : 0.039 0.237 1851 Planarity : 0.003 0.034 1656 Dihedral : 18.987 147.587 2830 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.99 % Allowed : 11.94 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.26), residues: 1047 helix: 1.27 (0.24), residues: 463 sheet: 0.66 (0.42), residues: 138 loop : 0.64 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 665 TYR 0.012 0.001 TYR A1329 PHE 0.013 0.001 PHE A1420 TRP 0.010 0.001 TRP A 79 HIS 0.003 0.001 HIS A1579 Details of bonding type rmsd covalent geometry : bond 0.00287 (11648) covalent geometry : angle 0.54421 (16250) SS BOND : bond 0.01488 ( 4) SS BOND : angle 5.69058 ( 8) hydrogen bonds : bond 0.03891 ( 499) hydrogen bonds : angle 3.95822 ( 1299) *********************** 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 91 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 370 LYS cc_start: 0.8888 (tppt) cc_final: 0.8415 (mtpp) REVERT: A 407 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8388 (tp-100) REVERT: A 515 GLU cc_start: 0.8794 (tt0) cc_final: 0.8508 (tt0) REVERT: A 516 TYR cc_start: 0.8714 (m-80) cc_final: 0.8294 (m-80) REVERT: A 521 GLN cc_start: 0.8897 (tp40) cc_final: 0.8529 (tp40) REVERT: A 1115 ASP cc_start: 0.8705 (m-30) cc_final: 0.8273 (m-30) REVERT: A 1167 MET cc_start: 0.8358 (mtm) cc_final: 0.8146 (mtp) REVERT: A 1260 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8606 (mp0) REVERT: A 1416 ASP cc_start: 0.8210 (t0) cc_final: 0.7911 (t0) REVERT: A 1442 SER cc_start: 0.9048 (p) cc_final: 0.8791 (t) REVERT: A 1491 GLU cc_start: 0.7944 (tt0) cc_final: 0.7634 (mt-10) REVERT: A 1540 ARG cc_start: 0.8984 (mmm160) cc_final: 0.8738 (tpp80) REVERT: A 1544 ILE cc_start: 0.9428 (mt) cc_final: 0.9035 (pp) REVERT: A 1570 ASP cc_start: 0.8809 (p0) cc_final: 0.8504 (t70) outliers start: 19 outliers final: 5 residues processed: 86 average time/residue: 0.4554 time to fit residues: 42.8984 Evaluate side-chains 72 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 1117 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 10 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN A 522 GLN A1157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.085858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.065934 restraints weight = 25108.601| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.75 r_work: 0.2826 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11652 Z= 0.141 Angle : 0.545 9.250 16258 Z= 0.295 Chirality : 0.039 0.234 1851 Planarity : 0.003 0.033 1656 Dihedral : 18.914 148.205 2828 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.88 % Allowed : 13.72 % Favored : 84.40 % 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: 1.46 (0.26), residues: 1047 helix: 1.47 (0.24), residues: 463 sheet: 0.82 (0.43), residues: 138 loop : 0.65 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 665 TYR 0.011 0.001 TYR A1329 PHE 0.017 0.001 PHE A1209 TRP 0.009 0.001 TRP A 79 HIS 0.005 0.001 HIS A1162 Details of bonding type rmsd covalent geometry : bond 0.00310 (11648) covalent geometry : angle 0.53365 (16250) SS BOND : bond 0.01400 ( 4) SS BOND : angle 5.05576 ( 8) hydrogen bonds : bond 0.03762 ( 499) hydrogen bonds : angle 3.83390 ( 1299) *********************** 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 88 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 370 LYS cc_start: 0.8892 (tppt) cc_final: 0.8433 (mtpp) REVERT: A 407 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8400 (tp-100) REVERT: A 486 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8793 (mttp) REVERT: A 515 GLU cc_start: 0.8784 (tt0) cc_final: 0.8429 (tt0) REVERT: A 516 TYR cc_start: 0.8691 (m-80) cc_final: 0.8118 (m-80) REVERT: A 521 GLN cc_start: 0.8977 (tp40) cc_final: 0.8624 (tp40) REVERT: A 522 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.7681 (tm-30) REVERT: A 596 GLN cc_start: 0.8513 (pm20) cc_final: 0.8044 (pp30) REVERT: A 1115 ASP cc_start: 0.8682 (m-30) cc_final: 0.8251 (m-30) REVERT: A 1260 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8621 (mp0) REVERT: A 1416 ASP cc_start: 0.8192 (t0) cc_final: 0.7870 (t0) REVERT: A 1442 SER cc_start: 0.9057 (p) cc_final: 0.8828 (t) REVERT: A 1491 GLU cc_start: 0.7934 (tt0) cc_final: 0.7615 (mt-10) REVERT: A 1539 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8785 (mm) REVERT: A 1540 ARG cc_start: 0.8954 (mmm160) cc_final: 0.8688 (tpp80) REVERT: A 1544 ILE cc_start: 0.9440 (mt) cc_final: 0.9049 (pp) REVERT: A 1570 ASP cc_start: 0.8765 (p0) cc_final: 0.8484 (t70) outliers start: 18 outliers final: 7 residues processed: 86 average time/residue: 0.5375 time to fit residues: 50.3812 Evaluate side-chains 74 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1539 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 16 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN A 327 ASN A 522 GLN A1157 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.086345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.066415 restraints weight = 24859.409| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.75 r_work: 0.2834 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11652 Z= 0.136 Angle : 0.537 10.104 16258 Z= 0.289 Chirality : 0.039 0.233 1851 Planarity : 0.003 0.039 1656 Dihedral : 18.868 148.743 2828 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.68 % Allowed : 14.45 % Favored : 83.87 % 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: 1.58 (0.26), residues: 1047 helix: 1.61 (0.24), residues: 463 sheet: 0.87 (0.43), residues: 138 loop : 0.66 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 665 TYR 0.010 0.001 TYR A1329 PHE 0.017 0.001 PHE A1209 TRP 0.009 0.001 TRP A 79 HIS 0.007 0.001 HIS A1162 Details of bonding type rmsd covalent geometry : bond 0.00301 (11648) covalent geometry : angle 0.52648 (16250) SS BOND : bond 0.01292 ( 4) SS BOND : angle 4.68371 ( 8) hydrogen bonds : bond 0.03642 ( 499) hydrogen bonds : angle 3.75382 ( 1299) *********************** 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 85 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 LYS cc_start: 0.8889 (tppt) cc_final: 0.8433 (mtpp) REVERT: A 407 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8409 (tp-100) REVERT: A 515 GLU cc_start: 0.8760 (tt0) cc_final: 0.8404 (tt0) REVERT: A 516 TYR cc_start: 0.8676 (m-80) cc_final: 0.8091 (m-80) REVERT: A 521 GLN cc_start: 0.8972 (tp40) cc_final: 0.8612 (tp40) REVERT: A 522 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.7824 (tm-30) REVERT: A 596 GLN cc_start: 0.8513 (pm20) cc_final: 0.8022 (pp30) REVERT: A 1115 ASP cc_start: 0.8699 (m-30) cc_final: 0.8269 (m-30) REVERT: A 1416 ASP cc_start: 0.8183 (t0) cc_final: 0.7862 (t0) REVERT: A 1442 SER cc_start: 0.9085 (p) cc_final: 0.8881 (t) REVERT: A 1491 GLU cc_start: 0.7946 (tt0) cc_final: 0.7621 (mt-10) REVERT: A 1539 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8770 (mm) REVERT: A 1540 ARG cc_start: 0.8940 (mmm160) cc_final: 0.8668 (tpp80) REVERT: A 1544 ILE cc_start: 0.9442 (mt) cc_final: 0.9038 (pp) REVERT: A 1570 ASP cc_start: 0.8757 (p0) cc_final: 0.8485 (t70) outliers start: 16 outliers final: 