Starting phenix.real_space_refine on Wed Feb 4 19:00:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ehg_48053/02_2026/9ehg_48053.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ehg_48053/02_2026/9ehg_48053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ehg_48053/02_2026/9ehg_48053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ehg_48053/02_2026/9ehg_48053.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ehg_48053/02_2026/9ehg_48053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ehg_48053/02_2026/9ehg_48053.map" } resolution = 3.0 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= 0.010 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 131 5.49 5 Mg 2 5.21 5 S 23 5.16 5 C 7236 2.51 5 N 2127 2.21 5 O 2621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 12140 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1128, 9353 Classifications: {'peptide': 1128} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 29, 'TRANS': 1098} Chain breaks: 6 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 1987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1987 Classifications: {'RNA': 94} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 8, 'rna3p_pur': 39, 'rna3p_pyr': 43} Link IDs: {'rna2p': 11, 'rna3p': 82} Chain: "C" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 242 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} 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: "c" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 370 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.89, per 1000 atoms: 0.24 Number of scatterers: 12140 At special positions: 0 Unit cell: (89.1524, 111.649, 142.477, 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 23 16.00 P 131 15.00 Mg 2 11.99 O 2621 8.00 N 2127 7.00 C 7236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 460 " - pdb=" SG CYS A 817 " distance=2.05 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 817 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 430.3 milliseconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 11 sheets defined 51.5% alpha, 9.6% beta 51 base pairs and 90 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 52 through 81 removed outlier: 4.176A 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: 3.971A pdb=" N LEU A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 4.054A pdb=" N LYS A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 Processing helix chain 'A' and resid 416 through 431 removed outlier: 3.886A 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 removed outlier: 3.610A pdb=" N ASP A 495 " --> pdb=" O GLN A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 504 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 Processing helix chain 'A' and resid 606 through 623 Processing helix chain 'A' and resid 649 through 652 Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'A' and resid 679 through 688 removed outlier: 4.011A pdb=" N LYS A 686 " --> pdb=" O PHE A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 702 removed outlier: 3.599A pdb=" N HIS A 702 " --> pdb=" O TRP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 721 Processing helix chain 'A' and resid 723 through 734 Processing helix chain 'A' and resid 739 through 750 Processing helix chain 'A' and resid 763 through 773 removed outlier: 4.006A pdb=" N LEU A 770 " --> pdb=" O GLU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 778 No H-bonds generated for 'chain 'A' and resid 776 through 778' Processing helix chain 'A' and resid 779 through 788 removed outlier: 4.228A pdb=" N ARG A 785 " --> pdb=" O PRO A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 804 removed outlier: 3.797A pdb=" N PHE A 796 " --> pdb=" O SER A 792 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 797 " --> pdb=" O ILE A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 825 removed outlier: 3.613A pdb=" N ALA A 819 " --> pdb=" O ALA A 815 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN A 821 " --> pdb=" O CYS A 817 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 822 " --> pdb=" O SER A 818 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HIS A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 944 Processing helix chain 'A' and resid 992 through 999 removed outlier: 3.815A pdb=" N LYS A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'A' and resid 1009 through 1018 Processing helix chain 'A' and resid 1021 through 1034 Processing helix chain 'A' and resid 1048 through 1052 Processing helix chain 'A' and resid 1053 through 1063 Processing helix chain 'A' and resid 1064 through 1066 No H-bonds generated for 'chain 'A' and resid 1064 through 1066' Processing helix chain 'A' and resid 1070 through 1081 Processing helix chain 'A' and resid 1082 through 1087 Processing helix chain 'A' and resid 1282 through 1292 Processing helix chain 'A' and resid 1293 through 1296 removed outlier: 3.567A 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: 3.526A pdb=" N LEU A1312 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1346 removed outlier: 3.539A 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 1362 Processing helix chain 'A' and resid 1375 through 1384 removed outlier: 3.552A pdb=" N VAL A1379 " --> pdb=" O SER A1375 " (cutoff:3.500A) 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 1570 through 1577 Processing helix chain 'A' and resid 1586 through 1595 removed outlier: 4.113A pdb=" N ILE A1593 " --> pdb=" O LYS A1589 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS A1595 " --> pdb=" O LEU A1591 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1624 removed outlier: 3.689A pdb=" N LYS A1618 " --> pdb=" O MET A1614 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 463 through 465 removed outlier: 3.527A pdb=" N THR A 655 " --> pdb=" O ILE A 464 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 513 through 514 Processing sheet with id=AA3, first strand: chain 'A' and resid 597 through 598 Processing sheet with id=AA4, first strand: chain 'A' and resid 630 through 635 removed outlier: 7.614A pdb=" N GLU A 631 " --> pdb=" O THR A 644 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 640 " --> pdb=" O ASP A 635 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 965 through 969 Processing sheet with id=AA6, first strand: chain 'A' and resid 1441 through 1446 removed outlier: 4.736A pdb=" N PHE A1441 " --> pdb=" O ILE A1373 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU A1443 " --> pdb=" O VAL A1371 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG A1370 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N ILE A1244 " --> pdb=" O ARG A1370 " (cutoff:3.500A) removed outlier: 13.795A pdb=" N LYS A1372 " --> pdb=" O ASP A1242 " (cutoff:3.500A) removed outlier: 17.829A pdb=" N ASP A1242 " --> pdb=" O LYS A1372 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY A1243 " --> pdb=" O ASN A1469 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN A1469 " --> pdb=" O GLY A1243 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE A1467 " --> pdb=" O TYR A1245 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N GLU A1247 " --> pdb=" O TYR A1465 " (cutoff:3.500A) removed outlier: 11.040A pdb=" N TYR A1465 " --> pdb=" O GLU A1247 " (cutoff:3.500A) removed outlier: 18.111A pdb=" N TYR A1249 " --> pdb=" O PHE A1463 " (cutoff:3.500A) removed outlier: 22.703A pdb=" N PHE A1463 " --> pdb=" O TYR A1249 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A1452 " --> pdb=" O LEU A1468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1270 through 1273 removed outlier: 4.796A 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 1492 through 1496 Processing sheet with id=AB2, first strand: chain 'A' and resid 1531 through 1533 removed outlier: 3.608A pdb=" N ILE A1547 " --> pdb=" O VAL A1533 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS A1562 " --> pdb=" O ALA A1545 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE A1547 " --> pdb=" O ARG A1560 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ARG A1560 " --> pdb=" O ILE A1547 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR A1549 " --> pdb=" O LYS A1558 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS A1558 " --> pdb=" O TYR A1549 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1158 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 129 hydrogen bonds 246 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 90 stacking parallelities Total time for adding SS restraints: 3.19 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1930 1.32 - 1.45: 4069 1.45 - 1.58: 6360 1.58 - 1.71: 258 1.71 - 1.84: 31 Bond restraints: 12648 Sorted by residual: bond pdb=" C LEU A1508 " pdb=" N PRO A1509 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.34e-02 1.83e+03 5.91e+00 bond pdb=" CB ILE A 742 " pdb=" CG2 ILE A 742 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.90e+00 bond pdb=" CA PHE A 960 " pdb=" CB PHE A 960 " ideal model delta sigma weight residual 1.524 1.549 -0.024 1.22e-02 6.72e+03 3.88e+00 bond pdb=" O5' DC c 24 " pdb=" C5' DC c 24 " ideal model delta sigma weight residual 1.423 1.364 0.059 3.00e-02 1.11e+03 3.81e+00 bond pdb=" CB ASN A 744 " pdb=" CG ASN A 744 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.67e+00 ... (remaining 12643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 17311 3.36 - 6.71: 285 6.71 - 10.07: 42 10.07 - 13.43: 11 13.43 - 16.79: 3 Bond angle restraints: 17652 Sorted by residual: angle pdb=" CA GLN A 539 " pdb=" CB GLN A 539 " pdb=" CG GLN A 539 " ideal model delta sigma weight residual 114.10 130.89 -16.79 2.00e+00 2.50e-01 7.04e+01 angle pdb=" CA LYS A1572 " pdb=" CB LYS A1572 " pdb=" CG LYS A1572 " ideal model delta sigma weight residual 114.10 126.87 -12.77 2.00e+00 2.50e-01 4.08e+01 angle pdb=" CA GLU A1018 " pdb=" CB GLU A1018 " pdb=" CG GLU A1018 " ideal model delta sigma weight residual 114.10 126.77 -12.67 2.00e+00 2.50e-01 4.01e+01 angle pdb=" CA GLU A 582 " pdb=" CB GLU A 582 " pdb=" CG GLU A 582 " ideal model delta sigma weight residual 114.10 124.47 -10.37 2.00e+00 2.50e-01 2.69e+01 angle pdb=" CB LYS A1520 " pdb=" CG LYS A1520 " pdb=" CD LYS A1520 " ideal model delta sigma weight residual 111.30 123.03 -11.73 2.30e+00 1.89e-01 2.60e+01 ... (remaining 17647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.45: 7249 33.45 - 66.89: 390 66.89 - 100.34: 53 100.34 - 133.79: 2 133.79 - 167.23: 2 Dihedral angle restraints: 7696 sinusoidal: 4351 harmonic: 3345 Sorted by residual: 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 64.77 167.23 1 1.70e+01 3.46e-03 6.56e+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 -160.00 -69.97 -90.03 1 1.50e+01 4.44e-03 4.27e+01 dihedral pdb=" CB CYS A 460 " pdb=" SG CYS A 460 " pdb=" SG CYS A 817 " pdb=" CB CYS A 817 " ideal model delta sinusoidal sigma weight residual -86.00 -138.44 52.44 1 1.00e+01 1.00e-02 3.75e+01 ... (remaining 7693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1789 0.100 - 0.200: 183 0.200 - 0.300: 19 0.300 - 0.400: 5 0.400 - 0.500: 3 Chirality restraints: 1999 Sorted by residual: chirality pdb=" CB ILE A 742 " pdb=" CA ILE A 742 " pdb=" CG1 ILE A 742 " pdb=" CG2 ILE A 742 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.50 2.00e-01 2.50e+01 6.26e+00 chirality pdb=" CA GLN A 539 " pdb=" N GLN A 539 " pdb=" C