Starting phenix.real_space_refine on Thu Aug 6 00:35:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ehg_48053/08_2026/9ehg_48053.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ehg_48053/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ehg_48053/08_2026/9ehg_48053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ehg_48053/08_2026/9ehg_48053.map" model { file = "/net/cci-nas-00/data/ceres_data/9ehg_48053/08_2026/9ehg_48053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ehg_48053/08_2026/9ehg_48053.cif" } 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-2.2rc3-6140/lib/python3.11/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: 1.87, per 1000 atoms: 0.15 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: 0.70 Conformation dependent library (CDL) restraints added in 443.0 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: 1.23 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: 2.90 Time building geometry restraints manager: 0.93 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=" C3' DA c 16 " pdb=" O3' DA c 16 " ideal model delta sigma weight residual 1.435 1.393 0.042 1.30e-02 5.92e+03 1.03e+01 bond pdb=" C1' DC c 24 " pdb=" N1 DC c 24 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.03e+01 bond pdb=" C1' DT D 4 " pdb=" N1 DT D 4 " ideal model delta sigma weight residual 1.468 1.510 -0.042 1.40e-02 5.10e+03 8.86e+00 bond pdb=" C4' DC c 24 " pdb=" C3' DC c 24 " ideal model delta sigma weight residual 1.529 1.500 0.029 1.00e-02 1.00e+04 8.56e+00 bond pdb=" C1' DC c 23 " pdb=" N1 DC c 23 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.92e+00 ... (remaining 12643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 17293 3.36 - 6.71: 302 6.71 - 10.07: 43 10.07 - 13.43: 11 13.43 - 16.79: 3 Bond angle restraints: 17652 Sorted by residual: angle pdb=" O5' G B 90 " pdb=" C5' G B 90 " pdb=" C4' G B 90 " ideal model delta sigma weight residual 109.40 116.18 -6.78 8.00e-01 1.56e+00 7.19e+01 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=" O4' DG c 25 " pdb=" C1' DG c 25 " pdb=" N9 DG c 25 " ideal model delta sigma weight residual 108.00 113.44 -5.44 7.00e-01 2.04e+00 6.04e+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 ... (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: 1676 0.100 - 0.200: 296 0.200 - 0.300: 19 0.300 - 0.400: 4 0.400 - 0.500: 4 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: 5.010 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.210 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:7.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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= 0.371 Angle : 1.189 16.786 17656 Z= 0.790 Chirality : 0.074 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/Z covalent geometry : bond 0.00590 / 0.37 (12648) covalent geometry : angle 1.18854 / 0.79 (17652) SS BOND : bond 0.01411 / 0.74 ( 2) SS BOND : angle 2.52092 / 1.36 ( 4) hydrogen bonds : bond 0.12982 / 8.50 ( 531) hydrogen bonds : angle 6.01600 / 4.40 ( 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 : 0.276 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: 0.4137 time to fit residues: 52.5584 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 : 0.321 ------------------------------------------------------------------------------- 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: 0.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 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: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 GLN A 725 ASN ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1515 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.134974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.107333 restraints weight = 24971.341| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.77 r_work: 0.3580 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.0954 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= 0.159 Angle : 0.650 8.241 17656 Z= 0.367 Chirality : 0.044 0.211 1999 Planarity : 0.004 0.030 1785 Dihedral : 19.461 168.833 3113 