Starting phenix.real_space_refine on Thu Mar 5 15:09:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b2m_11988/03_2026/7b2m_11988_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b2m_11988/03_2026/7b2m_11988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7b2m_11988/03_2026/7b2m_11988_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b2m_11988/03_2026/7b2m_11988_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7b2m_11988/03_2026/7b2m_11988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b2m_11988/03_2026/7b2m_11988.map" } resolution = 3.39 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= 0.001 sd= 0.023 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: 5 Type Number sf(0) Gaussians S 41 5.16 5 C 7390 2.51 5 N 2016 2.21 5 O 2217 1.98 5 H 11534 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23198 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 10023 Classifications: {'peptide': 650} Link IDs: {'PCIS': 3, 'PTRANS': 41, 'TRANS': 605} Chain: "B" Number of atoms: 9444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 9444 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 27, 'TRANS': 586} Chain breaks: 4 Chain: "C" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1984 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "D" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1691 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.91, per 1000 atoms: 0.17 Number of scatterers: 23198 At special positions: 0 Unit cell: (167.645, 120.334, 109.021, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 41 16.00 O 2217 8.00 N 2016 7.00 C 7390 6.00 H 11534 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS B 820 " distance=2.03 Simple disulfide: pdb=" SG CYS A 635 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 876 " - pdb=" SG CYS C1590 " distance=2.03 Simple disulfide: pdb=" SG CYS B1394 " - pdb=" SG CYS C1566 " distance=2.03 Simple disulfide: pdb=" SG CYS C1471 " - pdb=" SG CYS C1535 " distance=2.04 Simple disulfide: pdb=" SG CYS C1583 " - pdb=" SG CYS C1588 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " 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 Links applied NAG-ASN " NAG A1801 " - " ASN A 226 " " NAG B1801 " - " ASN B 862 " " NAG B1802 " - " ASN B1328 " " NAG B1803 " - " ASN B1391 " Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 702.2 milliseconds 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2774 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 30 sheets defined 19.3% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 114 through 120 removed outlier: 4.346A pdb=" N LYS A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 327 Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 642 through 651 Processing helix chain 'B' and resid 996 through 1003 removed outlier: 3.576A pdb=" N VAL B1000 " --> pdb=" O SER B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1032 Proline residue: B1020 - end of helix Processing helix chain 'B' and resid 1038 through 1058 removed outlier: 3.980A pdb=" N LYS B1042 " --> pdb=" O PRO B1038 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP B1043 " --> pdb=" O PRO B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1090 Processing helix chain 'B' and resid 1096 through 1111 removed outlier: 3.938A pdb=" N LEU B1100 " --> pdb=" O SER B1096 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN B1110 " --> pdb=" O TRP B1106 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN B1111 " --> pdb=" O LEU B1107 " (cutoff:3.500A) Processing helix chain 'B' and resid 1126 through 1130 removed outlier: 3.819A pdb=" N GLY B1130 " --> pdb=" O SER B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1152 Processing helix chain 'B' and resid 1161 through 1185 removed outlier: 3.702A pdb=" N LYS B1165 " --> pdb=" O ALA B1161 " (cutoff:3.500A) Processing helix chain 'B' and resid 1189 through 1203 Processing helix chain 'B' and resid 1206 through 1221 Processing helix chain 'B' and resid 1258 through 1275 Processing helix chain 'B' and resid 1281 through 1294 removed outlier: 3.667A pdb=" N TRP B1288 " --> pdb=" O GLN B1284 " (cutoff:3.500A) Processing helix chain 'B' and resid 1302 through 1320 Processing helix chain 'C' and resid 1497 through 1507 removed outlier: 4.006A pdb=" N LEU C1504 " --> pdb=" O ASP C1500 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR C1505 " --> pdb=" O LEU C1501 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C1506 " --> pdb=" O GLU C1502 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C1507 " --> pdb=" O LYS C1503 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 removed outlier: 3.581A pdb=" N LYS D 64 " --> pdb=" O ASN D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.935A pdb=" N THR D 90 " --> pdb=" O PRO D 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 87 removed outlier: 7.455A pdb=" N SER A 38 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32 removed outlier: 3.689A pdb=" N ASN A 60 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 66 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 32 Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 145 Processing sheet with id=AA5, first strand: chain 'A' and resid 149 through 150 Processing sheet with id=AA6, first strand: chain 'A' and resid 185 through 192 removed outlier: 6.060A pdb=" N VAL A 178 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS A 188 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 176 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU A 190 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A 174 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 241 through 247 removed outlier: 4.054A pdb=" N MET A 262 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 251 through 253 removed outlier: 5.374A pdb=" N ILE A 252 " --> pdb=" O VAL A 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 293 through 295 Processing sheet with id=AB1, first strand: chain 'A' and resid 293 through 295 removed outlier: 4.495A pdb=" N TYR A 281 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 355 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 367 through 370 removed outlier: 3.562A pdb=" N ARG A 391 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 419 through 423 removed outlier: 3.892A pdb=" N GLU A 443 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A 450 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 472 through 476 removed outlier: 4.156A pdb=" N THR A 527 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 515 through 522 removed outlier: 3.605A pdb=" N PHE A 517 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N HIS A 504 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TYR A 548 " --> pdb=" O HIS A 504 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 510 " --> pdb=" O TYR A 542 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 545 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HIS A 552 " --> pdb=" O HIS A 549 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 515 through 522 removed outlier: 3.605A pdb=" N PHE A 517 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N HIS A 504 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TYR A 548 " --> pdb=" O HIS A 504 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 510 " --> pdb=" O TYR A 542 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 572 through 574 removed outlier: 3.539A pdb=" N GLU A 592 