GLN A 539 " pdb=" CB GLN A 539 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" CB VAL A 503 " pdb=" CA VAL A 503 " pdb=" CG1 VAL A 503 " pdb=" CG2 VAL A 503 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.63e+00 ... (remaining 1996 not shown) Planarity restraints: 1785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 824 " -0.465 9.50e-02 1.11e+02 2.10e-01 3.44e+01 pdb=" NE ARG A 824 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG A 824 " -0.043 2.00e-02 2.50e+03 pdb=" NH1 ARG A 824 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG A 824 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 46 " -0.049 2.00e-02 2.50e+03 3.32e-02 2.48e+01 pdb=" N1 C B 46 " 0.039 2.00e-02 2.50e+03 pdb=" C2 C B 46 " -0.007 2.00e-02 2.50e+03 pdb=" O2 C B 46 " 0.007 2.00e-02 2.50e+03 pdb=" N3 C B 46 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C B 46 " -0.002 2.00e-02 2.50e+03 pdb=" N4 C B 46 " -0.003 2.00e-02 2.50e+03 pdb=" C5 C B 46 " -0.048 2.00e-02 2.50e+03 pdb=" C6 C B 46 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1530 " -0.029 2.00e-02 2.50e+03 2.86e-02 2.05e+01 pdb=" CG TRP A1530 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP A1530 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP A1530 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A1530 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A1530 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1530 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1530 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1530 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP A1530 " 0.000 2.00e-02 2.50e+03 ... (remaining 1782 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 44 2.62 - 3.19: 10423 3.19 - 3.76: 20248 3.76 - 4.33: 28516 4.33 - 4.90: 42567 Nonbonded interactions: 101798 Sorted by model distance: nonbonded pdb=" OP2 C B 46 " pdb="MG MG A1701 " model vdw 2.051 2.170 nonbonded pdb=" O ASN A1081 " pdb=" ND2 ASN A1081 " model vdw 2.339 3.120 nonbonded pdb=" NH1 ARG A1370 " pdb="MG MG A1701 " model vdw 2.349 2.250 nonbonded pdb=" NH2 ARG A1370 " pdb="MG MG A1701 " model vdw 2.476 2.250 nonbonded pdb=" O4' C B 18 " pdb=" C6 C B 18 " model vdw 2.515 2.672 ... (remaining 101793 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.310 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 0.006 0.065 12650 Z= 0.269 Angle : 1.140 16.786 17656 Z= 0.629 Chirality : 0.067 0.500 1999 Planarity : 0.010 0.210 1785 Dihedral : 18.887 167.233 5518 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.98 % Allowed : 16.10 % Favored : 82.93 % Cbeta Deviations : 0.37 % 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: -0.69 (0.23), residues: 1114 helix: -0.87 (0.21), residues: 522 sheet: -0.15 (0.52), residues: 84 loop : 0.22 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.003 ARG A 824 TYR 0.039 0.004 TYR A 794 PHE 0.041 0.003 PHE A 602 TRP 0.077 0.004 TRP A1530 HIS 0.005 0.001 HIS A 597 Details of bonding type rmsd covalent geometry : bond 0.00562 (12648) covalent geometry : angle 1.13928 (17652) SS BOND : bond 0.01411 ( 2) SS BOND : angle 2.52092 ( 4) hydrogen bonds : bond 0.12982 ( 531) hydrogen bonds : angle 6.01600 ( 1404) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.266 Fit side-chains REVERT: A 52 MET cc_start: 0.7552 (mmt) cc_final: 0.7069 (mmt) REVERT: A 494 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8505 (mm) REVERT: A 528 ARG cc_start: 0.7108 (mtm180) cc_final: 0.6511 (mtm180) REVERT: A 629 MET cc_start: 0.6434 (tpt) cc_final: 0.6062 (ttp) REVERT: A 631 GLU cc_start: 0.7651 (tt0) cc_final: 0.7437 (tt0) REVERT: A 712 ASP cc_start: 0.7772 (m-30) cc_final: 0.7529 (m-30) REVERT: A 788 LYS cc_start: 0.9095 (mmmt) cc_final: 0.8744 (mppt) REVERT: A 942 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7871 (mm-30) REVERT: A 976 LYS cc_start: 0.8606 (mttt) cc_final: 0.7879 (pmtt) REVERT: A 988 ILE cc_start: 0.8076 (tt) cc_final: 0.7835 (tt) REVERT: A 992 ARG cc_start: 0.6833 (ttm170) cc_final: 0.6552 (ttp80) REVERT: A 1006 ARG cc_start: 0.8237 (ptt180) cc_final: 0.7876 (ptp-170) REVERT: A 1047 ARG cc_start: 0.8037 (mtt90) cc_final: 0.7422 (tpt170) REVERT: A 1069 GLU cc_start: 0.7345 (pm20) cc_final: 0.7096 (pm20) REVERT: A 1358 MET cc_start: 0.7537 (tpp) cc_final: 0.7135 (tpp) REVERT: A 1440 ASP cc_start: 0.8309 (m-30) cc_final: 0.7830 (m-30) REVERT: A 1563 LEU cc_start: 0.8688 (mm) cc_final: 0.8025 (pp) outliers start: 10 outliers final: 5 residues processed: 115 average time/residue: 0.4732 time to fit residues: 59.8868 Evaluate side-chains 104 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 1031 ASP Chi-restraints excluded: chain A residue 1395 THR Chi-restraints excluded: chain A residue 1540 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.0980 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 HIS A 725 ASN ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1515 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.131866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.103975 restraints weight = 25048.198| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.79 r_work: 0.3530 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12650 Z= 0.200 Angle : 0.658 7.480 17656 Z= 0.355 Chirality : 0.043 0.222 1999 Planarity : 0.004 0.034 1785 Dihedral : 19.346 165.618 3113 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.63 % Allowed : 13.37 % Favored : 84.00 % 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: 0.23 (0.25), residues: 1114 helix: 0.12 (0.22), residues: 536 sheet: 0.09 (0.50), residues: 102 loop : 0.48 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1078 TYR 0.016 0.002 TYR A1418 PHE 