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.05 % Allowed : 14.05 % Favored : 83.90 % 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: 0.10 (0.25), residues: 1114 helix: -0.04 (0.22), residues: 537 sheet: -0.08 (0.52), residues: 96 loop : 0.50 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 622 TYR 0.014 0.002 TYR A1418 PHE 0.014 0.002 PHE A1576 TRP 0.029 0.002 TRP A1530 HIS 0.004 0.001 HIS A 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (12648) covalent geometry : angle 0.64935 / 0.37 (17652) SS BOND : bond 0.01025 / 0.54 ( 2) SS BOND : angle 1.73204 / 0.94 ( 4) hydrogen bonds : bond 0.05226 / 3.48 ( 531) hydrogen bonds : angle 4.81987 / 3.51 ( 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 128 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.280 Fit side-chains REVERT: A 495 ASP cc_start: 0.8010 (t0) cc_final: 0.7777 (t0) REVERT: A 629 MET cc_start: 0.6541 (tpt) cc_final: 0.6119 (ttt) REVERT: A 631 GLU cc_start: 0.7327 (tt0) cc_final: 0.7077 (tt0) REVERT: A 648 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7953 (m-30) REVERT: A 652 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7875 (mm-40) REVERT: A 712 ASP cc_start: 0.7785 (m-30) cc_final: 0.7542 (m-30) REVERT: A 788 LYS cc_start: 0.9157 (mmmt) cc_final: 0.8860 (mppt) REVERT: A 938 ASN cc_start: 0.7756 (m-40) cc_final: 0.7528 (m-40) REVERT: A 942 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7957 (mm-30) REVERT: A 976 LYS cc_start: 0.8632 (mttt) cc_final: 0.7895 (pmtt) REVERT: A 992 ARG cc_start: 0.6896 (ttm170) cc_final: 0.6610 (ttp80) REVERT: A 1006 ARG cc_start: 0.8286 (ptt180) cc_final: 0.8040 (ptp-170) REVERT: A 1029 ILE cc_start: 0.7127 (OUTLIER) cc_final: 0.6607 (mp) REVERT: A 1047 ARG cc_start: 0.8096 (mtt90) cc_final: 0.7505 (tpt170) REVERT: A 1069 GLU cc_start: 0.7493 (pm20) cc_final: 0.7229 (pm20) REVERT: A 1081 ASN cc_start: 0.7903 (t0) cc_final: 0.7451 (t0) REVERT: A 1510 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8166 (pttp) REVERT: A 1563 LEU cc_start: 0.8566 (mm) cc_final: 0.7951 (pp) outliers start: 21 outliers final: 6 residues processed: 121 average time/residue: 0.3916 time to fit residues: 52.6232 Evaluate side-chains 100 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 GLN Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 818 SER 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 1510 LYS 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: 4.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 GLN ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS A 639 HIS ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.132301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.104575 restraints weight = 24993.627| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.81 r_work: 0.3531 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12650 Z= 0.171 Angle : 0.626 8.294 17656 Z= 0.347 Chirality : 0.043 0.208 1999 Planarity : 0.004 0.043 1785 Dihedral : 19.244 175.120 3105 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.02 % Allowed : 14.93 % Favored : 82.05 % 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: 0.44 (0.25), residues: 1114 helix: 0.39 (0.23), residues: 534 sheet: -0.18 (0.50), residues: 112 loop : 0.56 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1078 TYR 0.016 0.002 TYR A1565 PHE 0.019 0.002 PHE A1576 TRP 0.021 0.002 TRP A1530 HIS 0.004 0.001 HIS A1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (12648) covalent geometry : angle 0.62547 / 0.35 (17652) SS BOND : bond 0.00824 / 0.43 ( 2) SS BOND : angle 1.64272 / 0.92 ( 4) hydrogen bonds : bond 0.04772 / 3.17 ( 531) hydrogen bonds : angle 4.59447 / 3.33 ( 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 136 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.378 Fit side-chains REVERT: A 484 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7795 (mt) REVERT: A 495 ASP cc_start: 0.8096 (t0) cc_final: 0.7791 (t0) REVERT: A 528 ARG cc_start: 0.6886 (mtm180) cc_final: 0.6282 (mtm180) REVERT: A 629 MET cc_start: 0.6544 (tpt) cc_final: 0.5979 (ttp) REVERT: A 631 GLU cc_start: 0.6954 (tt0) cc_final: 0.6718 (tt0) REVERT: A 648 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8067 (m-30) REVERT: A 652 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7886 (mm-40) REVERT: A 712 ASP cc_start: 0.7794 (m-30) cc_final: 0.7578 (m-30) REVERT: A 726 HIS cc_start: 0.8005 (OUTLIER) cc_final: 0.7659 (t70) REVERT: A 788 LYS cc_start: 0.9198 (mmmt) cc_final: 0.8889 (mppt) REVERT: A 806 GLU cc_start: 0.7832 (pm20) cc_final: 0.7629 (pm20) REVERT: A 938 ASN cc_start: 0.7666 (m-40) cc_final: 0.7381 (m-40) REVERT: A 942 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7835 (mm-30) REVERT: A 976 LYS cc_start: 0.8640 (mttt) cc_final: 0.7859 (pmtt) REVERT: A 992 ARG cc_start: 0.6796 (ttm170) cc_final: 0.6467 (ttp80) REVERT: A 1006 ARG cc_start: 0.8275 (ptt180) cc_final: 0.8028 (ptp-170) REVERT: A 1029 ILE cc_start: 0.6965 (OUTLIER) cc_final: 0.6421 (mp) REVERT: A 1043 PHE cc_start: 0.7148 (t80) cc_final: 0.6900 (t80) REVERT: A 1047 ARG cc_start: 0.8180 (mtt90) cc_final: 0.7531 (tpt170) REVERT: A 1069 GLU cc_start: 0.7634 (pm20) cc_final: 0.7323 (pm20) REVERT: A 1081 ASN cc_start: 0.7776 (t0) cc_final: 0.7359 (t0) REVERT: A 1552 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8169 (m-30) REVERT: A 1563 LEU cc_start: 0.8499 (mm) cc_final: 0.7909 (pp) outliers start: 31 outliers final: 10 residues processed: 126 average time/residue: 0.3754 time to fit residues: 52.9231 Evaluate side-chains 108 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 597 HIS 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 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 1045 ASN Chi-restraints excluded: chain A residue 1308 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: 3.9990 chunk 37 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS A 812 ASN A1287 ASN A1305 GLN ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.128937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.101064 restraints weight = 25440.162| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.79 r_work: 0.3471 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12650 Z= 0.234 Angle : 0.660 9.111 17656 Z= 0.362 Chirality : 0.046 0.284 1999 Planarity : 0.004 0.036 1785 Dihedral : 19.329 176.689 3103 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.51 % Allowed : 15.02 % Favored : 81.46 % 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: 0.32 (0.25), residues: 1114 helix: 0.45 (0.23), residues: 532 sheet: -0.53 (0.48), residues: 114 loop : 0.36 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1078 TYR 0.017 0.002 TYR A1329 PHE 0.019 0.002 PHE A 97 TRP 0.023 0.002 TRP A1530 HIS 0.026 0.002 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 (12648) covalent geometry : angle 0.65918 / 0.36 (17652) SS BOND : bond 0.00893 / 0.47 ( 2) SS BOND : angle 1.77575 / 0.99 ( 4) hydrogen bonds : bond 0.05179 / 3.46 ( 531) hydrogen bonds : angle 4.62233 / 3.34 ( 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 129 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 495 ASP cc_start: 0.8201 (t0) cc_final: 0.7887 (t0) REVERT: A 528 ARG cc_start: 0.6927 (mtm180) cc_final: 0.6585 (mtm180) REVERT: A 629 MET cc_start: 0.6422 (tpt) cc_final: 0.5900 (ttp) REVERT: A 631 GLU cc_start: 0.6985 (tt0) cc_final: 0.6733 (tt0) REVERT: A 648 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8145 (m-30) REVERT: A 652 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7924 (mm-40) REVERT: A 694 PHE cc_start: 0.8280 (t80) cc_final: 0.8017 (t80) REVERT: A 712 ASP cc_start: 0.7941 (m-30) cc_final: 0.7731 (m-30) REVERT: A 726 HIS cc_start: 0.8038 (OUTLIER) cc_final: 0.7647 (t70) REVERT: A 788 LYS cc_start: 0.9246 (mmmt) cc_final: 0.8955 (mppt) REVERT: A 806 GLU cc_start: 0.7932 (pm20) cc_final: 0.7645 (pm20) REVERT: A 938 ASN cc_start: 0.7855 (m-40) cc_final: 0.7546 (m-40) REVERT: A 942 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7788 (mm-30) REVERT: A 976 LYS cc_start: 0.8664 (mttt) cc_final: 0.7838 (pmtt) REVERT: A 992 ARG cc_start: 0.6862 (ttm170) cc_final: 0.6488 (ttp80) REVERT: A 1006 ARG cc_start: 0.8275 (ptt180) cc_final: 0.7995 (ptp-170) REVERT: A 1047 ARG cc_start: 0.8202 (mtt90) cc_final: 0.7529 (tpt170) REVERT: A 1069 GLU cc_start: 0.7683 (pm20) cc_final: 0.7389 (pm20) REVERT: A 1552 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8259 (m-30) outliers start: 36 outliers final: 15 residues processed: 121 average time/residue: 0.3892 time to fit residues: 52.6566 Evaluate side-chains 105 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 428 VAL Chi-restraints excluded: chain A residue 453 ASN 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 795 SER Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1031 ASP Chi-restraints excluded: chain A residue 1045 ASN Chi-restraints excluded: chain A residue 1308 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 1565 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 7 optimal weight: 0.7980 chunk 50 optimal weight: 0.0870 chunk 99 optimal weight: 6.9990 chunk 104 optimal weight: 0.4980 chunk 27 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 ASN A1319 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.131703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.103978 restraints weight = 25234.521| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.80 r_work: 0.3520 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12650 Z= 0.135 Angle : 0.589 9.703 17656 Z= 0.328 Chirality : 0.041 0.212 1999 Planarity : 0.003 0.029 1785 Dihedral : 19.310 178.996 3102 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.73 % Allowed : 16.39 % Favored : 80.88 % 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: 0.57 (0.23), residues: 537 sheet: -0.36 (0.48), residues: 108 loop : 0.43 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1078 TYR 0.013 0.001 TYR A1329 PHE 0.018 0.001 PHE A 960 TRP 0.019 0.002 TRP A1530 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (12648) covalent geometry : angle 0.58807 / 0.33 (17652) SS BOND : bond 0.00755 / 0.39 ( 2) SS BOND : angle 1.70653 / 1.01 ( 4) hydrogen bonds : bond 0.04394 / 2.95 ( 531) hydrogen bonds : angle 4.39019 / 3.16 ( 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 129 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 495 ASP cc_start: 0.8130 (t0) cc_final: 0.7831 (t0) REVERT: A 528 ARG cc_start: 0.6779 (mtm180) cc_final: 0.6428 (mtm180) REVERT: A 629 MET cc_start: 0.6514 (tpt) cc_final: 0.6061 (ttp) REVERT: A 631 GLU cc_start: 0.6908 (tt0) cc_final: 0.6665 (tt0) REVERT: A 694 PHE cc_start: 0.8296 (t80) cc_final: 0.8010 (t80) REVERT: A 712 ASP cc_start: 0.7968 (m-30) cc_final: 0.7751 (m-30) REVERT: A 726 HIS cc_start: 0.8040 (OUTLIER) cc_final: 0.7646 (t70) REVERT: A 788 LYS cc_start: 0.9226 (mmmt) cc_final: 0.8940 (mppt) REVERT: A 806 GLU cc_start: 0.7932 (pm20) cc_final: 0.7652 (pm20) REVERT: A 938 ASN cc_start: 0.7802 (m-40) cc_final: 0.7501 (m-40) REVERT: A 942 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7826 (mm-30) REVERT: A 976 LYS cc_start: 0.8654 (mttt) cc_final: 0.7826 (pmtt) REVERT: A 992 ARG cc_start: 0.6909 (ttm170) cc_final: 0.6507 (ttp80) REVERT: A 1006 ARG cc_start: 0.8279 (ptt180) cc_final: 0.7995 (ptp-170) REVERT: A 1047 ARG cc_start: 0.8149 (mtt90) cc_final: 0.7515 (tpt170) REVERT: A 1069 GLU cc_start: 0.7616 (pm20) cc_final: 0.7351 (pm20) REVERT: A 1552 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8264 (m-30) REVERT: A 1563 LEU cc_start: 0.8538 (mm) cc_final: 0.8146 (pp) outliers start: 28 outliers final: 9 residues processed: 122 average time/residue: 0.4330 time to fit residues: 58.4521 Evaluate side-chains 98 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 726 HIS Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 1031 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 113 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 50 optimal weight: 0.1980 chunk 60 optimal weight: 0.0030 chunk 61 optimal weight: 0.8980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1288 ASN ** 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 = 0.4128 r_free = 0.4128 target = 