Starting phenix.real_space_refine on Fri Jul 3 13:45:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i2h_52585/07_2026/9i2h_52585.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i2h_52585/07_2026/9i2h_52585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9i2h_52585/07_2026/9i2h_52585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i2h_52585/07_2026/9i2h_52585.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i2h_52585/07_2026/9i2h_52585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i2h_52585/07_2026/9i2h_52585.map" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Cu 1 5.60 5 S 86 5.16 5 Na 1 4.78 5 C 8780 2.51 5 N 2353 2.21 5 O 2694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13917 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1868 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain: "L" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1070 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "A" Number of atoms: 5406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5406 Classifications: {'peptide': 670} Link IDs: {'CIS': 1, 'PTRANS': 35, 'TRANS': 633} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 5305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5305 Classifications: {'peptide': 651} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 621} Chain: "X" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Ad-hoc single atom residues: {' CA': 1, ' NA': 1} Classifications: {'peptide': 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CU': 1} Chain breaks: 1 Time building chain proxies: 2.35, per 1000 atoms: 0.17 Number of scatterers: 13917 At special positions: 0 Unit cell: (94.62, 128.65, 128.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cu 1 28.99 Ca 2 19.99 S 86 16.00 Na 1 11.00 O 2694 8.00 N 2353 7.00 C 8780 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 27 " distance=2.03 Simple disulfide: pdb=" SG CYS H 42 " - pdb=" SG CYS H 58 " distance=2.03 Simple disulfide: pdb=" SG CYS H 122 " - pdb=" SG CYS L 132 " distance=2.03 Simple disulfide: pdb=" SG CYS H 168 " - pdb=" SG CYS H 182 " distance=2.03 Simple disulfide: pdb=" SG CYS H 191 " - pdb=" SG CYS H 220 " distance=2.03 Simple disulfide: pdb=" SG CYS L 17 " - pdb=" SG CYS L 22 " distance=2.03 Simple disulfide: pdb=" SG CYS L 50 " - pdb=" SG CYS L 61 " distance=2.03 Simple disulfide: pdb=" SG CYS L 55 " - pdb=" SG CYS L 70 " distance=2.03 Simple disulfide: pdb=" SG CYS L 72 " - pdb=" SG CYS L 81 " distance=2.03 Simple disulfide: pdb=" SG CYS L 89 " - pdb=" SG CYS L 100 " distance=2.03 Simple disulfide: pdb=" SG CYS L 96 " - pdb=" SG CYS L 109 " distance=2.03 Simple disulfide: pdb=" SG CYS L 111 " - pdb=" SG CYS L 124 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 472 " - pdb=" SG CYS A 498 " distance=2.03 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 656 " distance=2.03 Simple disulfide: pdb=" SG CYS B1697 " - pdb=" SG CYS B1723 " distance=2.03 Simple disulfide: pdb=" SG CYS B1879 " - pdb=" SG CYS B2033 " distance=2.03 Simple disulfide: pdb=" SG CYS B2038 " - pdb=" SG CYS B2193 " 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=2, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA D 3 " - " MAN D 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " " BMA D 3 " - " MAN D 6 " " MAN D 4 " - " MAN D 5 " " MAN D 6 " - " MAN D 7 " " BMA X 3 " - " MAN X 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " BETA1-6 " NAG E 1 " - " FUC E 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG X 1 " - " FUC X 6 " NAG-ASN " NAG C 1 " - " ASN B1982 " " NAG D 1 " - " ASN A 211 " " NAG E 1 " - " ASN B1675 " " NAG X 1 " - " ASN A 269 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 481.9 milliseconds 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3160 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 26 sheets defined 12.2% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'H' and resid 55 through 61A removed outlier: 3.508A pdb=" N CYS H 58 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR H 60 " --> pdb=" O HIS H 57 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA H 61A" --> pdb=" O LEU