10 residues processed: 84 average time/residue: 0.5400 time to fit residues: 49.3963 Evaluate side-chains 77 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1539 LEU Chi-restraints excluded: chain A residue 1598 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 56 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 chunk 52 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN A1157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.085986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.066053 restraints weight = 25054.938| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.75 r_work: 0.2825 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11652 Z= 0.148 Angle : 0.541 10.963 16258 Z= 0.290 Chirality : 0.039 0.230 1851 Planarity : 0.003 0.043 1656 Dihedral : 18.860 149.214 2828 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.47 % Allowed : 15.39 % Favored : 83.14 % 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: 1.61 (0.24), residues: 470 sheet: 0.97 (0.43), residues: 138 loop : 0.59 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 665 TYR 0.010 0.001 TYR A1329 PHE 0.019 0.001 PHE A1095 TRP 0.009 0.001 TRP A 79 HIS 0.006 0.001 HIS A1162 Details of bonding type rmsd covalent geometry : bond 0.00326 (11648) covalent geometry : angle 0.53172 (16250) SS BOND : bond 0.01294 ( 4) SS BOND : angle 4.51947 ( 8) hydrogen bonds : bond 0.03646 ( 499) hydrogen bonds : angle 3.72251 ( 1299) *********************** 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 81 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 LYS cc_start: 0.8902 (tppt) cc_final: 0.8526 (ttpp) REVERT: A 407 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8440 (tp-100) REVERT: A 515 GLU cc_start: 0.8770 (tt0) cc_final: 0.8465 (tt0) REVERT: A 516 TYR cc_start: 0.8661 (m-80) cc_final: 0.8101 (m-80) REVERT: A 521 GLN cc_start: 0.8955 (tp40) cc_final: 0.8584 (tp40) REVERT: A 522 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8017 (tm-30) REVERT: A 596 GLN cc_start: 0.8481 (pm20) cc_final: 0.8018 (pp30) REVERT: A 1115 ASP cc_start: 0.8748 (m-30) cc_final: 0.8278 (m-30) REVERT: A 1304 ILE cc_start: 0.9207 (tp) cc_final: 0.8934 (pp) REVERT: A 1416 ASP cc_start: 0.8173 (t0) cc_final: 0.7846 (t0) REVERT: A 1442 SER cc_start: 0.9076 (p) cc_final: 0.8873 (t) REVERT: A 1491 GLU cc_start: 0.7941 (tt0) cc_final: 0.7615 (mt-10) REVERT: A 1539 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8752 (mm) REVERT: A 1540 ARG cc_start: 0.8947 (mmm160) cc_final: 0.8665 (tpp80) REVERT: A 1544 ILE cc_start: 0.9452 (mt) cc_final: 0.9044 (pp) REVERT: A 1570 ASP cc_start: 0.8747 (p0) cc_final: 0.8516 (t70) outliers start: 14 outliers final: 7 residues processed: 79 average time/residue: 0.4992 time to fit residues: 43.1820 Evaluate side-chains 73 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1539 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 15 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN A 522 GLN A1157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.086025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.066248 restraints weight = 24912.957| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.73 r_work: 0.2832 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11652 Z= 0.138 Angle : 0.540 12.871 16258 Z= 0.288 Chirality : 0.038 0.228 1851 Planarity : 0.003 0.050 1656 Dihedral : 18.860 149.557 2828 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.57 % Allowed : 15.50 % Favored : 82.93 % 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: 1.59 (0.26), residues: 1047 helix: 1.67 (0.24), residues: 470 sheet: 0.94 (0.43), residues: 138 loop : 0.56 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 665 TYR 0.010 0.001 TYR A1329 PHE 0.012 0.001 PHE A1420 TRP 0.009 0.001 TRP A 79 HIS 0.005 0.001 HIS A1162 Details of bonding type rmsd covalent geometry : bond 0.00304 (11648) covalent geometry : angle 0.53098 (16250) SS BOND : bond 0.01234 ( 4) SS BOND : angle 4.39137 ( 8) hydrogen bonds : bond 0.03596 ( 499) hydrogen bonds : angle 3.69815 ( 1299) *********************** 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 82 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 LYS cc_start: 0.8896 (tppt) cc_final: 0.8522 (ttpp) REVERT: A 407 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8418 (tp-100) REVERT: A 486 LYS cc_start: 0.9166 (mtmp) cc_final: 0.8895 (mtmm) REVERT: A 515 GLU cc_start: 0.8755 (tt0) cc_final: 0.8447 (tt0) REVERT: A 516 TYR cc_start: 0.8644 (m-80) cc_final: 0.8081 (m-80) REVERT: A 521 GLN cc_start: 0.8950 (tp40) cc_final: 0.8579 (tp40) REVERT: A 522 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: A 596 GLN cc_start: 0.8468 (pm20) cc_final: 0.8051 (pp30) REVERT: A 1115 ASP cc_start: 0.8753 (m-30) cc_final: 0.8322 (m-30) REVERT: A 1304 ILE cc_start: 0.9216 (tp) cc_final: 0.8942 (pp) REVERT: A 1358 MET cc_start: 0.8794 (tpp) cc_final: 0.8125 (ttp) REVERT: A 1416 ASP cc_start: 0.8157 (t0) cc_final: 0.7824 (t0) REVERT: A 1491 GLU cc_start: 0.7953 (tt0) cc_final: 0.7626 (mt-10) REVERT: A 1540 ARG cc_start: 0.8940 (mmm160) cc_final: 0.8664 (tpp80) REVERT: A 1544 ILE cc_start: 0.9456 (mt) cc_final: 0.9075 (pp) REVERT: A 1570 ASP cc_start: 0.8724 (p0) cc_final: 0.8502 (t70) outliers start: 15 outliers final: 6 residues processed: 80 average time/residue: 0.5151 time to fit residues: 44.9553 Evaluate side-chains 69 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1307 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 98 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.085795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.066035 restraints weight = 24916.186| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.72 r_work: 0.2832 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11652 Z= 0.135 Angle : 0.537 13.462 16258 Z= 0.286 Chirality : 0.038 0.226 1851 Planarity : 0.003 0.042 1656 Dihedral : 18.850 149.885 2828 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.15 % Allowed : 15.71 % Favored : 83.14 % 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: 1.66 (0.26), residues: 1047 helix: 1.72 (0.24), residues: 470 sheet: 1.03 (0.44), residues: 138 loop : 0.58 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 32 TYR 0.010 0.001 TYR A1329 PHE 0.012 0.001 PHE A1420 TRP 0.009 0.001 TRP A 79 HIS 0.004 0.001 HIS A1162 Details of bonding type rmsd covalent geometry : bond 0.00298 (11648) covalent geometry : angle 0.52811 (16250) SS BOND : bond 0.01201 ( 4) SS BOND : angle 4.30785 ( 8) hydrogen bonds : bond 0.03546 ( 499) hydrogen bonds : angle 3.66517 ( 1299) *********************** 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 75 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 LYS cc_start: 0.8894 (tppt) cc_final: 0.8520 (ttpp) REVERT: A 390 GLU cc_start: 0.8689 (tt0) cc_final: 0.8341 (mm-30) REVERT: A 407 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8423 (tp-100) REVERT: A 515 GLU cc_start: 0.8756 (tt0) cc_final: 0.8442 (tt0) REVERT: A 516 TYR cc_start: 0.8631 (m-80) cc_final: 0.8068 (m-80) REVERT: A 521 GLN cc_start: 0.8946 (tp40) cc_final: 