0.018 0.002 PHE A 497 TRP 0.029 0.002 TRP A1530 HIS 0.004 0.001 HIS A1062 Details of bonding type rmsd covalent geometry : bond 0.00431 (12648) covalent geometry : angle 0.65777 (17652) SS BOND : bond 0.00852 ( 2) SS BOND : angle 1.58329 ( 4) hydrogen bonds : bond 0.04663 ( 531) hydrogen bonds : angle 4.72239 ( 1404) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.429 Fit side-chains REVERT: A 495 ASP cc_start: 0.8148 (t0) cc_final: 0.7915 (t0) REVERT: A 528 ARG cc_start: 0.7067 (mtm180) cc_final: 0.6407 (mtm180) REVERT: A 629 MET cc_start: 0.6468 (tpt) cc_final: 0.5920 (ttp) REVERT: A 631 GLU cc_start: 0.7023 (tt0) cc_final: 0.6775 (tt0) REVERT: A 648 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.8037 (m-30) REVERT: A 712 ASP cc_start: 0.7811 (m-30) cc_final: 0.7567 (m-30) REVERT: A 726 HIS cc_start: 0.7964 (OUTLIER) cc_final: 0.7495 (t70) REVERT: A 788 LYS cc_start: 0.9194 (mmmt) cc_final: 0.8924 (tppt) REVERT: A 793 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7648 (tt) REVERT: A 806 GLU cc_start: 0.7942 (pm20) cc_final: 0.7735 (pm20) REVERT: A 938 ASN cc_start: 0.7896 (m-40) cc_final: 0.7505 (m-40) REVERT: A 940 ILE cc_start: 0.8151 (mm) cc_final: 0.7793 (mt) REVERT: A 942 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7901 (mm-30) REVERT: A 976 LYS cc_start: 0.8692 (mttt) cc_final: 0.7893 (pmtt) REVERT: A 992 ARG cc_start: 0.6839 (ttm170) cc_final: 0.6527 (ttp80) REVERT: A 1006 ARG cc_start: 0.8319 (ptt180) cc_final: 0.8055 (ptp-170) REVERT: A 1029 ILE cc_start: 0.7048 (OUTLIER) cc_final: 0.6583 (mp) REVERT: A 1047 ARG cc_start: 0.8134 (mtt90) cc_final: 0.7519 (tpt170) REVERT: A 1069 GLU cc_start: 0.7595 (pm20) cc_final: 0.7307 (pm20) REVERT: A 1081 ASN cc_start: 0.7844 (t0) cc_final: 0.7354 (t0) REVERT: A 1510 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8401 (ptmm) REVERT: A 1563 LEU cc_start: 0.8553 (mm) cc_final: 0.7921 (pp) outliers start: 27 outliers final: 11 residues processed: 126 average time/residue: 0.4838 time to fit residues: 67.1560 Evaluate side-chains 108 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1031 ASP Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1395 THR Chi-restraints excluded: chain A residue 1471 SER Chi-restraints excluded: chain A residue 1510 LYS Chi-restraints excluded: chain A residue 1540 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 10 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 74 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.133409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.105741 restraints weight = 25244.290| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.80 r_work: 0.3560 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12650 Z= 0.138 Angle : 0.587 8.434 17656 Z= 0.313 Chirality : 0.040 0.220 1999 Planarity : 0.003 0.031 1785 Dihedral : 19.251 174.026 3109 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.83 % Allowed : 14.83 % Favored : 82.34 % 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: 0.64 (0.26), residues: 1114 helix: 0.61 (0.23), residues: 537 sheet: -0.16 (0.49), residues: 108 loop : 0.60 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1078 TYR 0.031 0.001 TYR A1565 PHE 0.017 0.001 PHE A1576 TRP 0.020 0.001 TRP A1530 HIS 0.005 0.001 HIS A1236 Details of bonding type rmsd covalent geometry : bond 0.00297 (12648) covalent geometry : angle 0.58622 (17652) SS BOND : bond 0.00802 ( 2) SS BOND : angle 1.55207 ( 4) hydrogen bonds : bond 0.03925 ( 531) hydrogen bonds : angle 4.37130 ( 1404) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 484 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7718 (mt) REVERT: A 495 ASP cc_start: 0.8086 (t0) cc_final: 0.7784 (t0) REVERT: A 591 GLN cc_start: 0.9346 (tp-100) cc_final: 0.9118 (tp40) REVERT: A 629 MET cc_start: 0.6520 (tpt) cc_final: 0.6071 (ttp) REVERT: A 631 GLU cc_start: 0.6919 (tt0) cc_final: 0.6692 (tt0) REVERT: A 652 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7869 (mm-40) REVERT: A 694 PHE cc_start: 0.8278 (t80) cc_final: 0.8009 (t80) REVERT: A 712 ASP cc_start: 0.7883 (m-30) cc_final: 0.7640 (m-30) REVERT: A 726 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.7537 (t70) REVERT: A 788 LYS cc_start: 0.9209 (mmmt) cc_final: 0.8936 (mppt) REVERT: A 806 GLU cc_start: 0.7859 (pm20) cc_final: 0.7597 (pm20) REVERT: A 938 ASN cc_start: 0.7865 (m-40) cc_final: 0.7502 (m-40) REVERT: A 940 ILE cc_start: 0.8053 (mm) cc_final: 0.7735 (mt) REVERT: A 942 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7893 (mm-30) REVERT: A 976 LYS cc_start: 0.8631 (mttt) cc_final: 0.7844 (pmtt) REVERT: A 992 ARG cc_start: 0.6915 (ttm170) cc_final: 0.6557 (ttp80) REVERT: A 1006 ARG cc_start: 0.8283 (ptt180) cc_final: 0.8046 (ptp-170) REVERT: A 1029 ILE cc_start: 0.6900 (OUTLIER) cc_final: 0.6430 (mp) REVERT: A 1043 PHE cc_start: 0.6844 (t80) cc_final: 0.6508 (t80) REVERT: A 1047 ARG cc_start: 0.8134 (mtt90) cc_final: 0.7509 (tpt170) REVERT: A 1069 GLU cc_start: 0.7623 (pm20) cc_final: 0.7359 (pm20) REVERT: A 1552 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8222 (m-30) REVERT: A 1563 LEU cc_start: 0.8511 (mm) cc_final: 0.7916 (pp) outliers start: 29 outliers final: 9 residues processed: 129 average time/residue: 0.5170 time to fit residues: 73.5102 Evaluate side-chains 108 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1045 ASN Chi-restraints excluded: chain A residue 1334 THR Chi-restraints excluded: chain A residue 1395 THR Chi-restraints excluded: chain A residue 1458 THR Chi-restraints excluded: chain A residue 1552 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 57 optimal weight: 0.0570 chunk 37 optimal weight: 0.0670 chunk 