H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 124A through 131 Processing helix chain 'H' and resid 131A through 133 Processing helix chain 'H' and resid 164 through 172 removed outlier: 3.691A pdb=" N LEU H 170 " --> pdb=" O HIS H 166 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER H 171 " --> pdb=" O SER H 167 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER H 172 " --> pdb=" O CYS H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 242 Processing helix chain 'L' and resid 12 through 17 Processing helix chain 'L' and resid 23 through 32 removed outlier: 3.602A pdb=" N GLU L 29 " --> pdb=" O GLU L 25 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL L 30 " --> pdb=" O GLU L 26 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE L 31 " --> pdb=" O ALA L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 33 through 47 removed outlier: 3.609A pdb=" N LYS L 43 " --> pdb=" O GLU L 39 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS L 45 " --> pdb=" O TRP L 41 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP L 46 " --> pdb=" O ASN L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 52 removed outlier: 3.640A pdb=" N THR L 52 " --> pdb=" O GLN L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 96 Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.517A pdb=" N LYS A 46 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 157 removed outlier: 3.515A pdb=" N GLY A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 344 through 352 removed outlier: 3.834A pdb=" N GLN A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 464 removed outlier: 3.751A pdb=" N GLU A 464 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 488 removed outlier: 3.597A pdb=" N ALA A 488 " --> pdb=" O MET A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 Processing helix chain 'A' and resid 530 through 539 removed outlier: 3.625A pdb=" N LYS A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A 538 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.707A pdb=" N GLU A 544 " --> pdb=" O ASN A 541 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 545 " --> pdb=" O PRO A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 541 through 545' Processing helix chain 'A' and resid 565 through 569 removed outlier: 3.863A pdb=" N ILE A 569 " --> pdb=" O PRO A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 660 through 663 Processing helix chain 'B' and resid 1566 through 1573 removed outlier: 4.848A pdb=" N GLN B1570 " --> pdb=" O GLU B1567 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG B1571 " --> pdb=" O PHE B1568 " (cutoff:3.500A) Processing helix chain 'B' and resid 1666 through 1670 removed outlier: 3.861A pdb=" N ASP B1669 " --> pdb=" O PHE B1666 " (cutoff:3.500A) Processing helix chain 'B' and resid 1685 through 1689 Processing helix chain 'B' and resid 1707 through 1712 Processing helix chain 'B' and resid 1749 through 1753 removed outlier: 3.503A pdb=" N LYS B1752 " --> pdb=" O ASP B1749 " (cutoff:3.500A) Processing helix chain 'B' and resid 1861 through 1866 removed outlier: 3.827A pdb=" N ARG B1865 " --> pdb=" O GLY B1861 " (cutoff:3.500A) Processing helix chain 'B' and resid 1891 through 1893 No H-bonds generated for 'chain 'B' and resid 1891 through 1893' Processing helix chain 'B' and resid 1905 through 1909 Processing helix chain 'B' and resid 2050 through 2052 No H-bonds generated for 'chain 'B' and resid 2050 through 2052' Processing helix chain 'B' and resid 2069 through 2073 Processing sheet with id=AA1, first strand: chain 'H' and resid 20 through 21 removed outlier: 3.901A pdb=" N SER H 139 " --> pdb=" O PRO H 198 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N HIS H 199 " --> pdb=" O THR H 210 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE H 227 " --> pdb=" O SER H 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 81 through 83 removed outlier: 3.976A pdb=" N CYS H 42 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASN H 35 " --> pdb=" O GLY H 40 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLY H 40 " --> pdb=" O ASN H 35 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS H 90 " --> pdb=" O GLU A 666 