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 814 " --> pdb=" O GLY B 818 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 785 through 798 removed outlier: 3.951A pdb=" N ARG B 791 " --> pdb=" O SER A 595 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N SER A 595 " --> pdb=" O ARG B 791 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLN B 793 " --> pdb=" O THR A 593 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N THR A 593 " --> pdb=" O GLN B 793 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU B 795 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU A 591 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU B 797 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU A 589 " --> pdb=" O LEU B 797 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 774 through 775 removed outlier: 6.996A pdb=" N VAL B 843 " --> pdb=" O GLU B 934 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 774 through 775 removed outlier: 3.546A pdb=" N VAL B 909 " --> pdb=" O LEU B 931 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 867 " --> pdb=" O GLN B 885 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 833 through 836 Processing sheet with id=AC3, first strand: chain 'B' and resid 849 through 851 removed outlier: 3.712A pdb=" N VAL B 902 " --> pdb=" O CYS B 876 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS B 876 " --> pdb=" O VAL B 902 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 938 through 945 Processing sheet with id=AC5, first strand: chain 'B' and resid 959 through 960 Processing sheet with id=AC6, first strand: chain 'B' and resid 1397 through 1405 Processing sheet with id=AC7, first strand: chain 'B' and resid 1397 through 1405 removed outlier: 3.574A pdb=" N VAL C1536 " --> pdb=" O VAL C1470 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1512 through 1518 removed outlier: 3.744A pdb=" N HIS C1514 " --> pdb=" O TYR C1525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1581 through 1583 Processing sheet with id=AD1, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.561A pdb=" N THR D 77 " --> pdb=" O ASP D 72 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 57 through 59 removed outlier: 3.528A pdb=" N VAL D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N SER D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 57 through 59 removed outlier: 3.528A pdb=" N VAL D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N SER D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA D 91 " --> pdb=" O VAL D 112 " (cutoff:3.500A) 522 hydrogen bonds defined for protein. 1416 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.05 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 11532 1.04 - 1.23: 771 1.23 - 1.43: 4229 1.43 - 1.63: 6851 1.63 - 1.83: 64 Bond restraints: 23447 Sorted by residual: bond pdb=" C1 NAG B1801 " pdb=" O5 NAG B1801 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.40e+00 bond pdb=" C1 NAG B1803 " pdb=" O5 NAG B1803 " ideal model delta sigma weight residual 1.406 1.429 -0.023 2.00e-02 2.50e+03 1.31e+00 bond pdb=" C5 NAG B1801 " pdb=" O5 NAG B1801 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.25e+00 bond pdb=" C5 NAG B1803 " pdb=" O5 NAG B1803 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.15e+00 bond pdb=" C5 NAG A1801 " pdb=" O5 NAG A1801 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.10e+00 ... (remaining 23442 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 39766 0.98 - 1.97: 2421 1.97 - 2.95: 117 2.95 - 3.93: 69 3.93 - 4.92: 8 Bond angle restraints: 42381 Sorted by residual: angle pdb=" N CYS C1535 " pdb=" CA CYS C1535 " pdb=" C CYS C1535 " ideal model delta sigma weight residual 108.14 111.38 -3.24 1.52e+00 4.33e-01 4.56e+00 angle pdb=" C GLU C1534 " pdb=" N CYS C1535 " pdb=" CA CYS C1535 " ideal model delta sigma weight residual 122.09 118.48 3.61 1.86e+00 2.89e-01 3.77e+00 angle pdb=" CA PRO C1530 " pdb=" C PRO C1530 " pdb=" N THR C1531 " ideal model delta sigma weight residual 114.74 116.71 -1.97 1.03e+00 9.43e-01 3.65e+00 angle pdb=" N SER A 613 " pdb=" CA SER A 613 " pdb=" C SER A 613 " ideal model delta sigma weight residual 108.14 111.01 -2.87 1.52e+00 4.33e-01 3.57e+00 angle pdb=" N ARG A 494 " pdb=" CA ARG A 494 " pdb=" C ARG A 494 " ideal model delta sigma weight residual 108.13 111.29 -3.16 1.72e+00 3.38e-01 3.37e+00 ... (remaining 42376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.32: 10256 20.32 - 40.64: 664 40.64 - 60.96: 199 60.96 - 81.27: 14 81.27 - 101.59: 13 Dihedral angle restraints: 11146 sinusoidal: 6130 harmonic: 5016 Sorted by residual: dihedral pdb=" CB CYS A 635 " pdb=" SG CYS A 635 " pdb=" SG CYS A 669 " pdb=" CB CYS A 669 " ideal model delta sinusoidal sigma weight residual 93.00 35.32 57.68 1 1.00e+01 1.00e-02 4.47e+01 dihedral pdb=" CB CYS A 567 " pdb=" SG CYS A 567 " pdb=" SG CYS B 820 " pdb=" CB CYS B 820 " ideal model delta sinusoidal sigma weight residual 93.00 37.73 55.27 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CB CYS C1471 " pdb=" SG CYS C1471 " pdb=" SG CYS C1535 " pdb=" CB CYS C1535 " ideal model delta sinusoidal sigma weight residual 93.00 39.27 53.73 1 1.00e+01 1.00e-02 3.92e+01 ... (remaining 11143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1645 0.069 - 0.138: 192 0.138 - 0.207: 3 0.207 - 0.276: 1 0.276 - 0.344: 1 Chirality restraints: 1842 Sorted by residual: chirality pdb=" C1 NAG B1803 " pdb=" ND2 ASN B1391 " pdb=" C2 NAG B1803 " pdb=" O5 NAG B1803 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C1 NAG B1802 " pdb=" ND2 ASN B1328 " pdb=" C2 NAG B1802 " pdb=" O5 NAG B1802 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE C1485 " pdb=" N ILE C1485 " pdb=" C ILE C1485 " pdb=" CB ILE C1485 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.42e-01 ... (remaining 1839 not shown) Planarity restraints: 3512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1391 " -0.015 2.00e-02 2.50e+03 1.44e-02 2.57e+00 pdb=" CG ASN B1391 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN B1391 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B1391 " 0.017 2.00e-02 2.50e+03 pdb=" C1 NAG B1803 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 452 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO A 453 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 453 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 453 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 548 " 0.015 2.00e-02 2.50e+03 8.55e-03 2.19e+00 pdb=" CG TYR A 548 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 548 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 548 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 548 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 548 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 548 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 548 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TYR A 548 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 TYR A 548 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TYR A 548 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 TYR A 548 " 0.001 2.00e-02 2.50e+03 ... (remaining 3509 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1124 2.18 - 2.78: 46684 2.78 - 3.39: 62522 3.39 - 3.99: 83065 3.99 - 4.60: 127593 Nonbonded interactions: 320988 Sorted by model distance: nonbonded pdb=" O LEU A 23 " pdb="HE22 GLN A 128 " model vdw 1.574 2.450 nonbonded pdb=" O LYS A 53 " pdb=" HG SER A 