0.132703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.105042 restraints weight = 25186.155| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.80 r_work: 0.3538 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12650 Z= 0.128 Angle : 0.574 9.083 17656 Z= 0.320 Chirality : 0.040 0.193 1999 Planarity : 0.003 0.042 1785 Dihedral : 19.268 179.905 3102 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.73 % Allowed : 17.27 % Favored : 80.00 % 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: 0.55 (0.25), residues: 1114 helix: 0.65 (0.23), residues: 538 sheet: -0.30 (0.48), residues: 108 loop : 0.42 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 622 TYR 0.012 0.001 TYR A1329 PHE 0.018 0.001 PHE A 960 TRP 0.021 0.002 TRP A1530 HIS 0.003 0.001 HIS A1236 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (12648) covalent geometry : angle 0.57401 / 0.32 (17652) SS BOND : bond 0.00715 / 0.37 ( 2) SS BOND : angle 1.63054 / 0.97 ( 4) hydrogen bonds : bond 0.04193 / 2.82 ( 531) hydrogen bonds : angle 4.30905 / 3.10 ( 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 126 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 495 ASP cc_start: 0.8103 (t0) cc_final: 0.7797 (t0) REVERT: A 528 ARG cc_start: 0.6743 (mtm180) cc_final: 0.6376 (mtm180) REVERT: A 629 MET cc_start: 0.6551 (tpt) cc_final: 0.6055 (ttp) REVERT: A 631 GLU cc_start: 0.6870 (tt0) cc_final: 0.6631 (tt0) REVERT: A 694 PHE cc_start: 0.8306 (t80) cc_final: 0.8001 (t80) REVERT: A 712 ASP cc_start: 0.8009 (m-30) cc_final: 0.7801 (m-30) REVERT: A 726 HIS cc_start: 0.8035 (OUTLIER) cc_final: 0.7658 (t70) REVERT: A 788 LYS cc_start: 0.9216 (mmmt) cc_final: 0.8927 (mppt) REVERT: A 806 GLU cc_start: 0.7919 (pm20) cc_final: 0.7619 (pm20) REVERT: A 812 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8456 (t0) REVERT: A 938 ASN cc_start: 0.7744 (m-40) cc_final: 0.7474 (m-40) REVERT: A 942 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7785 (mm-30) REVERT: A 976 LYS cc_start: 0.8645 (mttt) cc_final: 0.7822 (pmtt) REVERT: A 992 ARG cc_start: 0.6878 (ttm170) cc_final: 0.6496 (ttp80) REVERT: A 1006 ARG cc_start: 0.8284 (ptt180) cc_final: 0.8003 (ptp-170) REVERT: A 1047 ARG cc_start: 0.8149 (mtt90) cc_final: 0.7509 (tpt170) REVERT: A 1069 GLU cc_start: 0.7608 (pm20) cc_final: 0.7341 (pm20) REVERT: A 1552 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8239 (m-30) outliers start: 28 outliers final: 11 residues processed: 116 average time/residue: 0.4055 time to fit residues: 52.3410 Evaluate side-chains 107 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 597 HIS 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 1031 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 73 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 0.4980 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 104 optimal weight: 8.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1319 ASN ** 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 = 0.4121 r_free = 0.4121 target = 0.132175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.104648 restraints weight = 25177.456| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.75 r_work: 0.3534 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12650 Z= 0.137 Angle : 0.576 8.967 17656 Z= 0.320 Chirality : 0.041 0.190 1999 Planarity : 0.003 0.034 1785 Dihedral : 19.242 179.973 3102 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.44 % Allowed : 17.37 % Favored : 80.20 % 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 (0.25), residues: 1114 helix: 0.72 (0.23), residues: 537 sheet: -0.32 (0.48), residues: 108 loop : 0.38 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 622 TYR 0.014 0.001 TYR A1406 PHE 0.018 0.001 PHE A 542 TRP 0.022 0.002 TRP A1530 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (12648) covalent geometry : angle 0.57541 / 0.32 (17652) SS BOND : bond 0.00694 / 0.36 ( 2) SS BOND : angle 1.58433 / 0.93 ( 4) hydrogen bonds : bond 0.04186 / 2.82 ( 531) hydrogen bonds : angle 4.28728 / 3.08 ( 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: 