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 60 through 63 Processing sheet with id=AA4, first strand: chain 'L' and resid 115 through 117 Processing sheet with id=AA5, first strand: chain 'A' and resid 3 through 8 removed outlier: 3.710A pdb=" N LYS A 75 " --> pdb=" O VAL A 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 14 through 15 Processing sheet with id=AA7, first strand: chain 'A' and resid 62 through 64 removed outlier: 6.062A pdb=" N LEU A 62 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 162 " --> pdb=" O HIS A 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 209 through 210 Processing sheet with id=AA9, first strand: chain 'A' and resid 218 through 220 removed outlier: 6.038A pdb=" N VAL A 219 " --> pdb=" O LYS A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 257 through 261 Processing sheet with id=AB2, first strand: chain 'A' and resid 323 through 324 Processing sheet with id=AB3, first strand: chain 'A' and resid 327 through 334 removed outlier: 3.619A pdb=" N THR A 369 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 329 " --> pdb=" O MET A 367 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 408 through 409 Processing sheet with id=AB5, first strand: chain 'A' and resid 472 through 475 removed outlier: 3.531A pdb=" N ARG A 475 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 514 through 522 removed outlier: 6.793A pdb=" N ILE A 514 " --> pdb=" O GLN A 581 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N HIS A 583 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLN A 516 " --> pdb=" O HIS A 583 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N CYS A 585 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ALA A 518 " --> pdb=" O CYS A 585 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N VAL A 587 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE A 520 " --> pdb=" O VAL A 587 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR A 624 " --> pdb=" O ILE A 604 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 572 through 573 removed outlier: 3.578A pdb=" N ILE A 596 " --> pdb=" O LEU A 613 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1586 through 1594 removed outlier: 3.520A pdb=" N ILE B1561 " --> pdb=" O LYS B1589 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ARG B1552 " --> pdb=" O GLN B1629 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ARG B1631 " --> pdb=" O ARG B1552 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N TYR B1554 " --> pdb=" O ARG B1631 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP B1626 " --> pdb=" O ALA B1684 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1620 through 1621 removed outlier: 6.241A pdb=" N ILE B1620 " --> pdb=" O LEU B1721 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N CYS B1723 " --> pdb=" O ILE B1620 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1778 through 1780 removed outlier: 3.533A pdb=" N ALA B1779 " --> pdb=" O MET B1746 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET B1746 " --> pdb=" O ALA B1779 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ARG B1739 " --> pdb=" O ARG B1799 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N HIS B1801 " --> pdb=" O ARG B1739 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N PHE B1741 " --> pdb=" O HIS B1801 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU B1803 " --> pdb=" O PHE B1741 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LEU B1743 " --> pdb=" O LEU B1803 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B1842 " --> pdb=" O LEU B1802 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS B1847 " --> pdb=" O THR B1820 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR B1820 " --> pdb=" O LYS B1847 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1791 through 1792 Processing sheet with id=AC3, first strand: chain 'B' and resid 1833 through 1836 removed outlier: 3.573A pdb=" N HIS B1812 " --> pdb=" O LEU B1836 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1895 through 1897 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1935 through 1938 current: chain 'B' and resid 1977 through 1978 Processing sheet