114 " model vdw 1.599 2.450 nonbonded pdb=" OE1 GLU A 209 " pdb=" H GLU A 209 " model vdw 1.601 2.450 nonbonded pdb=" O SER B1065 " pdb=" HG1 THR B1079 " model vdw 1.613 2.450 nonbonded pdb="HE22 GLN B 848 " pdb=" HG SER B 900 " model vdw 1.613 2.100 ... (remaining 320983 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: 1.860 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: 0.080 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.370 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 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 : 0.003 0.034 11925 Z= 0.144 Angle : 0.499 5.450 16204 Z= 0.266 Chirality : 0.043 0.344 1842 Planarity : 0.003 0.038 2090 Dihedral : 14.434 101.593 4410 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.15 (0.22), residues: 1488 helix: 1.65 (0.34), residues: 243 sheet: -0.15 (0.24), residues: 508 loop : -0.59 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C1564 TYR 0.024 0.001 TYR A 548 PHE 0.008 0.001 PHE A 296 TRP 0.014 0.001 TRP A 360 HIS 0.003 0.001 HIS B1191 Details of bonding type rmsd covalent geometry : bond 0.00313 (11913) covalent geometry : angle 0.49341 (16176) SS BOND : bond 0.00284 ( 8) SS BOND : angle 1.06589 ( 16) hydrogen bonds : bond 0.23333 ( 466) hydrogen bonds : angle 9.67410 ( 1416) link_NAG-ASN : bond 0.00562 ( 4) link_NAG-ASN : angle 2.45212 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 SER cc_start: 0.7642 (p) cc_final: 0.7252 (m) REVERT: A 57 PHE cc_start: 0.8079 (p90) cc_final: 0.7810 (p90) REVERT: A 63 ARG cc_start: 0.6811 (tpp80) cc_final: 0.6511 (ttm110) REVERT: A 77 SER cc_start: 0.7722 (t) cc_final: 0.7460 (p) REVERT: A 82 PHE cc_start: 0.7108 (p90) cc_final: 0.6862 (p90) REVERT: A 116 TRP cc_start: 0.7744 (t60) cc_final: 0.7519 (t60) REVERT: A 125 THR cc_start: 0.7833 (t) cc_final: 0.7627 (p) REVERT: A 126 ASN cc_start: 0.8103 (p0) cc_final: 0.7877 (p0) REVERT: A 137 ARG cc_start: 0.7685 (ttt90) cc_final: 0.7439 (ttt-90) REVERT: A 138 ARG cc_start: 0.7907 (ptt90) cc_final: 0.7688 (ttp-110) REVERT: A 188 LYS cc_start: 0.7650 (tttp) cc_final: 0.7424 (ttmm) REVERT: A 234 LYS cc_start: 0.8013 (ttpp) cc_final: 0.7720 (ttpt) REVERT: A 251 TYR cc_start: 0.7948 (p90) cc_final: 0.7607 (p90) REVERT: A 269 ARG cc_start: 0.7446 (ttm-80) cc_final: 0.7238 (ttm-80) REVERT: A 270 TYR cc_start: 0.7775 (m-80) cc_final: 0.7298 (m-10) REVERT: A 346 GLU cc_start: 0.6854 (pt0) cc_final: 0.6540 (pt0) REVERT: A 353 GLU cc_start: 0.6824 (tp30) cc_final: 0.6608 (tp30) REVERT: A 364 SER cc_start: 0.8272 (p) cc_final: 0.7689 (t) REVERT: A 378 LEU cc_start: 0.7694 (pt) cc_final: 0.7474 (pp) REVERT: A 530 SER cc_start: 0.8359 (t) cc_final: 0.8137 (p) REVERT: A 532 PHE cc_start: 0.8098 (t80) cc_final: 0.7892 (t80) REVERT: A 534 ASP cc_start: 0.7421 (t0) cc_final: 0.7183 (m-30) REVERT: A 547 TYR cc_start: 0.8129 (p90) cc_final: 0.7913 (p90) REVERT: A 549 HIS cc_start: 0.7619 (t70) cc_final: 0.6613 (t-170) REVERT: A 570 LYS cc_start: 0.7347 (tmtt) cc_final: 0.7077 (tmtt) REVERT: A 656 ASP cc_start: 0.6843 (p0) cc_final: 0.6609 (p0) REVERT: B 809 HIS cc_start: 0.7126 (p-80) cc_final: 0.6803 (p-80) REVERT: B 811 LEU cc_start: 0.8247 (mt) cc_final: 0.7982 (mt) REVERT: B 858 TYR cc_start: 0.8450 (m-80) cc_final: 0.8145 (m-10) REVERT: B 930 VAL cc_start: 0.7970 (m) cc_final: 0.7734 (p) REVERT: B 1050 GLN cc_start: 0.7703 (tp40) cc_final: 0.7307 (tp40) REVERT: B 1053 TYR cc_start: 0.7653 (t80) cc_final: 0.7269 (t80) REVERT: B 1057 GLN cc_start: 0.7502 (tp40) cc_final: 0.7184 (mm-40) REVERT: B 1066 TYR cc_start: 0.7840 (m-80) cc_final: 0.7239 (m-80) REVERT: B 1084 LYS cc_start: 0.7667 (ttmt) cc_final: 0.7364 (tttt) REVERT: B 1101 GLN cc_start: 0.6697 (mt0) cc_final: 0.6495 (mt0) REVERT: B 1128 MET cc_start: 0.6844 (ptm) cc_final: 0.6638 (ptm) REVERT: B 1137 GLU cc_start: 0.6471 (mp0) cc_final: 0.5952 (mp0) REVERT: B 1165 LYS cc_start: 0.8240 (mtmt) cc_final: 0.7920 (mttt) REVERT: B 1262 ILE cc_start: 0.8611 (tp) cc_final: 0.8343 (mt) REVERT: B 1267 TYR cc_start: 0.8397 (m-80) cc_final: 0.8004 (m-80) REVERT: B 1355 GLU cc_start: 0.7073 (mp0) cc_final: 0.6550 (mp0) REVERT: B 1360 PHE cc_start: 0.6789 (p90) cc_final: 0.6348 (p90) REVERT: D 81 GLN cc_start: 0.7680 (tt0) cc_final: 0.7465 (tt0) REVERT: D 102 ILE cc_start: 0.8298 (tt) cc_final: 0.7949 (tp) outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.2773 time to fit residues: 143.3711 Evaluate side-chains 342 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.0670 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.0470 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 HIS B 932 GLN B 963 ASN D 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.099974 restraints weight = 56467.301| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.57 r_work: 0.3168 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11925 Z= 0.176 Angle : 0.574 7.449 16204 Z= 0.298 Chirality : 0.044 0.206 1842 Planarity : 0.004 0.045 2090 Dihedral : 6.752 64.131 1703 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.87 % Allowed : 9.38 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.18 (0.22), residues: 1488 helix: 1.55 (0.32), residues: 263 sheet: -0.10 (0.23), residues: 512 loop : -0.70 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 895 TYR 0.020 0.001 TYR A 548 PHE 0.013 0.001 PHE A 74 TRP 0.014 0.001 TRP A 360 HIS 0.005 0.001 HIS B 834 Details of bonding type rmsd covalent geometry : bond 0.00390 (11913) covalent geometry : angle 0.56822 (16176) SS BOND : bond 0.00394 ( 8) SS BOND : angle 1.76286 ( 16) hydrogen bonds : bond 0.04988 ( 466) hydrogen bonds : angle 6.59354 ( 1416) link_NAG-ASN : bond 0.00373 ( 4) link_NAG-ASN : angle 2.50393 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 355 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7334 (mtpt) cc_final: 0.6956 (mtmm) REVERT: A 55 SER cc_start: 0.7787 (p) cc_final: 0.7362 (m) REVERT: A 57 PHE cc_start: 0.8056 (p90) cc_final: 0.7784 (p90) REVERT: A 63 ARG cc_start: 0.7526 (tpp80) cc_final: 0.7055 (ttm110) REVERT: A 116 TRP cc_start: 0.7678 (t60) cc_final: 0.7359 (t60) REVERT: A 119 ASP cc_start: 0.7192 (p0) cc_final: 0.6795 (p0) REVERT: A 125 THR cc_start: 0.8206 (t) cc_final: 0.7870 (p) REVERT: A 137 ARG cc_start: 0.8077 (ttt90) cc_final: 0.7627 (ttt-90) REVERT: A 138 ARG cc_start: 0.8235 (ptt90) cc_final: 0.7894 (ttp-110) REVERT: A 188 LYS cc_start: 0.8097 (tttp) cc_final: 0.7879 (ttmm) REVERT: A 234 LYS cc_start: 0.8184 (ttpp) cc_final: 0.7799 (ttpt) REVERT: A 251 TYR cc_start: 0.8099 (p90) cc_final: 0.7765 (p90) REVERT: A 270 TYR cc_start: 0.8134 (m-80) cc_final: 0.7678 (m-10) REVERT: A 346 GLU cc_start: 0.7694 (pt0) cc_final: 0.7267 (pt0) REVERT: A 353 GLU cc_start: 0.7542 (tp30) cc_final: 0.7151 (mm-30) REVERT: A 364 SER cc_start: 0.8408 (p) cc_final: 0.7832 (t) REVERT: A 404 LYS cc_start: 0.8345 (mmmt) cc_final: 0.8024 (ttmm) REVERT: A 424 ASN cc_start: 0.7822 (t0) cc_final: 0.7426 (t0) REVERT: A 494 ARG cc_start: 0.7861 (ttm110) cc_final: 0.7625 (ttm110) REVERT: A 521 GLU cc_start: 0.7895 (tp30) cc_final: 0.7672 (tp30) REVERT: A 585 GLU cc_start: 0.7728 (mm-30) cc_final: 0.6949 (mm-30) REVERT: A 648 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7397 (mm110) REVERT: B 807 GLU cc_start: 0.7524 (tm-30) cc_final: 0.7176 (tm-30) REVERT: B 811 LEU cc_start: 0.8274 (mt) cc_final: 0.8002 (mt) REVERT: B 858 TYR cc_start: 0.8507 (m-80) cc_final: 0.8180 (m-10) REVERT: B 1013 GLN cc_start: 0.6820 (tt0) cc_final: 0.6589 (tp40) REVERT: B 1050 GLN cc_start: 0.7931 (tp40) cc_final: 0.7610 (tp40) REVERT: B 1057 GLN cc_start: 0.7700 (tp40) cc_final: 0.7487 (mm-40) REVERT: B 1066 TYR cc_start: 0.8123 (m-80) cc_final: 0.7577 (m-80) REVERT: B 1101 GLN cc_start: 0.7140 (mt0) cc_final: 0.6883 (mt0) REVERT: B 1102 GLU cc_start: 0.8000 (tt0) cc_final: 0.7774 (mt-10) REVERT: B 1125 ASP cc_start: 0.7936 (t0) cc_final: 0.7586 (t0) REVERT: B 1128 MET cc_start: 0.7342 (ptm) cc_final: 0.7119 (ptm) REVERT: B 1137 GLU cc_start: 0.7012 (mp0) cc_final: 0.6731 (mp0) REVERT: B 1162 GLU cc_start: 0.7484 (mp0) cc_final: 0.7192 (mp0) REVERT: B 1166 GLN cc_start: 0.8408 (mm-40) cc_final: 0.7917 (mm-40) REVERT: B 1267 TYR cc_start: 0.8460 (m-80) cc_final: 0.8247 (m-80) REVERT: B 1355 GLU cc_start: 0.7390 (mp0) cc_final: 0.7091 (mp0) REVERT: B 1356 GLU cc_start: 0.8037 (tt0) cc_final: 0.7575 (tp30) REVERT: B 1360 PHE cc_start: 0.7100 (p90) cc_final: 0.6871 (p90) REVERT: C 1483 MET cc_start: 0.6916 (ptp) cc_final: 0.6145 (ptp) REVERT: C 1575 LYS cc_start: 0.7736 (mmtm) cc_final: 0.7498 (mmtp) REVERT: D 81 GLN cc_start: 0.7894 (tt0) cc_final: 0.7625 (tt0) REVERT: D 102 ILE cc_start: 0.8276 (tt) cc_final: 0.7926 (tp) outliers start: 11 outliers final: 9 residues processed: 357 average time/residue: 0.2872 time to fit residues: 138.5294 Evaluate side-chains 350 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 341 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1292 GLN Chi-restraints excluded: chain D residue 60 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 129 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 85 optimal weight: 0.0010 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 HIS B1176 ASN B1367 ASN D 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.117955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.100891 restraints weight = 54866.998| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.48 r_work: 0.3148 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 11925 Z= 0.251 Angle : 0.602 7.105 16204 Z= 0.314 Chirality : 0.044 0.240 1842 Planarity : 0.005 0.047 2090 Dihedral : 5.619 54.871 1703 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.05 % Allowed : 11.75 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.41 (0.22), residues: 1488 helix: 1.50 (0.32), residues: 263 sheet: -0.31 (0.23), residues: 513 loop : -0.86 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 157 TYR 0.030 0.002 TYR A 548 PHE 0.019 0.002 PHE A 74 TRP 0.017 0.002 TRP A 360 HIS 0.007 0.001 HIS B 834 Details of bonding type rmsd covalent geometry : bond 0.00559 (11913) covalent geometry : angle 0.59363 (16176) SS BOND : bond 0.00505 ( 8) SS BOND : angle 2.05311 ( 16) hydrogen bonds : bond 0.04666 ( 466) hydrogen bonds : angle 6.05783 ( 1416) link_NAG-ASN : bond 0.00287 ( 4) link_NAG-ASN : angle 2.94640 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 361 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7389 (mtpt) cc_final: 0.6996 (mtmm) REVERT: A 55 SER cc_start: 0.7844 (p) cc_final: 0.7386 (m) REVERT: A 57 PHE cc_start: 0.8090 (p90) cc_final: 0.7860 (p90) REVERT: A 63 ARG cc_start: 0.7539 (tpp80) cc_final: 0.7128 (ttm110) REVERT: A 116 TRP cc_start: 0.7712 (t60) cc_final: 0.7339 (t60) REVERT: A 119 ASP cc_start: 0.7126 (p0) cc_final: 0.6684 (p0) REVERT: A 125 THR cc_start: 0.8242 (t) cc_final: 0.7894 (p) REVERT: A 137 ARG cc_start: 0.8112 (ttt90) cc_final: 0.7908 (ttt90) REVERT: A 138 ARG cc_start: 0.8284 (ptt90) cc_final: 0.8034 (ptt-90) REVERT: A 188 LYS cc_start: 0.8193 (tttp) cc_final: 0.7975 (ttmm) REVERT: A 270 TYR cc_start: 0.8168 (m-80) cc_final: 0.7706 (m-10) REVERT: A 346 GLU cc_start: 0.7757 (pt0) cc_final: 0.7343 (pt0) REVERT: A 353 GLU cc_start: 0.7627 (tp30) cc_final: 0.7235 (mm-30) REVERT: A 356 GLU cc_start: 0.7301 (mm-30) cc_final: 0.7025 (mm-30) REVERT: A 364 SER cc_start: 0.8468 (p) cc_final: 0.7913 (t) REVERT: A 404 LYS cc_start: 0.8351 (mmmt) cc_final: 0.8002 (ttpp) REVERT: A 424 ASN cc_start: 0.7889 (t0) cc_final: 0.7577 (t0) REVERT: A 521 GLU cc_start: 0.7984 (tp30) cc_final: 0.7778 (tp30) REVERT: A 648 GLN cc_start: 0.7660 (mm-40) cc_final: 0.7444 (mm110) REVERT: B 811 LEU cc_start: 0.8269 (mt) cc_final: 0.8055 (mt) REVERT: B 858 TYR cc_start: 0.8522 (m-80) cc_final: 0.8168 (m-10) REVERT: B 943 GLU cc_start: 0.7244 (tm-30) cc_final: 0.7027 (tm-30) REVERT: B 1013 GLN cc_start: 0.6894 (tt0) cc_final: 0.6649 (tp40) REVERT: B 1050 GLN cc_start: 0.7919 (tp40) cc_final: 0.7586 (tp-100) REVERT: B 1057 GLN cc_start: 0.7762 (tp40) cc_final: 0.7484 (mm-40) REVERT: B 1101 GLN cc_start: 0.7120 (mt0) cc_final: 0.6862 (mt0) REVERT: B 1102 GLU cc_start: 0.7897 (tt0) cc_final: 0.7503 (mt-10) REVERT: B 1125 ASP cc_start: 0.7872 (t0) cc_final: 0.7487 (t0) REVERT: B 1128 MET cc_start: 0.7313 (ptm) cc_final: 0.7041 (ptm) REVERT: B 1137 GLU cc_start: 0.7044 (mp0) cc_final: 0.6755 (mp0) REVERT: B 1165 LYS cc_start: 0.8204 (mtmt) cc_final: 0.8001 (mttp) REVERT: B 1292 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.7242 (tp40) REVERT: B 1313 SER cc_start: 0.7593 (t) cc_final: 0.7028 (p) REVERT: B 1356 GLU cc_start: 0.8039 (tt0) cc_final: 0.7665 (tp30) REVERT: B 1389 MET cc_start: 0.6420 (ptp) cc_final: 0.5966 (ptt) REVERT: C 1516 GLU cc_start: 0.7874 (tp30) cc_final: 0.7651 (tp30) REVERT: C 1575 LYS cc_start: 0.7792 (mmtm) cc_final: 0.7557 (mmtp) REVERT: D 81 GLN cc_start: 0.7924 (tt0) cc_final: 0.7618 (tt0) REVERT: D 102 ILE cc_start: 0.8295 (tt) cc_final: 0.7892 (tp) outliers start: 26 outliers final: 20 residues processed: 368 average time/residue: 0.2938 time to fit residues: 145.7326 Evaluate side-chains 370 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 349 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1292 GLN Chi-restraints excluded: chain B residue 1302 THR Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain B residue 1381 LEU Chi-restraints excluded: chain C residue 1578 LEU Chi-restraints excluded: chain D residue 60 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 22 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 135 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN B 809 HIS D 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.120247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.103372 restraints weight = 54561.492| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.43 r_work: 0.3159 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11925 Z= 0.184 Angle : 0.568 8.040 16204 Z= 0.292 Chirality : 0.043 0.188 1842 Planarity : 0.004 0.050 2090 Dihedral : 5.225 46.656 1703 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.05 % Allowed : 13.96 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.37 (0.22), residues: 1488 helix: 1.63 (0.32), residues: 264 sheet: -0.27 (0.23), residues: 502 loop : -0.89 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 494 TYR 0.013 0.001 TYR A 507 PHE 0.015 0.001 PHE A 74 TRP 0.011 0.001 TRP A 360 HIS 0.033 0.002 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00406 (11913) covalent geometry : angle 0.55898 (16176) SS BOND : bond 0.00405 ( 8) SS BOND : angle 1.86535 ( 16) hydrogen bonds : bond 0.03967 ( 466) hydrogen bonds : angle 5.71212 ( 1416) link_NAG-ASN : bond 0.00357 ( 4) link_NAG-ASN : angle 3.13788 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 362 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7216 (t0) cc_final: 0.6944 (t70) REVERT: A 53 LYS