25 poor density : 99 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 495 ASP cc_start: 0.8073 (t0) cc_final: 0.7780 (t0) REVERT: A 528 ARG cc_start: 0.6753 (mtm180) cc_final: 0.6362 (mtm180) REVERT: A 629 MET cc_start: 0.6523 (tpt) cc_final: 0.6092 (ttp) REVERT: A 631 GLU cc_start: 0.6923 (tt0) cc_final: 0.6667 (tt0) REVERT: A 694 PHE cc_start: 0.8339 (t80) cc_final: 0.8016 (t80) REVERT: A 726 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7659 (t70) REVERT: A 788 LYS cc_start: 0.9232 (mmmt) cc_final: 0.8951 (mppt) REVERT: A 806 GLU cc_start: 0.7922 (pm20) cc_final: 0.7649 (pm20) REVERT: A 812 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8423 (t0) REVERT: A 942 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7821 (mm-30) REVERT: A 976 LYS cc_start: 0.8650 (mttt) cc_final: 0.7824 (pmtt) REVERT: A 992 ARG cc_start: 0.6910 (ttm170) cc_final: 0.6541 (ttp80) REVERT: A 1006 ARG cc_start: 0.8284 (ptt180) cc_final: 0.8019 (ptp-170) REVERT: A 1029 ILE cc_start: 0.6911 (OUTLIER) cc_final: 0.6369 (mp) REVERT: A 1047 ARG cc_start: 0.8132 (mtt90) cc_final: 0.7527 (tpt170) REVERT: A 1069 GLU cc_start: 0.7622 (pm20) cc_final: 0.7369 (pm20) REVERT: A 1309 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8535 (tm) REVERT: A 1552 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8221 (m-30) outliers start: 25 outliers final: 14 residues processed: 115 average time/residue: 0.4015 time to fit residues: 51.2826 Evaluate side-chains 112 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 597 HIS Chi-restraints excluded: chain A residue 683 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 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 1552 ASP Chi-restraints excluded: chain A residue 1554 ASN Chi-restraints excluded: chain A residue 1567 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 81 optimal weight: 2.9990 chunk 25 optimal weight: 0.0270 chunk 89 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 554 ASN ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4123 r_free = 0.4123 target = 0.132384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.104777 restraints weight = 25030.261| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.75 r_work: 0.3540 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12650 Z= 0.135 Angle : 0.581 9.397 17656 Z= 0.322 Chirality : 0.040 0.187 1999 Planarity : 0.003 0.028 1785 Dihedral : 19.232 179.726 3102 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.24 % Allowed : 17.66 % 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: 0.60 (0.25), residues: 1114 helix: 0.75 (0.23), residues: 537 sheet: -0.30 (0.48), residues: 108 loop : 0.37 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1078 TYR 0.014 0.001 TYR A1549 PHE 0.020 0.001 PHE A 960 TRP 0.022 0.002 TRP A1530 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (12648) covalent geometry : angle 0.58013 / 0.32 (17652) SS BOND : bond 0.00665 / 0.35 ( 2) SS BOND : angle 1.55040 / 0.91 ( 4) hydrogen bonds : bond 0.04141 / 2.79 ( 531) hydrogen bonds : angle 4.26984 / 3.06 ( 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 119 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 495 ASP cc_start: 0.8068 (t0) cc_final: 0.7782 (t0) REVERT: A 528 ARG cc_start: 0.6723 (mtm180) cc_final: 0.6064 (mtm180) REVERT: A 629 MET cc_start: 0.6512 (tpt) cc_final: 0.6035 (ttm) REVERT: A 631 GLU cc_start: 0.6915 (tt0) cc_final: 0.6686 (tt0) REVERT: A 694 PHE cc_start: 0.8361 (t80) cc_final: 0.8087 (t80) REVERT: A 726 HIS cc_start: 0.8026 (OUTLIER) cc_final: 0.7648 (t70) REVERT: A 788 LYS cc_start: 0.9234 (mmmt) cc_final: 0.8954 (mppt) REVERT: A 806 GLU cc_start: 0.7952 (pm20) cc_final: 0.7665 (pm20) REVERT: A 812 ASN cc_start: 0.8683 (OUTLIER) cc_final: 0.8384 (t0) REVERT: A 938 ASN cc_start: 0.7920 (m-40) cc_final: 0.7406 (m-40) REVERT: A 942 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7825 (mm-30) REVERT: A 976 LYS cc_start: 0.8658 (mttt) cc_final: 0.7826 (pmtt) REVERT: A 992 ARG cc_start: 0.6836 (ttm170) cc_final: 0.6487 (ttp80) REVERT: A 1006 ARG cc_start: 