with id=AC5, first strand: chain 'B' and resid 1920 through 1921 Processing sheet with id=AC6, first strand: chain 'B' and resid 1944 through 1945 Processing sheet with id=AC7, first strand: chain 'B' and resid 1953 through 1954 Processing sheet with id=AC8, first strand: chain 'B' and resid 2054 through 2056 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2095 through 2110 current: chain 'B' and resid 2119 through 2130 removed outlier: 3.601A pdb=" N TYR B2129 " --> pdb=" O LYS B2137 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 582 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: 2.52 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4419 1.34 - 1.46: 2670 1.46 - 1.58: 7035 1.58 - 1.70: 1 1.70 - 1.81: 128 Bond restraints: 14253 Sorted by residual: bond pdb=" C1 0GJ H 303 " pdb=" N2 0GJ H 303 " ideal model delta sigma weight residual 1.342 1.430 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" CA CYS L 89 " pdb=" C CYS L 89 " ideal model delta sigma weight residual 1.523 1.557 -0.034 1.34e-02 5.57e+03 6.48e+00 bond pdb=" CG 0GJ H 303 " pdb=" CD 0GJ H 303 " ideal model delta sigma weight residual 1.538 1.516 0.022 2.00e-02 2.50e+03 1.18e+00 bond pdb=" N ASP A 659 " pdb=" CA ASP A 659 " ideal model delta sigma weight residual 1.458 1.478 -0.020 1.90e-02 2.77e+03 1.11e+00 bond pdb=" N GLY A 231 " pdb=" CA GLY A 231 " ideal model delta sigma weight residual 1.456 1.444 0.012 1.16e-02 7.43e+03 1.04e+00 ... (remaining 14248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.01: 19261 5.01 - 10.01: 9 10.01 - 15.02: 1 15.02 - 20.03: 1 20.03 - 25.03: 1 Bond angle restraints: 19273 Sorted by residual: angle pdb=" C1 0GJ H 303 " pdb=" N2 0GJ H 303 " pdb=" CA2 0GJ H 303 " ideal model delta sigma weight residual 124.62 99.59 25.03 3.00e+00 1.11e-01 6.96e+01 angle pdb=" CA1 0GJ H 303 " pdb=" C1 0GJ H 303 " pdb=" N2 0GJ H 303 " ideal model delta sigma weight residual 113.95 98.26 15.69 3.00e+00 1.11e-01 2.73e+01 angle pdb=" C PRO A 658 " pdb=" N ASP A 659 " pdb=" CA ASP A 659 " ideal model delta sigma weight residual 121.70 127.91 -6.21 1.80e+00 3.09e-01 1.19e+01 angle pdb=" C2 NAG D 1 " pdb=" N2 NAG D 1 " pdb=" C7 NAG D 1 " ideal model delta sigma weight residual 124.56 134.90 -10.34 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C PHE A 424 " pdb=" N SER A 425 " pdb=" CA SER A 425 " ideal model delta sigma weight residual 121.61 126.02 -4.41 1.39e+00 5.18e-01 1.01e+01 ... (remaining 19268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.64: 8371 23.64 - 47.28: 365 47.28 - 70.92: 52 70.92 - 94.56: 11 94.56 - 118.20: 17 Dihedral angle restraints: 8816 sinusoidal: 3891 harmonic: 4925 Sorted by residual: dihedral pdb=" CA GLN L 104 " pdb=" C GLN L 104 " pdb=" N SER L 105 " pdb=" CA SER L 105 " ideal model delta harmonic sigma weight residual -180.00 -139.39 -40.61 0 5.00e+00 4.00e-02 6.60e+01 dihedral pdb=" CA LYS A 310 " pdb=" C LYS A 310 " pdb=" N ILE A 311 " pdb=" CA ILE A 311 " ideal model delta harmonic sigma weight residual 180.00 -158.09 -21.91 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ARG L 102 " pdb=" C ARG L 102 " pdb=" N VAL L 103 " pdb=" CA VAL L 103 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 8813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1651 0.050 - 0.100: 344 0.100 - 0.151: 89 0.151 - 0.201: 2 0.201 - 0.251: 2 Chirality restraints: 2088 Sorted by residual: chirality pdb=" C4 NAG X 1 " pdb=" C3 NAG X 1 " pdb=" C5 NAG X 1 " pdb=" O4 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.28 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" N2 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.27 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C3 NAG D 1 " pdb=" C2 NAG D 1 " pdb=" C4 NAG D 1 " pdb=" O3 NAG D 1 " both_signs ideal model delta sigma weight residual False 2.45 2.27 0.18 2.00e-01 2.50e+01 8.42e-01 ... (remaining 2085 not shown) Planarity restraints: 2461 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 0GJ H 303 " -0.234 2.00e-02 2.50e+03 1.27e-01 2.02e+02 pdb=" CA1 0GJ H 303 " 0.042 2.00e-02 2.50e+03 pdb=" CA2 0GJ H 303 " -0.026 2.00e-02 2.50e+03 pdb=" N2 0GJ H 303 " 0.105 2.00e-02 