cc_start: 0.7341 (mtpt) cc_final: 0.6961 (mtmm) REVERT: A 55 SER cc_start: 0.7851 (p) cc_final: 0.7397 (m) REVERT: A 119 ASP cc_start: 0.7140 (p0) cc_final: 0.6727 (p0) REVERT: A 125 THR cc_start: 0.8255 (t) cc_final: 0.7898 (p) REVERT: A 137 ARG cc_start: 0.8094 (ttt90) cc_final: 0.7887 (ttt90) REVERT: A 146 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6735 (t0) REVERT: A 252 ILE cc_start: 0.7812 (mm) cc_final: 0.7560 (mp) REVERT: A 270 TYR cc_start: 0.8175 (m-80) cc_final: 0.7751 (m-80) REVERT: A 346 GLU cc_start: 0.7658 (pt0) cc_final: 0.7280 (pt0) REVERT: A 353 GLU cc_start: 0.7589 (tp30) cc_final: 0.7237 (mm-30) REVERT: A 356 GLU cc_start: 0.7279 (mm-30) cc_final: 0.7013 (mm-30) REVERT: A 364 SER cc_start: 0.8419 (p) cc_final: 0.7887 (t) REVERT: A 404 LYS cc_start: 0.8326 (mmmt) cc_final: 0.8018 (ttpp) REVERT: A 424 ASN cc_start: 0.7847 (t0) cc_final: 0.7557 (t0) REVERT: A 494 ARG cc_start: 0.7885 (ttm110) cc_final: 0.7676 (ttm110) REVERT: A 521 GLU cc_start: 0.8073 (tp30) cc_final: 0.7866 (tp30) REVERT: A 547 TYR cc_start: 0.8452 (p90) cc_final: 0.8222 (p90) REVERT: A 563 GLN cc_start: 0.7350 (mm-40) cc_final: 0.7140 (mm-40) REVERT: A 570 LYS cc_start: 0.7503 (tmtt) cc_final: 0.7199 (tptp) REVERT: A 585 GLU cc_start: 0.7766 (mm-30) cc_final: 0.6964 (mm-30) REVERT: B 847 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7296 (mt-10) REVERT: B 852 ARG cc_start: 0.8235 (ttp-170) cc_final: 0.7901 (ttm110) REVERT: B 858 TYR cc_start: 0.8506 (m-80) cc_final: 0.8214 (m-10) REVERT: B 1013 GLN cc_start: 0.6909 (tt0) cc_final: 0.6684 (tp40) REVERT: B 1050 GLN cc_start: 0.7917 (tp40) cc_final: 0.7580 (tp-100) REVERT: B 1057 GLN cc_start: 0.7736 (tp40) cc_final: 0.7496 (mm-40) REVERT: B 1063 ASP cc_start: 0.6813 (p0) cc_final: 0.6411 (p0) REVERT: B 1101 GLN cc_start: 0.7151 (mt0) cc_final: 0.6898 (mt0) REVERT: B 1102 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7453 (mt-10) REVERT: B 1166 GLN cc_start: 0.8345 (mm-40) cc_final: 0.8093 (mm110) REVERT: B 1288 TRP cc_start: 0.7750 (t60) cc_final: 0.7543 (t60) REVERT: B 1313 SER cc_start: 0.7619 (t) cc_final: 0.7059 (p) REVERT: B 1355 GLU cc_start: 0.7377 (mp0) cc_final: 0.6940 (mp0) REVERT: B 1356 GLU cc_start: 0.8056 (tt0) cc_final: 0.7751 (tp30) REVERT: B 1389 MET cc_start: 0.6345 (ptp) cc_final: 0.5900 (ptt) REVERT: C 1483 MET cc_start: 0.7034 (ptp) cc_final: 0.6324 (ptp) REVERT: C 1575 LYS cc_start: 0.7835 (mmtm) cc_final: 0.7588 (mmtp) REVERT: D 81 GLN cc_start: 0.7932 (tt0) cc_final: 0.7665 (tt0) REVERT: D 102 ILE cc_start: 0.8276 (tt) cc_final: 0.7956 (tp) outliers start: 26 outliers final: 15 residues processed: 369 average time/residue: 0.2861 time to fit residues: 142.4801 Evaluate side-chains 368 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 351 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1292 GLN Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1330 THR Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain C residue 1578 LEU Chi-restraints excluded: chain D residue 60 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 117 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 137 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1359 GLN B1367 ASN D 39 GLN D 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.120301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.103672 restraints weight = 54313.411| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.43 r_work: 0.3186 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11925 Z= 0.152 Angle : 0.547 8.355 16204 Z= 0.279 Chirality : 0.043 0.178 1842 Planarity : 0.004 0.051 2090 Dihedral : 4.956 47.290 1703 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.05 % Allowed : 14.43 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.35 (0.22), residues: 1488 helix: 1.74 (0.32), residues: 264 sheet: -0.38 (0.23), residues: 524 loop : -0.82 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 155 TYR 0.011 0.001 TYR A 507 PHE 0.014 0.001 PHE A 74 TRP 0.010 0.001 TRP A 360 HIS 0.004 0.001 HIS B1150 Details of bonding type rmsd covalent geometry : bond 0.00345 (11913) covalent geometry : angle 0.53750 (16176) SS BOND : bond 0.00404 ( 8) SS BOND : angle 1.74587 ( 16) hydrogen bonds : bond 0.03694 ( 466) hydrogen bonds : angle 5.48329 ( 1416) link_NAG-ASN : bond 0.00373 ( 4) link_NAG-ASN : angle 3.22804 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 359 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7333 (mtpt) cc_final: 0.6949 (mtmm) REVERT: A 55 SER cc_start: 0.7838 (p) cc_final: 0.7383 (m) REVERT: A 116 TRP cc_start: 0.7589 (t60) cc_final: 0.7310 (t60) REVERT: A 119 ASP cc_start: 0.7113 (p0) cc_final: 0.6668 (p0) REVERT: A 125 THR cc_start: 0.8208 (t) cc_final: 0.7845 (p) REVERT: A 138 ARG cc_start: 0.8263 (ptt90) cc_final: 0.8045 (ptt-90) REVERT: A 146 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.6921 (t0) REVERT: A 252 ILE cc_start: 0.7826 (mm) cc_final: 0.7584 (mp) REVERT: A 270 TYR cc_start: 0.8172 (m-80) cc_final: 0.7779 (m-80) REVERT: A 346 GLU cc_start: 0.7654 (pt0) cc_final: 0.7269 (pt0) REVERT: A 353 GLU cc_start: 0.7583 (tp30) cc_final: 0.7333 (tp30) REVERT: A 356 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6984 (mm-30) REVERT: A 364 SER cc_start: 0.8402 (p) cc_final: 0.7887 (t) REVERT: A 404 LYS cc_start: 0.8296 (mmmt) cc_final: 0.7994 (ttpp) REVERT: A 424 ASN cc_start: 0.7825 (t0) cc_final: 0.7511 (t0) REVERT: A 521 GLU cc_start: 0.8065 (tp30) cc_final: 0.7835 (tp30) REVERT: A 570 LYS cc_start: 0.7500 (tmtt) cc_final: 0.7173 (tptp) REVERT: B 827 LEU cc_start: 0.8089 (tp) cc_final: 0.7879 (tt) REVERT: B 847 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7354 (mt-10) REVERT: B 852 ARG cc_start: 0.8206 (ttp-170) cc_final: 0.7890 (ttm110) REVERT: B 858 TYR cc_start: 0.8494 (m-80) cc_final: 0.8230 (m-80) REVERT: B 1013 GLN cc_start: 0.6947 (tt0) cc_final: 0.6714 (tp40) REVERT: B 1050 GLN cc_start: 0.7887 (tp40) cc_final: 0.7553 (tp40) REVERT: B 1101 GLN cc_start: 0.7101 (mt0) cc_final: 0.6844 (mt0) REVERT: B 1102 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7455 (mt-10) REVERT: B 1137 GLU cc_start: 0.7260 (mp0) cc_final: 0.7002 (mp0) REVERT: B 1165 LYS cc_start: 0.8199 (mtmt) cc_final: 0.7869 (mttp) REVERT: B 1166 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8112 (mm110) REVERT: B 1288 TRP cc_start: 0.7776 (t60) cc_final: 0.7514 (t60) REVERT: B 1291 ARG cc_start: 0.7662 (ttp80) cc_final: 0.7403 (ttm110) REVERT: B 1313 SER cc_start: 0.7606 (t) cc_final: 0.7043 (p) REVERT: B 1355 GLU cc_start: 0.7371 (mp0) cc_final: 0.6815 (mp0) REVERT: B 1356 GLU cc_start: 0.8047 (tt0) cc_final: 0.7776 (tp30) REVERT: B 1389 MET cc_start: 0.6402 (ptp) cc_final: 0.5965 (ptt) REVERT: C 1483 MET cc_start: 0.7056 (ptp) cc_final: 0.6314 (ptp) REVERT: C 1575 LYS cc_start: 0.7878 (mmtm) cc_final: 0.7629 (mmtp) REVERT: D 81 GLN cc_start: 0.7880 (tt0) cc_final: 0.7635 (tt0) REVERT: D 102 ILE cc_start: 0.8251 (tt) cc_final: 0.7923 (tp) outliers start: 26 outliers final: 18 residues processed: 367 average time/residue: 0.2899 time to fit residues: 143.9524 Evaluate side-chains 371 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 351 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1030 LYS Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1292 GLN Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1367 ASN Chi-restraints excluded: chain C residue 1553 SER Chi-restraints excluded: chain D residue 60 