0.8570 (tp40) REVERT: A 596 GLN cc_start: 0.8436 (pm20) cc_final: 0.8012 (pp30) REVERT: A 1115 ASP cc_start: 0.8698 (m-30) cc_final: 0.8235 (m-30) REVERT: A 1167 MET cc_start: 0.8202 (mtm) cc_final: 0.7883 (mtp) REVERT: A 1304 ILE cc_start: 0.9224 (tp) cc_final: 0.8947 (pp) REVERT: A 1416 ASP cc_start: 0.8142 (t0) cc_final: 0.7826 (t0) REVERT: A 1491 GLU cc_start: 0.7961 (tt0) cc_final: 0.7631 (mt-10) REVERT: A 1540 ARG cc_start: 0.8932 (mmm160) cc_final: 0.8660 (tpp80) REVERT: A 1544 ILE cc_start: 0.9488 (mt) cc_final: 0.9115 (pp) REVERT: A 1570 ASP cc_start: 0.8722 (p0) cc_final: 0.8518 (t70) outliers start: 11 outliers final: 9 residues processed: 73 average time/residue: 0.4615 time to fit residues: 36.8849 Evaluate side-chains 71 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1458 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 chunk 93 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN A1157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.084925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.065034 restraints weight = 24762.116| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.74 r_work: 0.2803 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11652 Z= 0.174 Angle : 0.580 14.103 16258 Z= 0.305 Chirality : 0.039 0.221 1851 Planarity : 0.003 0.045 1656 Dihedral : 18.861 150.200 2828 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.15 % Allowed : 16.13 % 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: 1.70 (0.26), residues: 1047 helix: 1.82 (0.25), residues: 464 sheet: 1.07 (0.44), residues: 138 loop : 0.54 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 32 TYR 0.012 0.001 TYR A 656 PHE 0.030 0.002 PHE A1209 TRP 0.008 0.001 TRP A 79 HIS 0.006 0.001 HIS A1162 Details of bonding type rmsd covalent geometry : bond 0.00388 (11648) covalent geometry : angle 0.55448 (16250) SS BOND : bond 0.02185 ( 4) SS BOND : angle 7.70726 ( 8) hydrogen bonds : bond 0.03788 ( 499) hydrogen bonds : angle 3.70669 ( 1299) *********************** 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: 11 poor density : 61 time to evaluate : 0.266 Fit side-chains REVERT: A 370 LYS cc_start: 0.8925 (tppt) cc_final: 0.8566 (ttpp) REVERT: A 407 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8447 (tp-100) REVERT: A 515 GLU cc_start: 0.8746 (tt0) cc_final: 0.8464 (tt0) REVERT: A 521 GLN cc_start: 0.8898 (tp40) cc_final: 0.8491 (tp40) REVERT: A 522 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8010 (tm-30) REVERT: A 596 GLN cc_start: 0.8423 (pm20) cc_final: 0.8002 (pp30) REVERT: A 1115 ASP cc_start: 0.8770 (m-30) cc_final: 0.8301 (m-30) REVERT: A 1141 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8281 (mt-10) REVERT: A 1304 ILE cc_start: 0.9241 (tp) cc_final: 0.8973 (pp) REVERT: A 1358 MET cc_start: 0.8750 (tpp) cc_final: 0.8105 (ttp) REVERT: A 1416 ASP cc_start: 0.8148 (t0) cc_final: 0.7833 (t0) REVERT: A 1491 GLU cc_start: 0.7973 (tt0) cc_final: 0.7646 (mt-10) REVERT: A 1540 ARG cc_start: 0.8916 (mmm160) cc_final: 0.8639 (tpp80) REVERT: A 1544 ILE cc_start: 0.9493 (mt) cc_final: 0.9087 (pp) outliers start: 11 outliers final: 9 residues processed: 70 average time/residue: 0.5213 time to fit residues: 39.7553 Evaluate side-chains 68 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1458 THR Chi-restraints excluded: chain A residue 1512 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 67 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 86 optimal weight: 0.2980 chunk 59 optimal weight: 0.0010 chunk 61 