2.50e+03 pdb=" O1 0GJ H 303 " 0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B1581 " 0.027 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO B1582 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B1582 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B1582 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B2023 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO B2024 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B2024 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B2024 " 0.022 5.00e-02 4.00e+02 ... (remaining 2458 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 35 2.24 - 2.91: 6071 2.91 - 3.57: 19950 3.57 - 4.24: 34911 4.24 - 4.90: 58448 Nonbonded interactions: 119415 Sorted by model distance: nonbonded pdb=" O TYR H 185 " pdb=" O LYS H 224 " model vdw 1.576 3.040 nonbonded pdb=" NH1 ARG H 67 " pdb=" OD2 ASP H 70 " model vdw 1.696 3.120 nonbonded pdb=" C ASP H 185A" pdb="NA NA H 302 " model vdw 1.719 3.440 nonbonded pdb=" OD1 ASN B1857 " pdb=" OE2 GLU B1859 " model vdw 1.959 3.040 nonbonded pdb=" OE2 GLU B1859 " pdb="CU CU B2201 " model vdw 2.046 2.980 ... (remaining 119410 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 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 2 or resid 5 through 6)) selection = (chain 'X' and (resid 1 or resid 4 through 5)) } 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: 7.080 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.200 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 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 : 0.004 0.088 14294 Z= 0.174 Angle : 0.666 25.031 19371 Z= 0.318 Chirality : 0.045 0.251 2088 Planarity : 0.004 0.127 2457 Dihedral : 14.324 118.197 5599 Min Nonbonded Distance : 1.576 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 4.67 % Allowed : 8.81 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.32 (0.20), residues: 1681 helix: -1.40 (0.49), residues: 114 sheet: -1.91 (0.24), residues: 435 loop : -1.43 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1593 TYR 0.015 0.001 TYR A 144 PHE 0.014 0.002 PHE B1872 TRP 0.015 0.001 TRP B1665 HIS 0.003 0.001 HIS B2128 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (14253) covalent geometry : angle 0.63362 / 0.31 (19273) SS BOND : bond 0.00212 / 0.13 ( 19) SS BOND : angle 0.69149 / 0.46 ( 38) hydrogen bonds : bond 0.29584 / 19.16 ( 247) hydrogen bonds : angle 12.29485 / 8.36 ( 582) Misc. bond : bond 0.00114 / 0.06 ( 2) link_ALPHA1-3 : bond 0.00967 / 0.44 ( 3) link_ALPHA1-3 : angle 1.75390 / 0.91 ( 9) link_ALPHA1-6 : bond 0.00569 / 0.37 ( 5) link_ALPHA1-6 : angle 2.14270 / 1.41 ( 15) link_BETA1-4 : bond 0.00696 / 0.34 ( 6) link_BETA1-4 : angle 3.98471 / 2.09 ( 18) link_BETA1-6 : bond 0.00295 / 0.15 ( 2) link_BETA1-6 : angle 3.62806 / 1.87 ( 6) link_NAG-ASN : bond 0.00671 / 0.29 ( 4) link_NAG-ASN : angle 5.56141 / 3.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 243 time to evaluate : 0.342 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: H 134 ASP cc_start: 0.8494 (p0) cc_final: 0.8262 (p0) REVERT: H 135 THR cc_start: 0.8572 (p) cc_final: 0.8359 (p) REVERT: H 225 TYR cc_start: 0.7295 (OUTLIER) cc_final: 0.6795 (m-80) REVERT: L 88 LEU cc_start: 0.6998 (mm) cc_final: 0.6660 (mm) REVERT: L 97 ASP cc_start: 0.8049 (t0) cc_final: 0.7849 (t0) REVERT: L 102 ARG cc_start: 0.6093 (ttm170) cc_final: 0.4909 (tpt170) REVERT: L 136 THR cc_start: 0.8571 (p) cc_final: 0.7761 (p) REVERT: A 387 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.5350 (tp30) REVERT: A 396 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7136 (ttm110) REVERT: B 1900 PHE cc_start: 0.8342 (p90) cc_final: 0.7584 (p90) REVERT: B 1998 THR cc_start: 0.8445 (m) cc_final: 0.8112 (m) REVERT: B 2021 TYR cc_start: 0.7685 (t80) cc_final: 0.7375 (t80) REVERT: B 2044 MET cc_start: 0.8010 (tpp) cc_final: 0.7774 (tpp) REVERT: B 2113 CYS cc_start: 0.7933 (t) cc_final: 0.7551 (t) REVERT: B 2121 TYR cc_start: 0.8650 (p90) cc_final: 0.7860 (p90) REVERT: B 2123 LYS cc_start: 0.9106 (mmmm) cc_final: 0.8876 (mmmm) REVERT: B 2126 THR cc_start: 0.7658 (OUTLIER) cc_final: 0.7325 (m) REVERT: B 2186 LEU cc_start: 0.6178 (OUTLIER) cc_final: 