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.101452 restraints weight = 55315.746| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.46 r_work: 0.3137 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11925 Z= 0.187 Angle : 0.563 8.546 16204 Z= 0.289 Chirality : 0.043 0.188 1842 Planarity : 0.004 0.049 2090 Dihedral : 4.883 46.455 1703 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.13 % Allowed : 14.91 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.50 (0.22), residues: 1488 helix: 1.69 (0.32), residues: 265 sheet: -0.55 (0.22), residues: 543 loop : -0.88 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 137 TYR 0.013 0.001 TYR A 507 PHE 0.016 0.002 PHE A 74 TRP 0.011 0.001 TRP A 360 HIS 0.005 0.001 HIS B 834 Details of bonding type rmsd covalent geometry : bond 0.00422 (11913) covalent geometry : angle 0.55257 (16176) SS BOND : bond 0.00437 ( 8) SS BOND : angle 1.84014 ( 16) hydrogen bonds : bond 0.03722 ( 466) hydrogen bonds : angle 5.47336 ( 1416) link_NAG-ASN : bond 0.00317 ( 4) link_NAG-ASN : angle 3.35843 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 360 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7374 (mtpt) cc_final: 0.6963 (mtmm) REVERT: A 55 SER cc_start: 0.7825 (p) cc_final: 0.7346 (m) REVERT: A 77 SER cc_start: 0.7979 (t) cc_final: 0.7614 (p) REVERT: A 116 TRP cc_start: 0.7636 (t60) cc_final: 0.7373 (t60) REVERT: A 119 ASP cc_start: 0.7090 (p0) cc_final: 0.6643 (p0) REVERT: A 125 THR cc_start: 0.8226 (t) cc_final: 0.7853 (p) REVERT: A 138 ARG cc_start: 0.8300 (ptt90) cc_final: 0.8088 (ptt-90) REVERT: A 146 ASP cc_start: 0.7334 (OUTLIER) cc_final: 0.6988 (t0) REVERT: A 232 GLU cc_start: 0.7753 (tt0) cc_final: 0.7332 (tp30) REVERT: A 252 ILE cc_start: 0.7831 (mm) cc_final: 0.7600 (mp) REVERT: A 270 TYR cc_start: 0.8213 (m-80) cc_final: 0.7812 (m-80) REVERT: A 324 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7623 (tm-30) REVERT: A 346 GLU cc_start: 0.7703 (pt0) cc_final: 0.7358 (pt0) REVERT: A 353 GLU cc_start: 0.7673 (tp30) cc_final: 0.7431 (tp30) REVERT: A 364 SER cc_start: 0.8414 (p) cc_final: 0.7903 (t) REVERT: A 404 LYS cc_start: 0.8302 (mmmt) cc_final: 0.7930 (ttpp) REVERT: A 424 ASN cc_start: 0.7833 (t0) cc_final: 0.7517 (t0) REVERT: A 443 GLU cc_start: 0.7486 (pt0) cc_final: 0.7144 (pm20) REVERT: A 534 ASP cc_start: 0.7736 (t70) cc_final: 0.7229 (t70) REVERT: A 536 HIS cc_start: 0.7490 (m90) cc_final: 0.7108 (m90) REVERT: A 570 LYS cc_start: 0.7498 (tmtt) cc_final: 0.7164 (tptp) REVERT: B 827 LEU cc_start: 0.8071 (tp) cc_final: 0.7854 (tt) REVERT: B 832 GLU cc_start: 0.7373 (mp0) cc_final: 0.7020 (mp0) REVERT: B 852 ARG cc_start: 0.8270 (ttp-170) cc_final: 0.7932 (ttm110) REVERT: B 858 TYR cc_start: 0.8510 (m-80) cc_final: 0.8266 (m-80) REVERT: B 1050 GLN cc_start: 0.7861 (tp40) cc_final: 0.7522 (tp40) REVERT: B 1072 ARG cc_start: 0.6822 (mtp-110) cc_final: 0.6406 (ttp80) REVERT: B 1101 GLN cc_start: 0.7116 (mt0) cc_final: 0.6867 (mt0) REVERT: B 1102 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7446 (mt-10) REVERT: B 1137 GLU cc_start: 0.7283 (mp0) cc_final: 0.7034 (mp0) REVERT: B 1165 LYS cc_start: 0.8198 (mtmt) cc_final: 0.7946 (mttp) REVERT: B 1288 TRP cc_start: 0.7839 (t60) cc_final: 0.7590 (t60) REVERT: B 1291 ARG cc_start: 0.7666 (ttp80) cc_final: 0.7422 (ttm110) REVERT: B 1356 GLU cc_start: 0.8077 (tt0) cc_final: 0.7822 (tp30) REVERT: B 1360 PHE cc_start: 0.7084 (p90) cc_final: 0.6764 (p90) REVERT: B 1381 LEU cc_start: 0.7990 (pp) cc_final: 0.7764 (pp) REVERT: B 1389 MET cc_start: 0.6433 (ptp) cc_final: 0.6010 (ptt) REVERT: B 1411 MET cc_start: 0.5471 (mmm) cc_final: 0.5231 (mmp) REVERT: C 1483 MET cc_start: 0.7072 (ptp) cc_final: 0.6332 (ptp) REVERT: C 1575 LYS cc_start: 0.7880 (mmtm) cc_final: 0.7674 (mmtm) REVERT: D 56 ASN cc_start: 0.8211 (m-40) cc_final: 0.7774 (m110) REVERT: D 81 GLN cc_start: 0.7861 (tt0) cc_final: 0.7595 (tt0) REVERT: D 102 ILE cc_start: 0.8254 (tt) cc_final: 0.7902 (tp) outliers start: 27 outliers final: 23 residues processed: 368 average time/residue: 0.2934 time to fit residues: 144.7617 Evaluate side-chains 379 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 354 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1030 LYS Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1292 GLN Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain C residue 1553 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 60 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 11 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN B1129 GLN D 39 GLN D 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.119082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.102136 restraints weight = 55393.749| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.46 r_work: 0.3134 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11925 Z= 0.191 Angle : 0.565 8.664 16204 Z= 0.291 Chirality : 0.043 0.191 1842 Planarity : 0.004 0.049 2090 Dihedral : 4.857 46.003 1703 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.44 % Allowed : 15.85 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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 (0.22), residues: 1488 helix: 1.65 (0.32), residues: 265 sheet: -0.59 (0.22), residues: 544 loop : -0.94 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 155 TYR 0.014 0.001 TYR A 507 PHE 0.016 0.002 PHE A 74 TRP 0.010 0.001 TRP B 782 HIS 0.005 0.001 HIS B 834 Details of bonding type rmsd covalent geometry : bond 0.00430 (11913) covalent geometry : angle 0.55510 (16176) SS BOND : bond 0.00392 ( 8) SS BOND : angle 1.88997 ( 16) hydrogen bonds : bond 0.03696 ( 466) hydrogen bonds : angle 5.37364 ( 1416) link_NAG-ASN : bond 0.00329 ( 4) link_NAG-ASN : angle 3.37285 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 365 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8303 (m-80) cc_final: 0.8011 (m-80) REVERT: A 53 LYS cc_start: 0.7388 (mtpt) cc_final: 0.6969 (mtmm) REVERT: A 55 SER cc_start: 0.7835 (p) cc_final: 0.7333 (m) REVERT: A 77 SER cc_start: 0.8015 (t) cc_final: 0.7665 (p) REVERT: A 116 TRP cc_start: 0.7660 (t60) cc_final: 0.7412 (t60) REVERT: A 119 ASP cc_start: 0.7144 (p0) cc_final: 0.6672 (p0) REVERT: A 125 THR cc_start: 0.8240 (t) cc_final: 0.7878 (p) REVERT: A 138 ARG cc_start: 0.8333 (ptt90) cc_final: 0.8122 (ptt-90) REVERT: A 146 ASP cc_start: 0.7252 (OUTLIER) cc_final: 0.6840 (t0) REVERT: A 232 GLU cc_start: 0.7744 (tt0) cc_final: 0.7347 (tp30) REVERT: A 252 ILE cc_start: 0.7853 (mm) cc_final: 0.7639 (mp) REVERT: A 270 TYR cc_start: 0.8238 (m-80) cc_final: 0.7836 (m-80) REVERT: A 324 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7670 (tm-30) REVERT: A 353 GLU cc_start: 0.7691 (tp30) cc_final: 0.7456 (tp30) REVERT: A 364 SER cc_start: 0.8420 (p) cc_final: 0.7917 (t) REVERT: A 404 LYS cc_start: 0.8317 (mmmt) cc_final: 0.7942 (ttpp) REVERT: A 424 ASN cc_start: 0.7832 (t0) cc_final: 0.7515 (t0) REVERT: A 443 GLU cc_start: 0.7512 (pt0) cc_final: 0.7166 (pm20) REVERT: A 536 HIS cc_start: 0.7522 (m90) cc_final: 0.7256 (m170) REVERT: A 570 LYS cc_start: 0.7512 (tmtt) cc_final: 0.7190 (tptp) REVERT: B 827 LEU cc_start: 0.8088 (tp) cc_final: 0.7867 (tt) REVERT: B 832 GLU cc_start: 0.7402 (mp0) cc_final: 0.7011 (mp0) REVERT: B 852 ARG cc_start: 0.8272 (ttp-170) cc_final: 0.7938 (ttm110) REVERT: B 858 TYR cc_start: 0.8524 (m-80) cc_final: 0.8267 (m-80) REVERT: B 943 GLU cc_start: 0.7476 (tp30) cc_final: 0.7222 (tp30) REVERT: B 1050 GLN cc_start: 0.7865 (tp40) cc_final: 0.7548 (tp40) REVERT: B 1059 PHE cc_start: 0.7775 (m-80) cc_final: 0.7523 (m-80) REVERT: B 1072 ARG cc_start: 0.6813 (mtp-110) cc_final: 0.6296 (ttp80) REVERT: B 1101 GLN cc_start: 0.7110 (mt0) cc_final: 0.6859 (mt0) REVERT: B 1102 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: B 1137 GLU cc_start: 0.7330 (mp0) cc_final: 0.7094 (mp0) REVERT: B 1355 GLU cc_start: 0.7257 (mp0) cc_final: 0.7049 (mp0) REVERT: B 1360 PHE cc_start: 0.7078 (p90) cc_final: 0.6848 (p90) REVERT: B 1381 LEU cc_start: 0.7986 (pp) cc_final: 0.7646 (pp) REVERT: B 1389 MET cc_start: 0.6450 (ptp) cc_final: 0.6029 (ptt) REVERT: C 1483 MET cc_start: 0.7078 (ptp) cc_final: 0.6424 (ptp) REVERT: C 1575 LYS cc_start: 0.7875 (mmtm) cc_final: 0.7606 (mmtp) REVERT: D 56 ASN cc_start: 0.8204 (m-40) cc_final: 0.7760 (m110) REVERT: D 81 GLN cc_start: 0.7862 (tt0) cc_final: 0.7596 (tt0) REVERT: D 102 ILE cc_start: 0.8278 (tt) cc_final: 0.7902 (tp) outliers start: 31 outliers final: 26 residues processed: 376 average time/residue: 0.2887 time to fit residues: 146.4351 Evaluate side-chains 388 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 360 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 511 SER Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 1030 LYS Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1292 GLN Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain C residue 1553 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 80 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 76 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.118760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.101779 restraints weight = 54778.782| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.45 r_work: 0.3127 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11925 Z= 0.165 Angle : 0.562 8.965 16204 Z= 0.287 Chirality : 0.043 0.182 1842 Planarity : 0.004 0.050 2090 Dihedral : 4.769 47.157 1703 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.21 % Allowed : 16.32 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.54 (0.22), residues: 1488 helix: 1.67 (0.32), residues: 267 sheet: -0.58 (0.22), residues: 546 loop : -0.92 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 155 TYR 0.016 0.001 TYR B1409 PHE 0.015 0.002 PHE A 74 TRP 0.008 0.001 TRP B 782 HIS 0.004 0.001 HIS B1150 Details of bonding type rmsd covalent geometry : bond 0.00374 (11913) covalent geometry : angle 0.55206 (16176) SS BOND : bond 0.00503 ( 8) SS BOND : angle 1.78577 ( 16) hydrogen bonds : bond 0.03544 ( 466) hydrogen bonds : angle 5.25829 ( 1416) link_NAG-ASN : bond 0.00370 ( 4) link_NAG-ASN : angle 3.31228 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 357 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8300 (m-80) cc_final: 0.8006 (m-80) REVERT: A 53 LYS cc_start: 0.7377 (mtpt) cc_final: 0.6940 (mtmm) REVERT: A 55 SER cc_start: 0.7840 (p) cc_final: 0.7334 (m) REVERT: A 77 SER cc_start: 0.8015 (t) cc_final: 0.7679 (p) REVERT: A 119 ASP cc_start: 0.7027 (p0) cc_final: 0.6550 (p0) REVERT: A 125 THR cc_start: 0.8224 (t) cc_final: 0.7874 (p) REVERT: A 146 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.6855 (t0) REVERT: A 252 ILE cc_start: 0.7847 (mm) cc_final: 0.7638 (mp) REVERT: A 324 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7656 (tm-30) REVERT: A 353 GLU cc_start: 0.7694 (tp30) cc_final: 0.7420 (tp30) REVERT: A 364 SER cc_start: 0.8379 (p) cc_final: 0.7900 (t) REVERT: A 404 LYS cc_start: 0.8297 (mmmt) cc_final: 0.7907 (ttpp) REVERT: A 424 ASN cc_start: 0.7815 (t0) cc_final: 0.7486 (t0) REVERT: A 443 GLU cc_start: 0.7484 (pt0) cc_final: 0.7132 (pm20) REVERT: A 536 HIS cc_start: 0.7537 (m90) cc_final: 0.7263 (m90) REVERT: A 570 LYS cc_start: 0.7493 (tmtt) cc_final: 0.7165 (tptp) REVERT: B 827 LEU cc_start: 0.8069 (tp) cc_final: 0.7832 (tt) REVERT: B 852 ARG cc_start: 0.8273 (ttp-170) cc_final: 0.7982 (ttm170) REVERT: B 858 TYR cc_start: 0.8520 (m-80) cc_final: 0.8286 (m-80) REVERT: B 943 GLU cc_start: 0.7484 (tp30) cc_final: 0.7225 (tp30) REVERT: B 1050 GLN cc_start: 0.7839 (tp40) cc_final: 0.7434 (tp-100) REVERT: B 1059 PHE cc_start: 0.7750 (m-80) cc_final: 0.7508 (m-80) REVERT: B 1101 GLN cc_start: 0.7085 (mt0) cc_final: 0.6841 (mt0) REVERT: B 1102 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7436 (mt-10) REVERT: B 1114 ASP cc_start: 0.7156 (p0) cc_final: 0.6863 (p0) REVERT: B 1137 GLU cc_start: 0.7356 (mp0) cc_final: 0.7091 (mp0) REVERT: B 1220 MET cc_start: 0.6977 (mpp) cc_final: 0.6656 (mpp) REVERT: B 1288 TRP cc_start: 0.7814 (t60) cc_final: 0.7436 (t60) REVERT: B 1291 ARG cc_start: 0.7651 (ttp80) cc_final: 0.7109 (ttp-110) REVERT: B 1360 PHE cc_start: 0.7055 (p90) cc_final: 0.6855 (p90) REVERT: B 1381 LEU cc_start: 0.7994 (pp) cc_final: 0.7657 (pp) REVERT: B 1389 MET cc_start: 0.6445 (ptp) cc_final: 0.6036 (ptt) REVERT: C 1483 MET cc_start: 0.7083 (ptp) cc_final: 0.6403 (ptp) REVERT: C 1497 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7954 (tp) REVERT: C 1575 LYS cc_start: 0.7837 (mmtm) cc_final: 0.7620 (mmtm) REVERT: D 56 ASN cc_start: 0.8188 (m-40) cc_final: 0.7741 (m110) REVERT: D 81 GLN cc_start: 0.7832 (tt0) cc_final: 0.7567 (tt0) REVERT: D 102 ILE cc_start: 0.8223 (tt) cc_final: 0.7903 (tp) outliers start: 28 outliers final: 23 residues processed: 368 average time/residue: 0.2893 time to fit residues: 143.7977 Evaluate side-chains 380 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 354 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1030 LYS Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1292 GLN Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1370 VAL Chi-restraints excluded: chain C residue 1497 LEU Chi-restraints excluded: chain C residue 1553 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 80 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 0.0060 chunk 112 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1129 GLN D 39 GLN D 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.098213 restraints weight = 55780.132| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.55 r_work: 0.3109 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11925 Z= 0.243 Angle : 0.606 8.714 16204 Z= 0.314 Chirality : 0.044 0.211 1842 Planarity : 0.005 0.051 2090 Dihedral : 4.992 47.683 1703 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.05 % Allowed : 17.19 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.22), residues: 1488 helix: 1.34 (0.31), residues: 271 sheet: -0.83 (0.22), residues: 551 loop : -1.02 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B1072 TYR 0.017 0.002 TYR A 507 PHE 0.021 0.002 PHE A 74 TRP 0.012 0.002 TRP B 782 HIS 0.007 0.001 HIS B1150 Details of bonding type rmsd covalent geometry : bond 0.00547 (11913) covalent geometry : angle 0.59509 (16176) SS BOND : bond 0.00542 ( 8) SS BOND : angle 2.16688 ( 16) hydrogen bonds : bond 0.03899 ( 466) hydrogen bonds : angle 5.42917 ( 1416) link_NAG-ASN : bond 0.00311 ( 4) link_NAG-ASN : angle 3.42823 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 361 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7423 (mtpt) cc_final: 0.6979 (mtmm) REVERT: A 55 SER cc_start: 0.7863 (p) cc_final: 0.7319 (m) REVERT: A 77 SER cc_start: 0.8015 (t) cc_final: 0.7691 (p) REVERT: A 119 ASP cc_start: 0.7104 (p0) cc_final: 0.6652 (p0) REVERT: A 125 THR cc_start: 0.8224 (t) cc_final: 0.7889 (p) REVERT: A 146 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6715 (t0) REVERT: A 324 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7711 (tm-30) REVERT: A 353 GLU cc_start: 0.7696 (tp30) cc_final: 0.7468 (tp30) REVERT: A 364 SER cc_start: 0.8413 (p) cc_final: 0.7917 (t) REVERT: A 404 LYS cc_start: 0.8347 (mmmt) cc_final: 0.7976 (ttmm) REVERT: A 424 ASN cc_start: 0.7792 (t0) cc_final: 0.7496 (t0) REVERT: A 521 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7673 (mm-30) REVERT: A 536 HIS cc_start: 0.7592 (m90) cc_final: 0.7343 (m90) REVERT: A 570 LYS cc_start: 0.7501 (tmtt) cc_final: 0.7240 (tptp) REVERT: A 587 VAL cc_start: 0.8288 (p) cc_final: 0.7939 (m) REVERT: B 852 ARG cc_start: 0.8325 (ttp-170) cc_final: 0.8012 (ttm110) REVERT: B 858 TYR cc_start: 0.8525 (m-80) cc_final: 0.8314 (m-80) REVERT: B 943 GLU cc_start: 0.7453 (tp30) cc_final: 0.7148 (tp30) REVERT: B 1050 GLN cc_start: 0.7877 (tp40) cc_final: 0.7463 (tm-30) REVERT: B 1101 GLN cc_start: 0.7106 (mt0) cc_final: 0.6857 (mt0) REVERT: B 1102 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: B 1291 ARG cc_start: 0.7753 (ttp80) cc_final: 0.7286 (ttp-110) REVERT: B 1360 PHE cc_start: 0.7118 (p90) cc_final: 0.6904 (p90) REVERT: B 1381 LEU cc_start: 0.8006 (pp) cc_final: 0.7647 (pp) REVERT: B 1389 MET cc_start: 0.6393 (ptp) cc_final: 0.5971 (ptt) REVERT: D 56 ASN cc_start: 0.8265 (m-40) cc_final: 0.7906 (m-40) REVERT: D 81 GLN cc_start: 0.7849 (tt0) cc_final: 0.7554 (tt0) REVERT: D 102 ILE cc_start: 0.8289 (tt) cc_final: 0.7979 (tp) outliers start: 26 outliers final: 22 residues processed: 372 average time/residue: 0.3057 time to fit residues: 154.3147 Evaluate side-chains 378 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 354 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 1030 LYS Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1292 GLN Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1370 VAL Chi-restraints excluded: chain C residue 1497 LEU Chi-restraints excluded: chain C residue 1553 SER Chi-restraints excluded: chain D residue 60 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 61 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 4 optimal weight: 0.1980 chunk 57 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 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 64 ASN A 147 GLN D 39 GLN D 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.118992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.101963 restraints weight = 54668.787| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.44 r_work: 0.3133 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11925 Z= 0.170 Angle : 0.578 8.738 16204 Z= 0.296 Chirality : 0.043 0.181 1842 Planarity : 0.005 0.069 2090 Dihedral : 4.847 47.633 1703 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.13 % Allowed : 17.43 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.73 (0.22), residues: 1488 helix: 1.36 (0.32), residues: 274 sheet: -0.73 (0.22), residues: 541 loop : -0.96 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 269 TYR 0.013 0.001 TYR B1267 PHE 0.016 0.002 PHE A 74 TRP 0.013 0.001 TRP C1473 HIS 0.004 0.001 HIS B1150 Details of bonding type rmsd covalent geometry : bond 0.00388 (11913) covalent geometry : angle 0.56854 (16176) SS BOND : bond 0.00408 ( 8) SS BOND : angle 1.84296 ( 16) hydrogen bonds : bond 0.03544 ( 466) hydrogen bonds : angle 5.21560 ( 1416) link_NAG-ASN : bond 0.00383 ( 4) link_NAG-ASN : angle 3.28963 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 358 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7408 (mtpt) cc_final: 0.6975 (mtmm) REVERT: A 55 SER cc_start: 0.7851 (p) cc_final: 0.7312 (m) REVERT: A 77 SER cc_start: 0.8033 (t) cc_final: 0.7718 (p) REVERT: A 119 ASP cc_start: 0.7049 (p0) cc_final: 0.6572 (p0) REVERT: A 125 THR cc_start: 0.8205 (t) cc_final: 0.7872 (p) REVERT: A 146 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.6897 (t0) REVERT: A 232 GLU cc_start: 0.7728 (tt0) cc_final: 0.7296 (tp30) REVERT: A 324 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7668 (tm-30) REVERT: A 364 SER cc_start: 0.8319 (p) cc_final: 0.7828 (t) REVERT: A 404 LYS cc_start: 0.8320 (mmmt) cc_final: 0.7946 (ttmm) REVERT: A 424 ASN cc_start: 0.7796 (t0) cc_final: 0.7466 (t0) REVERT: A 521 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7638 (mm-30) REVERT: A 536 HIS cc_start: 0.7595 (m90) cc_final: 0.7322 (m90) REVERT: A 570 LYS cc_start: 0.7452 (tmtt) cc_final: 0.7097 (tptp) REVERT: B 827 LEU cc_start: 0.8063 (tp) cc_final: 0.7821 (tt) REVERT: B 832 GLU cc_start: 0.7399 (mp0) cc_final: 0.7038 (mp0) REVERT: B 858 TYR cc_start: 0.8491 (m-80) cc_final: 0.8217 (m-80) REVERT: B 943 GLU cc_start: 0.7432 (tp30) cc_final: 0.7135 (tp30) REVERT: B 1050 GLN cc_start: 0.7858 (tp40) cc_final: 0.7449 (tm-30) REVERT: B 1072 ARG cc_start: 0.7056 (mmm-85) cc_final: 0.6623 (tmm-80) REVERT: B 1101 GLN cc_start: 0.7069 (mt0) cc_final: 0.6828 (mt0) REVERT: B 1102 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: B 1220 MET cc_start: 0.6932 (mpp) cc_final: 0.6611 (mpp) REVERT: B 1291 ARG cc_start: 0.7722 (ttp80) cc_final: 0.7365 (ttp-110) REVERT: B 1360 PHE cc_start: 0.7071 (p90) cc_final: 0.6841 (p90) REVERT: B 1381 LEU cc_start: 0.7969 (pp) cc_final: 0.7613 (pp) REVERT: B 1389 MET cc_start: 0.6341 (ptp) cc_final: 0.5931 (ptt) REVERT: D 81 GLN cc_start: 0.7837 (tt0) cc_final: 0.7560 (tt0) REVERT: D 102 ILE cc_start: 0.8222 (tt) cc_final: 0.7876 (tp) outliers start: 27 outliers final: 24 residues processed: 370 average time/residue: 0.2901 time to fit residues: 145.1871 Evaluate side-chains 383 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 357 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain B residue 1030 LYS Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1292 GLN Chi-restraints excluded: chain B residue 1309 LEU Chi-restraints excluded: chain B residue 1370 VAL Chi-restraints excluded: chain C residue 1497 LEU Chi-restraints excluded: chain C residue 1553 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 80 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 56 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 49 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 19 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.120362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.103284 restraints weight = 54562.718| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.43 r_work: 0.3138 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11925 Z= 0.137 Angle : 0.562 8.726 16204 Z= 0.286 Chirality : 0.043 0.173 1842 Planarity : 0.004 0.055 2090 Dihedral : 4.696 47.785 1703 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.81 % Allowed : 18.06 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: -0.56 (0.22), residues: 1488 helix: 1.54 (0.32), residues: 273 sheet: -0.61 (0.22), residues: 537 loop : -0.87 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 269 TYR 0.016 0.001 TYR B1267 PHE 0.013 0.001 PHE A 74 TRP 0.012 0.001 TRP C1473 HIS 0.003 0.001 HIS B1150 Details of bonding type rmsd covalent geometry : bond 0.00318 (11913) covalent geometry : angle 0.55262 (16176) SS BOND : bond 0.00366 ( 8) SS BOND : angle 1.65490 ( 16) hydrogen bonds : bond 0.03315 ( 466) hydrogen bonds : angle 5.06270 ( 1416) link_NAG-ASN : bond 0.00428 ( 4) link_NAG-ASN : angle 3.25407 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6363.17 seconds wall clock time: 108 minutes 10.76 seconds (6490.76 seconds total)