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.086801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.066939 restraints weight = 25009.536| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.75 r_work: 0.2843 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11652 Z= 0.115 Angle : 0.558 13.476 16258 Z= 0.294 Chirality : 0.038 0.223 1851 Planarity : 0.003 0.050 1656 Dihedral : 18.841 150.446 2828 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.94 % Allowed : 17.07 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.26), residues: 1047 helix: 1.87 (0.25), residues: 464 sheet: 1.08 (0.44), residues: 138 loop : 0.53 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 32 TYR 0.009 0.001 TYR A 614 PHE 0.028 0.001 PHE A1209 TRP 0.010 0.001 TRP A 79 HIS 0.006 0.001 HIS A1162 Details of bonding type rmsd covalent geometry : bond 0.00253 (11648) covalent geometry : angle 0.53569 (16250) SS BOND : bond 0.01887 ( 4) SS BOND : angle 7.06511 ( 8) hydrogen bonds : bond 0.03454 ( 499) hydrogen bonds : angle 3.58166 ( 1299) ********************** 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 72 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 370 LYS cc_start: 0.8901 (tppt) cc_final: 0.8526 (ttpp) REVERT: A 390 GLU cc_start: 0.8685 (tt0) cc_final: 0.8327 (mm-30) REVERT: A 407 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8451 (tp-100) REVERT: A 521 GLN cc_start: 0.8951 (tp40) cc_final: 0.8567 (tp40) REVERT: A 579 LYS cc_start: 0.8944 (tptm) cc_final: 0.8531 (tptp) REVERT: A 596 GLN cc_start: 0.8398 (pm20) cc_final: 0.7988 (pp30) REVERT: A 1304 ILE cc_start: 0.9247 (tp) cc_final: 0.8975 (pp) REVERT: A 1358 MET cc_start: 0.8751 (tpp) cc_final: 0.8145 (ttp) REVERT: A 1416 ASP cc_start: 0.8146 (t0) cc_final: 0.7790 (t0) REVERT: A 1491 GLU cc_start: 0.7954 (tt0) cc_final: 0.7628 (mt-10) REVERT: A 1540 ARG cc_start: 0.8904 (mmm160) cc_final: 0.8691 (tpp80) REVERT: A 1544 ILE cc_start: 0.9500 (mt) cc_final: 0.9119 (pp) outliers start: 9 outliers final: 6 residues processed: 70 average time/residue: 0.5057 time to fit residues: 38.6174 Evaluate side-chains 65 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1458 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 79 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 68 optimal weight: 0.0670 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN A1157 GLN ** A1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.085940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.066065 restraints weight = 25139.470| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.76 r_work: 0.2825 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11652 Z= 0.144 Angle : 0.554 13.211 16258 Z= 0.294 Chirality : 0.038 0.219 1851 Planarity : 0.003 0.051 1656 Dihedral : 18.805 150.768 2828 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.94 % Allowed : 17.70 % 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: 1.72 (0.26), residues: 1047 helix: 1.80 (0.25), residues: 471 sheet: 1.14 (0.44), residues: 138 loop : 0.54 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 32 TYR 0.016 0.001 TYR A 516 PHE 0.023 0.001 PHE A1209 TRP 0.008 0.001 TRP A 79 HIS 0.006 0.001 HIS A1162 Details of bonding type rmsd covalent geometry : bond 0.00320 (11648) covalent geometry : angle 0.53251 (16250) SS BOND : bond 0.01863 ( 4) SS BOND : angle 6.86955 ( 8) hydrogen bonds : bond 0.03583 ( 499) hydrogen bonds : angle 3.61540 ( 1299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2502.82 seconds wall clock time: 43 minutes 43.94 seconds (2623.94 seconds total)