0.5942 (mt) outliers start: 70 outliers final: 34 residues processed: 305 average time/residue: 0.1015 time to fit residues: 45.0122 Evaluate side-chains 220 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 182 CYS Chi-restraints excluded: chain H residue 205 ASP Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 225 TYR Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 420 HIS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 1573 THR Chi-restraints excluded: chain B residue 1634 ASN Chi-restraints excluded: chain B residue 1841 PHE Chi-restraints excluded: chain B residue 1858 THR Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1895 ILE Chi-restraints excluded: chain B residue 1954 LYS Chi-restraints excluded: chain B residue 2051 ASN Chi-restraints excluded: chain B residue 2106 THR Chi-restraints excluded: chain B residue 2126 THR Chi-restraints excluded: chain B residue 2186 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 178 GLN A 2 GLN A 103 HIS A 242 HIS A 251 ASN ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1629 GLN ** B1857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1869 GLN B1949 GLN B1975 ASN B2031 GLN ** B2076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2091 ASN ** B2111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2155 ASN B2181 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.113133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.087564 restraints weight = 41013.741| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 5.18 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14294 Z= 0.160 Angle : 0.730 13.526 19371 Z= 0.356 Chirality : 0.048 0.214 2088 Planarity : 0.004 0.044 2457 Dihedral : 10.549 105.519 2321 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.07 % Favored : 93.87 % Rotamer: Outliers : 3.94 % Allowed : 14.15 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.35 (0.20), residues: 1681 helix: -1.60 (0.42), residues: 139 sheet: -1.77 (0.24), residues: 441 loop : -1.49 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 348 TYR 0.017 0.001 TYR B2125 PHE 0.023 0.002 PHE A 574 TRP 0.018 0.002 TRP B1904 HIS 0.007 0.001 HIS B1955 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (14253) covalent geometry : angle 0.69401 / 0.35 (19273) SS BOND : bond 0.00415 / 0.25 ( 19) SS BOND : angle 1.22420 / 0.75 ( 38) hydrogen bonds : bond 0.04310 / 2.91 ( 247) hydrogen bonds : angle 8.62289 / 5.90 ( 582) Misc. bond : bond 0.00049 / 0.02 ( 2) link_ALPHA1-3 : bond 0.01456 / 0.65 ( 3) link_ALPHA1-3 : angle 2.23534 / 1.17 ( 9) link_ALPHA1-6 : bond 0.00534 / 0.33 ( 5) link_ALPHA1-6 : angle 2.10329 / 1.43 ( 15) link_BETA1-4 : bond 0.00674 / 0.37 ( 6) link_BETA1-4 : angle 4.10999 / 2.16 ( 18) link_BETA1-6 : bond 0.00119 / 0.06 ( 2) link_BETA1-6 : angle 4.17215 / 2.17 ( 6) link_NAG-ASN : bond 0.00687 / 0.31 ( 4) link_NAG-ASN : angle 6.26885 / 3.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 199 time to evaluate : 0.463 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: H 116 MET cc_start: 0.9099 (tpp) cc_final: 0.8628 (tpp) REVERT: H 157 MET cc_start: 0.8915 (ttp) cc_final: 0.8590 (ttp) REVERT: L 98 GLN cc_start: 0.8470 (mt0) cc_final: 0.7981 (tt0) REVERT: L 136 THR cc_start: 0.8298 (p) cc_final: 0.7763 (p) REVERT: A 270 MET cc_start: 0.6126 (OUTLIER) cc_final: 0.5226 (tpt) REVERT: A 387 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.5461 (tp30) REVERT: A 396 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.6902 (mtm110) REVERT: A 594 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7938 (mp) REVERT: B 1685 THR cc_start: 0.8176 (p) cc_final: 0.7970 (p) REVERT: B 1734 MET cc_start: 0.8497 (mmt) cc_final: 0.8033 (mmt) REVERT: B 1869 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8837 (pt0) REVERT: B 1904 TRP cc_start: 0.7830 (m-90) cc_final: 0.7580 (m-90) REVERT: B 1988 MET cc_start: 0.8350 (tpp) cc_final: 0.7952 (tpp) REVERT: B 1998 THR cc_start: 0.8714 (m) cc_final: 0.8333 (p) REVERT: B 2021 TYR cc_start: 0.7810 (t80) cc_final: 0.7417 (t80) REVERT: B 2044 MET cc_start: 0.7615 (tpp) cc_final: 0.7149 (tpp) REVERT: B 2113 CYS cc_start: 0.7958 (t) cc_final: 0.6937 (t) REVERT: B 2121 TYR cc_start: 0.8684 (p90) cc_final: 0.7780 (p90) outliers start: 59 outliers final: 36 residues processed: 244 average time/residue: 0.0977 time to fit residues: 35.3990 Evaluate side-chains 215 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 91 HIS Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 420 HIS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 ASN Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 1634 ASN Chi-restraints excluded: chain B residue 1841 PHE Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1895 ILE Chi-restraints excluded: chain B residue 1935 ILE Chi-restraints excluded: chain B residue 1954 LYS Chi-restraints excluded: chain B residue 2122 VAL Chi-restraints excluded: chain B residue 2173 ILE Chi-restraints excluded: chain B residue 2181 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 155 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1955 HIS B1975 ASN ** B2082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.112941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.087508 restraints weight = 40977.730| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 5.26 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14294 Z= 0.147 Angle : 0.678 13.514 19371 Z= 0.328 Chirality : 0.046 0.222 2088 Planarity : 0.004 0.044 2457 Dihedral : 9.401 102.617 2300 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.47 % Allowed : 16.15 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.34 (0.20), residues: 1681 helix: -1.43 (0.43), residues: 133 sheet: -1.75 (0.24), residues: 421 loop : -1.53 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B2072 TYR 0.015 0.001 TYR A 415 PHE 0.017 0.001 PHE A 154 TRP 0.021 0.001 TRP B2068 HIS 0.007 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (14253) covalent geometry : angle 0.64245 / 0.32 (19273) SS BOND : bond 0.00445 / 0.25 ( 19) SS BOND : angle 0.86005 / 0.56 ( 38) hydrogen bonds : bond 0.03898 / 2.66 ( 247) hydrogen bonds : angle 7.98811 / 5.47 ( 582) Misc. bond : bond 0.00043 / 0.02 ( 2) link_ALPHA1-3 : bond 0.01174 / 0.55 ( 3) link_ALPHA1-3 : angle 2.08038 / 1.06 ( 9) link_ALPHA1-6 : bond 0.00589 / 0.38 ( 5) link_ALPHA1-6 : angle 2.05134 / 1.39 ( 15) link_BETA1-4 : bond 0.00637 / 0.32 ( 6) link_BETA1-4 : angle 3.91551 / 2.01 ( 18) link_BETA1-6 : bond 0.00150 / 0.08 ( 2) link_BETA1-6 : angle 4.11521 / 2.11 ( 6) link_NAG-ASN : bond 0.00783 / 0.36 ( 4) link_NAG-ASN : angle 6.10937 / 3.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 191 time to evaluate : 0.454 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: H 75 GLN cc_start: 0.8897 (mt0) cc_final: 0.8605 (mt0) REVERT: H 116 MET cc_start: 0.9112 (tpp) cc_final: 0.8673 (tpp) REVERT: H 134 ASP cc_start: 0.8802 (p0) cc_final: 0.8586 (p0) REVERT: H 228 TYR cc_start: 0.8370 (m-80) cc_final: 0.8048 (m-80) REVERT: L 98 GLN cc_start: 0.8413 (mt0) cc_final: 0.7842 (tt0) REVERT: L 136 THR cc_start: 0.8347 (p) cc_final: 0.7722 (p) REVERT: A 194 LYS cc_start: 0.8675 (tppt) cc_final: 0.8465 (tppt) REVERT: A 270 MET cc_start: 0.6278 (OUTLIER) cc_final: 0.5451 (tpt) REVERT: A 387 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.5589 (tp30) REVERT: A 396 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7062 (mtm110) REVERT: A 577 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8099 (m-30) REVERT: A 594 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7931 (mp) REVERT: B 1734 MET cc_start: 0.8583 (mmt) cc_final: 0.8075 (mmt) REVERT: B 1869 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.7350 (pp30) REVERT: B 1892 ASP cc_start: 0.8582 (m-30) cc_final: 0.8010 (t0) REVERT: B 1998 THR cc_start: 0.8612 (m) cc_final: 0.8209 (p) REVERT: B 2021 TYR cc_start: 0.7830 (t80) cc_final: 0.7447 (t80) REVERT: B 2044 MET cc_start: 0.7577 (tpp) cc_final: 0.7115 (tpp) REVERT: B 2120 MET cc_start: 0.8382 (ptm) cc_final: 0.7943 (tmm) REVERT: B 2121 TYR cc_start: 0.8505 (p90) cc_final: 0.8196 (p90) REVERT: B 2123 LYS cc_start: 0.9210 (mmmm) cc_final: 0.8868 (mmmm) REVERT: B 2183 SER cc_start: 0.8002 (t) cc_final: 0.7219 (t) outliers start: 52 outliers final: 35 residues processed: 229 average time/residue: 0.0944 time