33 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS A 812 ASN A1287 ASN A1288 ASN A1305 GLN ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.130558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.102974 restraints weight = 25302.161| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.75 r_work: 0.3509 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12650 Z= 0.179 Angle : 0.602 8.348 17656 Z= 0.321 Chirality : 0.041 0.231 1999 Planarity : 0.003 0.040 1785 Dihedral : 19.210 175.762 3102 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.22 % Allowed : 15.22 % Favored : 81.56 % 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: 0.59 (0.25), residues: 1114 helix: 0.67 (0.23), residues: 538 sheet: -0.33 (0.48), residues: 108 loop : 0.48 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 622 TYR 0.014 0.001 TYR A1329 PHE 0.013 0.002 PHE A1576 TRP 0.022 0.002 TRP A1530 HIS 0.015 0.001 HIS A 597 Details of bonding type rmsd covalent geometry : bond 0.00390 (12648) covalent geometry : angle 0.60137 (17652) SS BOND : bond 0.00790 ( 2) SS BOND : angle 1.56190 ( 4) hydrogen bonds : bond 0.04129 ( 531) hydrogen bonds : angle 4.34972 ( 1404) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 484 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7714 (mt) REVERT: A 495 ASP cc_start: 0.8127 (t0) cc_final: 0.7845 (t0) REVERT: A 528 ARG cc_start: 0.6837 (mtm180) cc_final: 0.6120 (mtm180) REVERT: A 629 MET cc_start: 0.6329 (tpt) cc_final: 0.5826 (ttm) REVERT: A 631 GLU cc_start: 0.6917 (tt0) cc_final: 0.6684 (tt0) REVERT: A 652 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7831 (mm-40) REVERT: A 694 PHE cc_start: 0.8352 (t80) cc_final: 0.8088 (t80) REVERT: A 726 HIS cc_start: 0.7966 (OUTLIER) cc_final: 0.7532 (t70) REVERT: A 788 LYS cc_start: 0.9238 (mmmt) cc_final: 0.8967 (mppt) REVERT: A 806 GLU cc_start: 0.7949 (pm20) cc_final: 0.7696 (pm20) REVERT: A 812 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8375 (t0) REVERT: A 938 ASN cc_start: 0.7901 (m-40) cc_final: 0.7546 (m-40) REVERT: A 940 ILE cc_start: 0.8112 (mm) cc_final: 0.7783 (mt) REVERT: A 942 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7892 (mm-30) REVERT: A 976 LYS cc_start: 0.8670 (mttt) cc_final: 0.7856 (pmtt) REVERT: A 992 ARG cc_start: 0.6962 (ttm170) cc_final: 0.6590 (ttp80) REVERT: A 1006 ARG cc_start: 0.8277 (ptt180) cc_final: 0.7995 (ptp-170) REVERT: A 1029 ILE cc_start: 0.6894 (OUTLIER) cc_final: 0.6298 (mp) REVERT: A 1043 PHE cc_start: 0.6950 (t80) cc_final: 0.6538 (t80) REVERT: A 1047 ARG cc_start: 0.8136 (mtt90) cc_final: 0.7526 (tpt170) REVERT: A 1069 GLU cc_start: 0.7648 (pm20) cc_final: 0.7391 (pm20) REVERT: A 1552 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8254 (m-30) outliers start: 33 outliers final: 11 residues processed: 120 average time/residue: 0.4380 time to fit residues: 58.3955 Evaluate side-chains 108 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1045 ASN Chi-restraints excluded: chain A residue 1395 THR Chi-restraints excluded: chain A residue 1458 THR Chi-restraints excluded: chain A residue 1552 ASP Chi-restraints excluded: chain A residue 1554 ASN Chi-restraints excluded: chain A residue 1569 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 7 optimal weight: 0.4980 chunk 50 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 29 optimal weight: 0.3980 chunk 62 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.131129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.103601 restraints weight = 25247.929| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.76 r_work: 0.3520 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12650 Z= 0.153 Angle : 0.583 8.759 17656 Z= 0.311 Chirality : 0.040 0.228 1999 Planarity : 0.003 0.027 1785 Dihedral : 19.209 177.775 3102 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.32 % Allowed : 15.71 % Favored : 80.98 % 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: 0.64 (0.25), residues: 1114 helix: 0.76 (0.23), residues: 537 sheet: -0.33 (0.48), residues: 107 loop : 0.42 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 622 TYR 0.012 0.001 TYR A1329 PHE 0.014 0.001 PHE A 960 TRP 0.021 0.002 TRP A1530 HIS 0.003 0.001 HIS A1236 Details of bonding type rmsd covalent geometry : bond 0.00337 (12648) covalent geometry : angle 0.58195 (17652) SS BOND : bond 0.00782 ( 2) SS BOND : angle 2.03324 ( 4) hydrogen bonds : bond 0.03855 ( 531) hydrogen bonds : angle 4.27674 ( 1404) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.400 Fit side-chains REVERT: A 495 ASP cc_start: 0.8099 (t0) cc_final: 0.7819 (t0) REVERT: A 629 MET cc_start: 0.6236 (tpt) cc_final: 0.5809 (ttm) REVERT: A 631 GLU cc_start: 0.6872 (tt0) cc_final: 0.6620 (tt0) REVERT: A 694 PHE cc_start: 0.8377 (t80) cc_final: 0.8089 (t80) REVERT: A 726 HIS cc_start: 0.7967 (OUTLIER) cc_final: 0.7535 (t70) REVERT: A 788 LYS cc_start: 0.9238 (mmmt) cc_final: 0.8967 (mppt) REVERT: A 806 GLU cc_start: 0.8004 (pm20) cc_final: 0.7729 (pm20) REVERT: A 938 ASN cc_start: 0.7920 (m-40) cc_final: 0.7589 (m-40) REVERT: A 940 ILE cc_start: 0.8129 (mm) cc_final: 0.7837 (mt) REVERT: A 942 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7887 (mm-30) REVERT: A 976 LYS cc_start: 0.8687 (mttt) cc_final: 0.7847 (pmtt) REVERT: A 992 ARG cc_start: 0.6932 (ttm170) cc_final: 0.6574 (ttp80) REVERT: A 1006 ARG cc_start: 0.8295 (ptt180) cc_final: 0.8018 (ptp-170) REVERT: A 1029 ILE cc_start: 0.6889 (OUTLIER) cc_final: 0.6326 (mp) REVERT: A 1047 ARG cc_start: 0.8161 (mtt90) cc_final: 0.7530 (tpt170) REVERT: A 1069 GLU cc_start: 0.7698 (pm20) cc_final: 0.7448 (pm20) REVERT: A 1552 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8255 (m-30) outliers start: 34 outliers final: 13 residues processed: 123 average time/residue: 0.4844 time to fit residues: 66.3007 Evaluate side-chains 107 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1045 ASN Chi-restraints excluded: chain A residue 1334 THR Chi-restraints excluded: chain A residue 1395 THR Chi-restraints excluded: chain A residue 1458 THR Chi-restraints excluded: chain A residue 1540 ARG Chi-restraints excluded: chain A residue 1552 ASP Chi-restraints excluded: chain A residue 1554 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 113 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 96 optimal weight: 0.0010 chunk 50 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 61 optimal weight: 0.0670 overall best weight: 0.