0.8270 (ptt180) cc_final: 0.8003 (ptp-170) REVERT: A 1047 ARG cc_start: 0.8126 (mtt90) cc_final: 0.7525 (tpt170) REVERT: A 1069 GLU cc_start: 0.7605 (pm20) cc_final: 0.7346 (pm20) REVERT: A 1309 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8529 (tm) outliers start: 23 outliers final: 14 residues processed: 110 average time/residue: 0.3725 time to fit residues: 45.8022 Evaluate side-chains 111 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 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 812 ASN 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 1554 ASN Chi-restraints excluded: chain A residue 1567 ILE Chi-restraints excluded: chain A residue 1572 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 19 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1319 ASN ** 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 = 0.4118 r_free = 0.4118 target = 0.131918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.104353 restraints weight = 24955.560| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.75 r_work: 0.3537 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12650 Z= 0.142 Angle : 0.586 9.331 17656 Z= 0.325 Chirality : 0.040 0.187 1999 Planarity : 0.003 0.031 1785 Dihedral : 19.220 179.807 3102 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.44 % Allowed : 17.46 % 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: 0.61 (0.25), residues: 1114 helix: 0.78 (0.23), residues: 537 sheet: -0.29 (0.48), residues: 108 loop : 0.36 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1078 TYR 0.015 0.001 TYR A1549 PHE 0.018 0.001 PHE A 960 TRP 0.024 0.002 TRP A1530 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (12648) covalent geometry : angle 0.58610 / 0.32 (17652) SS BOND : bond 0.00661 / 0.34 ( 2) SS BOND : angle 1.53710 / 0.90 ( 4) hydrogen bonds : bond 0.04187 / 2.83 ( 531) hydrogen bonds : angle 4.29285 / 3.06 ( 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 119 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.245 Fit side-chains REVERT: A 495 ASP cc_start: 0.8095 (t0) cc_final: 0.7818 (t0) REVERT: A 528 ARG cc_start: 0.6735 (mtm180) cc_final: 0.6087 (mtm180) REVERT: A 629 MET cc_start: 0.6419 (tpt) cc_final: 0.5952 (ttm) REVERT: A 631 GLU cc_start: 0.6893 (tt0) cc_final: 0.6654 (tt0) REVERT: A 694 PHE cc_start: 0.8358 (t80) cc_final: 0.8063 (t80) REVERT: A 726 HIS cc_start: 0.8014 (OUTLIER) cc_final: 0.7638 (t70) REVERT: A 788 LYS cc_start: 0.9232 (mmmt) cc_final: 0.8962 (mppt) REVERT: A 806 GLU cc_start: 0.7967 (pm20) cc_final: 0.7678 (pm20) REVERT: A 812 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8375 (t0) REVERT: A 938 ASN cc_start: 0.7948 (m-40) cc_final: 0.7435 (m-40) REVERT: A 942 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7822 (mm-30) REVERT: A 976 LYS cc_start: 0.8668 (mttt) cc_final: 0.7826 (pmtt) REVERT: A 992 ARG cc_start: 0.6855 (ttm170) cc_final: 0.6483 (ttp80) REVERT: A 1006 ARG cc_start: 0.8271 (ptt180) cc_final: 0.7998 (ptp-170) REVERT: A 1043 PHE cc_start: 0.6576 (t80) cc_final: 0.6309 (t80) REVERT: A 1047 ARG cc_start: 0.8165 (mtt90) cc_final: 0.7528 (tpt170) REVERT: A 1069 GLU cc_start: 0.7621 (pm20) cc_final: 0.7350 (pm20) REVERT: A 1309 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8537 (tm) REVERT: A 1552 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8260 (m-30) outliers start: 25 outliers final: 12 residues processed: 108 average time/residue: 0.3863 time to fit residues: 46.4361 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 : 0.260 ------------------------------------------------------------------------------- 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 693 LEU Chi-restraints excluded: chain A residue 699 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 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: 4.9990 chunk 12 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1410 GLN ** A1515 GLN ** 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 = 0.4116 r_free = 0.4116 target = 0.131747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.104142 