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.133541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.105851 restraints weight = 25385.647| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.83 r_work: 0.3564 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12650 Z= 0.127 Angle : 0.572 8.452 17656 Z= 0.305 Chirality : 0.039 0.223 1999 Planarity : 0.003 0.027 1785 Dihedral : 19.162 179.789 3102 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.24 % Allowed : 16.98 % Favored : 80.78 % 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: 0.71 (0.26), residues: 1114 helix: 0.85 (0.23), residues: 537 sheet: -0.26 (0.49), residues: 107 loop : 0.43 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 785 TYR 0.012 0.001 TYR A1549 PHE 0.016 0.001 PHE A 542 TRP 0.021 0.001 TRP A1530 HIS 0.003 0.001 HIS A1236 Details of bonding type rmsd covalent geometry : bond 0.00279 (12648) covalent geometry : angle 0.57132 (17652) SS BOND : bond 0.00641 ( 2) SS BOND : angle 1.50102 ( 4) hydrogen bonds : bond 0.03563 ( 531) hydrogen bonds : angle 4.17566 ( 1404) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.467 Fit side-chains REVERT: A 495 ASP cc_start: 0.8116 (t0) cc_final: 0.7830 (t0) REVERT: A 528 ARG cc_start: 0.6603 (mtm180) cc_final: 0.5961 (mtm180) REVERT: A 629 MET cc_start: 0.6330 (tpt) cc_final: 0.5861 (ttm) REVERT: A 631 GLU cc_start: 0.6837 (tt0) cc_final: 0.6635 (tt0) REVERT: A 694 PHE cc_start: 0.8455 (t80) cc_final: 0.8163 (t80) REVERT: A 712 ASP cc_start: 0.7860 (m-30) cc_final: 0.7620 (m-30) REVERT: A 726 HIS cc_start: 0.7949 (OUTLIER) cc_final: 0.7533 (t70) REVERT: A 788 LYS cc_start: 0.9236 (mmmt) cc_final: 0.8958 (mppt) REVERT: A 806 GLU cc_start: 0.8017 (pm20) cc_final: 0.7757 (pm20) REVERT: A 812 ASN cc_start: 0.8598 (m-40) cc_final: 0.8271 (t0) REVERT: A 938 ASN cc_start: 0.7865 (m-40) cc_final: 0.7528 (m-40) REVERT: A 940 ILE cc_start: 0.8034 (mm) cc_final: 0.7755 (mt) REVERT: A 942 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7862 (mm-30) REVERT: A 976 LYS cc_start: 0.8658 (mttt) cc_final: 0.7804 (pmtt) REVERT: A 992 ARG cc_start: 0.6924 (ttm170) cc_final: 0.6550 (ttp80) REVERT: A 1006 ARG cc_start: 0.8285 (ptt180) cc_final: 0.8029 (ptp-170) REVERT: A 1029 ILE cc_start: 0.6812 (OUTLIER) cc_final: 0.6353 (mp) REVERT: A 1047 ARG cc_start: 0.8130 (mtt90) cc_final: 0.7474 (tpt170) REVERT: A 1069 GLU cc_start: 0.7714 (pm20) cc_final: 0.7456 (pm20) REVERT: A 1309 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8511 (tm) outliers start: 23 outliers final: 12 residues processed: 116 average time/residue: 0.4815 time to fit residues: 61.9532 Evaluate side-chains 105 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1031 ASP Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1334 THR Chi-restraints excluded: chain A residue 1395 THR Chi-restraints excluded: chain A residue 1458 THR Chi-restraints excluded: chain A residue 1540 ARG Chi-restraints excluded: chain A residue 1565 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 73 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 104 optimal weight: 0.0570 chunk 105 optimal weight: 2.9990 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1515 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.128659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.100766 restraints weight = 25674.557| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.83 r_work: 0.3474 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12650 Z= 0.235 Angle : 0.647 8.789 17656 Z= 0.343 Chirality : 0.042 0.237 1999 Planarity : 0.004 0.034 1785 Dihedral : 19.217 177.620 3102 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.12 % Allowed : 16.78 % Favored : 80.10 % 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: 0.48 (0.25), residues: 1114 helix: 0.73 (0.23), residues: 536 sheet: -0.51 (0.47), residues: 113 loop : 0.25 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 785 TYR 0.016 0.002 TYR A1329 PHE 0.022 0.002 PHE A 602 TRP 0.023 0.002 TRP A1530 HIS 0.004 0.001 HIS A1062 Details of bonding type rmsd covalent geometry : bond 0.00519 (12648) covalent geometry : angle 0.64661 (17652) SS BOND : bond 0.00829 ( 2) SS BOND : angle 1.55572 ( 4) hydrogen bonds : bond 0.04554 ( 531) hydrogen bonds : angle 4.38271 ( 1404) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.435 Fit side-chains REVERT: A 495 ASP cc_start: 0.8242 (t0) cc_final: 0.7976 (t0) REVERT: A 528 ARG cc_start: 0.6811 (mtm180) cc_final: 0.6170 (mtm180) REVERT: A 629 MET cc_start: 0.6308 (tpt) cc_final: 0.5802 (ttm) REVERT: A 631 GLU cc_start: 0.6961 (tt0) cc_final: 0.6690 (tt0) REVERT: A 694 PHE cc_start: 0.8456 (t80) cc_final: 0.8124 (t80) REVERT: A 726 HIS cc_start: 0.8015 (OUTLIER) cc_final: 0.7558 (t70) REVERT: A 788 LYS cc_start: 0.9253 (mmmt) cc_final: 0.8922 (mppt) REVERT: A 806 GLU cc_start: 0.8095 (pm20) cc_final: 0.7850 (pm20) REVERT: A 940 ILE cc_start: 0.8100 (mm) cc_final: 0.7734 (mt) REVERT: A 942 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7955 (mm-30) REVERT: A 976 LYS cc_start: 0.8730 (mttt) cc_final: 0.7869 (pmtt) REVERT: A 992 ARG cc_start: 0.6891 (ttm170) cc_final: 0.6479 (ttp80) REVERT: A 1029 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6380 (mp) REVERT: A 1047 ARG cc_start: 0.8143 (mtt90) cc_final: 0.7507 (tpt170) REVERT: A 1069 GLU cc_start: 0.7763 (pm20) cc_final: 0.7506 (pm20) REVERT: A 1080 ILE cc_start: 0.7569 (pt) cc_final: 0.7364 (pp) REVERT: A 1285 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7938 (mm110) REVERT: A 1552 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8334 (m-30) outliers start: 32 outliers final: 13 residues processed: 115 average time/residue: 0.5171 time to fit residues: 65.7243 Evaluate side-chains 103 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1285 GLN Chi-restraints excluded: chain A residue 1334 THR Chi-restraints excluded: chain A residue 1395 THR Chi-restraints excluded: chain A residue 1458 THR Chi-restraints excluded: chain A residue 1540 ARG Chi-restraints excluded: chain A residue 1552 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 81 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 0.0020 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.132027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.104201 restraints weight = 25283.251| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.84 r_work: 0.3537 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12650 Z= 0.135 Angle : 0.592 9.033 17656 Z= 0.314 Chirality : 0.039 0.222 1999 Planarity : 0.003 0.029 1785 Dihedral : 19.170 179.637 3102 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.02 % Allowed : 17.56 % Favored : 79.41 % 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: 0.55 (0.26), residues: 1114 helix: 0.77 (0.23), residues: 545 sheet: -0.30 (0.49), residues: 107 loop : 0.25 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 785 TYR 0.013 0.001 TYR A1549 PHE 0.018 0.001 PHE A 602 TRP 0.023 0.002 TRP A1530 HIS 0.003 0.001 HIS A1236 Details of bonding type rmsd covalent geometry : bond 0.00301 (12648) covalent geometry : angle 0.59158 (17652) SS BOND : bond 0.00680 ( 2) SS BOND : angle 1.52759 ( 4) hydrogen bonds : bond 0.03765 ( 531) hydrogen bonds : angle 4.21580 ( 1404) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.374 Fit side-chains REVERT: A 495 ASP cc_start: 0.8215 (t0) cc_final: 0.7943 (t0) REVERT: A 528 ARG cc_start: 0.6631 (mtm180) cc_final: 0.6017 (mtm180) REVERT: A 629 MET cc_start: 0.6285 (tpt) cc_final: 0.5788 (ttm) REVERT: A 631 GLU cc_start: 0.6778 (tt0) cc_final: 0.6539 (tt0) REVERT: A 694 PHE cc_start: 0.8473 (t80) cc_final: 0.8110 (t80) REVERT: A 788 LYS cc_start: 0.9244 (mmmt) cc_final: 0.8885 (mppt) REVERT: A 793 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7836 (tt) REVERT: A 806 GLU cc_start: 0.8084 (pm20) cc_final: 0.7828 (pm20) REVERT: A 812 ASN cc_start: 0.8605 (m-40) cc_final: 0.8312 (t0) REVERT: A 938 ASN cc_start: 0.7936 (m-40) cc_final: 0.7433 (m-40) REVERT: A 940 ILE cc_start: 0.8061 (mm) cc_final: 0.7722 (mt) REVERT: A 942 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7930 (mm-30) REVERT: A 976 LYS cc_start: 0.8654 (mttt) cc_final: 0.7776 (pmtt) REVERT: A 992 ARG cc_start: 0.6878 (ttm170) cc_final: 0.6490 (ttp80) REVERT: A 1029 ILE cc_start: 0.6818 (OUTLIER) cc_final: 0.6270 (mp) REVERT: A 1047 ARG cc_start: 0.8123 (mtt90) cc_final: 0.7457 (tpt170) REVERT: A 1069 GLU cc_start: 0.7767 (pm20) cc_final: 0.7499 (pm20) REVERT: A 1309 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8531 (tm) REVERT: A 1370 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7771 (mtt-85) REVERT: A 1552 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8190 (m-30) outliers start: 31 outliers final: 12 residues processed: 118 average time/residue: 0.4782 time to fit residues: 62.3181 Evaluate side-chains 106 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1334 THR Chi-restraints excluded: chain A residue 1370 ARG Chi-restraints excluded: chain A residue 1395 THR Chi-restraints excluded: chain A residue 1458 THR Chi-restraints excluded: chain A residue 1540 ARG Chi-restraints excluded: chain A residue 1552 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.130984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.103312 restraints weight = 25149.480| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.80 r_work: 0.3525 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12650 Z= 0.159 Angle : 0.610 9.904 17656 Z= 0.324 Chirality : 0.040 0.224 1999 Planarity : 0.003 0.030 1785 Dihedral : 19.147 179.456 3102 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.24 % Allowed : 18.63 % Favored : 79.12 % 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: 0.58 (0.26), residues: 1114 helix: 0.82 (0.23), residues: 538 sheet: -0.28 (0.48), residues: 107 loop : 0.23 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 785 TYR 0.013 0.001 TYR A1549 PHE 0.014 0.001 PHE A 542 TRP 0.022 0.002 TRP A1530 HIS 0.003 0.001 HIS A 597 Details of bonding type rmsd covalent geometry : bond 0.00354 (12648) covalent geometry : angle 0.60914 (17652) SS BOND : bond 0.00684 ( 2) SS BOND : angle 1.52386 ( 4) hydrogen bonds : bond 0.03966 ( 531) hydrogen bonds : angle 4.23210 ( 1404) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 495 ASP cc_start: 0.8277 (t0) cc_final: 0.8018 (t0) REVERT: A 528 ARG cc_start: 0.6638 (mtm180) cc_final: 0.6047 (mtm180) REVERT: A 629 MET cc_start: 0.6314 (tpt) cc_final: 0.5799 (ttm) REVERT: A 694 PHE cc_start: 0.8500 (t80) cc_final: 0.8142 (t80) REVERT: A 788 LYS cc_start: 0.9243 (mmmt) cc_final: 0.8901 (mppt) REVERT: A 793 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7857 (tt) REVERT: A 806 GLU cc_start: 0.8098 (pm20) cc_final: 0.7847 (pm20) REVERT: A 812 ASN cc_start: 0.8600 (m-40) cc_final: 0.8307 (t0) REVERT: A 938 ASN cc_start: 0.7958 (m-40) cc_final: 0.7484 (m-40) REVERT: A 940 ILE cc_start: 0.8065 (mm) cc_final: 0.7734 (mt) REVERT: A 942 GLU cc_start: 0.8457 (mm-30) cc_final: 0.7921 (mm-30) REVERT: A 976 LYS cc_start: 0.8674 (mttt) cc_final: 0.7796 (pmtt) REVERT: A 992 ARG cc_start: 0.6846 (ttm170) cc_final: 0.6450 (ttp80) REVERT: A 1029 ILE cc_start: 0.6882 (OUTLIER) cc_final: 0.6368 (mp) REVERT: A 1047 ARG cc_start: 0.8088 (mtt90) cc_final: 0.7424 (tpt170) REVERT: A 1069 GLU cc_start: 0.7806 (pm20) cc_final: 0.7535 (pm20) REVERT: A 1309 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8553 (tm) REVERT: A 1552 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8238 (m-30) outliers start: 23 outliers final: 16 residues processed: 107 average time/residue: 0.4942 time to fit residues: 58.5762 Evaluate side-chains 108 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1334 THR Chi-restraints excluded: chain A residue 1395 THR Chi-restraints excluded: chain A residue 1458 THR Chi-restraints excluded: chain A residue 1540 ARG Chi-restraints excluded: chain A residue 1552 ASP Chi-restraints excluded: chain A residue 1554 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 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 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.131413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.103751 restraints weight = 25373.851| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.82 r_work: 0.3528 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12650 Z= 0.151 Angle : 0.613 9.542 17656 Z= 0.324 Chirality : 0.039 0.221 1999 Planarity : 0.003 0.031 1785 Dihedral : 19.144 179.673 3102 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.05 % Allowed : 19.02 % Favored : 78.93 % 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: 0.55 (0.26), residues: 1114 helix: 0.79 (0.23), residues: 539 sheet: -0.26 (0.48), residues: 107 loop : 0.21 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 785 TYR 0.014 0.001 TYR A 516 PHE 0.020 0.001 PHE A1576 TRP 0.023 0.002 TRP A1530 HIS 0.003 0.001 HIS A1236 Details of bonding type rmsd covalent geometry : bond 0.00339 (12648) covalent geometry : angle 0.61248 (17652) SS BOND : bond 0.00673 ( 2) SS BOND : angle 1.51351 ( 4) hydrogen bonds : bond 0.03900 ( 531) hydrogen bonds : angle 4.23848 ( 1404) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 495 ASP cc_start: 0.8269 (t0) cc_final: 0.8018 (t0) REVERT: A 528 ARG cc_start: 0.6684 (mtm180) cc_final: 0.6086 (mtm180) REVERT: A 629 MET cc_start: 0.6313 (tpt) cc_final: 0.5807 (ttm) REVERT: A 694 PHE cc_start: 0.8468 (t80) cc_final: 0.8111 (t80) REVERT: A 788 LYS cc_start: 0.9265 (mmmt) cc_final: 0.8927 (mppt) REVERT: A 793 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7854 (tt) REVERT: A 806 GLU cc_start: 0.8103 (pm20) cc_final: 0.7848 (pm20) REVERT: A 812 ASN cc_start: 0.8585 (m-40) cc_final: 0.8292 (t0) REVERT: A 938 ASN cc_start: 0.7950 (m-40) cc_final: 0.7732 (m-40) REVERT: A 940 ILE cc_start: 0.8052 (mm) cc_final: 0.7728 (mt) REVERT: A 976 LYS cc_start: 0.8675 (mttt) cc_final: 0.7793 (pmtt) REVERT: A 992 ARG cc_start: 0.6878 (ttm170) cc_final: 0.6460 (ttp80) REVERT: A 1029 ILE cc_start: 0.6882 (OUTLIER) cc_final: 0.6434 (mp) REVERT: A 1047 ARG cc_start: 0.8070 (mtt90) cc_final: 0.7421 (tpt170) REVERT: A 1069 GLU cc_start: 0.7814 (pm20) cc_final: 0.7543 (pm20) REVERT: A 1309 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8540 (tm) REVERT: A 1552 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8195 (m-30) outliers start: 21 outliers final: 15 residues processed: 103 average time/residue: 0.4637 time to fit residues: 53.0638 Evaluate side-chains 107 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1334 THR Chi-restraints excluded: chain A residue 1395 THR Chi-restraints excluded: chain A residue 1458 THR Chi-restraints excluded: chain A residue 1540 ARG Chi-restraints excluded: chain A residue 1552 ASP Chi-restraints excluded: chain A residue 1554 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 122 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 53 optimal weight: 0.5980 chunk 109 optimal weight: 0.0050 chunk 26 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.132098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.104512 restraints weight = 25178.408| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.81 r_work: 0.3542 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12650 Z= 0.139 Angle : 0.608 10.913 17656 Z= 0.320 Chirality : 0.039 0.217 1999 Planarity : 0.003 0.034 1785 Dihedral : 19.129 179.932 3102 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.56 % Allowed : 19.71 % Favored : 78.73 % 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: 0.57 (0.25), residues: 1114 helix: 0.81 (0.23), residues: 539 sheet: -0.24 (0.48), residues: 107 loop : 0.22 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 785 TYR 0.014 0.001 TYR A1549 PHE 0.021 0.001 PHE A1576 TRP 0.023 0.002 TRP A1530 HIS 0.009 0.001 HIS A 597 Details of bonding type rmsd covalent geometry : bond 0.00312 (12648) covalent geometry : angle 0.60802 (17652) SS BOND : bond 0.00647 ( 2) SS BOND : angle 1.52176 ( 4) hydrogen bonds : bond 0.03780 ( 531) hydrogen bonds : angle 4.20779 ( 1404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4137.00 seconds wall clock time: 71 minutes 27.77 seconds (4287.77 seconds total)