restraints weight = 25260.594| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.76 r_work: 0.3529 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12650 Z= 0.145 Angle : 0.596 9.484 17656 Z= 0.328 Chirality : 0.041 0.185 1999 Planarity : 0.003 0.031 1785 Dihedral : 19.216 179.884 3102 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.95 % Allowed : 18.34 % Favored : 79.71 % 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: 0.61 (0.25), residues: 1114 helix: 0.79 (0.23), residues: 537 sheet: -0.30 (0.48), residues: 108 loop : 0.34 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1078 TYR 0.019 0.001 TYR A 516 PHE 0.019 0.001 PHE A 960 TRP 0.025 0.002 TRP A1530 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (12648) covalent geometry : angle 0.59560 / 0.33 (17652) SS BOND : bond 0.00637 / 0.33 ( 2) SS BOND : angle 1.53639 / 0.90 ( 4) hydrogen bonds : bond 0.04280 / 2.91 ( 531) hydrogen bonds : angle 4.30004 / 3.06 ( 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 116 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.408 Fit side-chains REVERT: A 495 ASP cc_start: 0.8148 (t0) cc_final: 0.7886 (t0) REVERT: A 629 MET cc_start: 0.6383 (tpt) cc_final: 0.5917 (ttm) REVERT: A 631 GLU cc_start: 0.6892 (tt0) cc_final: 0.6647 (tt0) REVERT: A 694 PHE cc_start: 0.8359 (t80) cc_final: 0.8067 (t80) REVERT: A 726 HIS cc_start: 0.7975 (OUTLIER) cc_final: 0.7588 (t70) REVERT: A 788 LYS cc_start: 0.9241 (mmmt) cc_final: 0.8974 (mppt) REVERT: A 806 GLU cc_start: 0.7974 (pm20) cc_final: 0.7691 (pm20) REVERT: A 812 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.8354 (t0) REVERT: A 938 ASN cc_start: 0.7952 (m-40) cc_final: 0.7444 (m-40) REVERT: A 942 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7813 (mm-30) REVERT: A 976 LYS cc_start: 0.8677 (mttt) cc_final: 0.7818 (pmtt) REVERT: A 992 ARG cc_start: 0.6855 (ttm170) cc_final: 0.6484 (ttp80) REVERT: A 1006 ARG cc_start: 0.8303 (ptt180) cc_final: 0.8026 (ptp-170) REVERT: A 1043 PHE cc_start: 0.6571 (t80) cc_final: 0.6302 (t80) REVERT: A 1047 ARG cc_start: 0.8169 (mtt90) cc_final: 0.7530 (tpt170) REVERT: A 1069 GLU cc_start: 0.7692 (pm20) cc_final: 0.7410 (pm20) REVERT: A 1309 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8547 (tm) REVERT: A 1552 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8271 (m-30) outliers start: 20 outliers final: 13 residues processed: 108 average time/residue: 0.4348 time to fit residues: 52.2488 Evaluate side-chains 107 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 597 HIS Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 699 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 855 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 122 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 109 optimal weight: 0.0020 chunk 26 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4118 r_free = 0.4118 target = 0.131783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.103988 restraints weight = 25125.323| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.83 r_work: 0.3527 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12650 Z= 0.143 Angle : 0.603 10.558 17656 Z= 0.331 Chirality : 0.040 0.184 1999 Planarity : 0.003 0.030 1785 Dihedral : 19.212 179.808 3102 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.05 % Allowed : 18.73 % Favored : 79.22 % 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: 0.61 (0.25), residues: 1114 helix: 0.79 (0.23), residues: 537 sheet: -0.30 (0.48), residues: 108 loop : 0.33 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1078 TYR 0.015 0.001 TYR A1549 PHE 0.019 0.001 PHE A 602 TRP 0.024 0.002 TRP A1530 HIS 0.010 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (12648) covalent geometry : angle 0.60238 / 0.33 (17652) SS BOND : bond 0.00649 / 0.34 ( 2) SS BOND : angle 1.53662 / 0.90 ( 4) hydrogen bonds : bond 0.04244 / 2.89 ( 531) hydrogen bonds : angle 4.27863 / 3.04 ( 1404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3236.53 seconds wall clock time: 55 minutes 55.84 seconds (3355.84 seconds total)