to fit residues: 32.3337 Evaluate side-chains 217 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 176 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 91 HIS Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 168 CYS Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 420 HIS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 ASN Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 1634 ASN Chi-restraints excluded: chain B residue 1841 PHE Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1895 ILE Chi-restraints excluded: chain B residue 1935 ILE Chi-restraints excluded: chain B residue 1954 LYS Chi-restraints excluded: chain B residue 1985 ARG Chi-restraints excluded: chain B residue 2013 ILE Chi-restraints excluded: chain B residue 2122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 44 optimal weight: 3.9990 chunk 136 optimal weight: 0.0050 chunk 27 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 109 optimal weight: 0.0370 chunk 152 optimal weight: 0.9990 overall best weight: 0.7876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 104 GLN ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 HIS ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2031 GLN ** B2082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2181 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.113073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.087325 restraints weight = 41147.516| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 5.19 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14294 Z= 0.140 Angle : 0.666 12.712 19371 Z= 0.322 Chirality : 0.046 0.236 2088 Planarity : 0.004 0.042 2457 Dihedral : 9.035 95.370 2297 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.41 % Allowed : 16.96 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.20 (0.20), residues: 1681 helix: -1.29 (0.44), residues: 133 sheet: -1.56 (0.25), residues: 407 loop : -1.49 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 90 TYR 0.032 0.001 TYR A 415 PHE 0.019 0.002 PHE A 603 TRP 0.019 0.001 TRP B2068 HIS 0.006 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (14253) covalent geometry : angle 0.62998 / 0.31 (19273) SS BOND : bond 0.00378 / 0.16 ( 19) SS BOND : angle 0.84990 / 0.54 ( 38) hydrogen bonds : bond 0.03531 / 2.41 ( 247) hydrogen bonds : angle 7.49593 / 5.12 ( 582) Misc. bond : bond 0.00042 / 0.02 ( 2) link_ALPHA1-3 : bond 0.01316 / 0.63 ( 3) link_ALPHA1-3 : angle 2.18834 / 1.14 ( 9) link_ALPHA1-6 : bond 0.00554 / 0.36 ( 5) link_ALPHA1-6 : angle 2.01031 / 1.35 ( 15) link_BETA1-4 : bond 0.00663 / 0.34 ( 6) link_BETA1-4 : angle 3.93816 / 2.00 ( 18) link_BETA1-6 : bond 0.00103 / 0.05 ( 2) link_BETA1-6 : angle 4.21310 / 2.15 ( 6) link_NAG-ASN : bond 0.00616 / 0.28 ( 4) link_NAG-ASN : angle 5.87524 / 3.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 191 time to evaluate : 0.369 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: H 116 MET cc_start: 0.9092 (tpp) cc_final: 0.8711 (tpp) REVERT: H 228 TYR cc_start: 0.8353 (m-80) cc_final: 0.7944 (m-80) REVERT: L 98 GLN cc_start: 0.8277 (mt0) cc_final: 0.7761 (tt0) REVERT: L 136 THR cc_start: 0.8418 (p) cc_final: 0.7748 (p) REVERT: A 40 GLU cc_start: 0.5977 (OUTLIER) cc_final: 0.5704 (mt-10) REVERT: A 194 LYS cc_start: 0.8685 (tppt) cc_final: 0.8451 (tppt) REVERT: A 270 MET cc_start: 0.6146 (OUTLIER) cc_final: 0.5405 (tpt) REVERT: A 387 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.5510 (tp30) REVERT: A 396 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7206 (mtm110) REVERT: A 479 SER cc_start: 0.7202 (OUTLIER) cc_final: 0.6562 (p) REVERT: A 577 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8151 (m-30) REVERT: A 594 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7792 (mt) REVERT: B 1656 LYS cc_start: 0.8706 (tttm) cc_final: 0.7836 (mtpt) REVERT: B 1734 MET cc_start: 0.8581 (mmt) cc_final: 0.8078 (mmt) REVERT: B 1869 GLN cc_start: 0.9248 (OUTLIER) cc_final: 0.7281 (pp30) REVERT: B 1900 PHE cc_start: 0.8536 (p90) cc_final: 0.7588 (p90) REVERT: B 1998 THR cc_start: 0.8587 (m) cc_final: 0.8196 (p) REVERT: B 2021 TYR cc_start: 0.7874 (t80) cc_final: 0.7492 (t80) REVERT: B 2044 MET cc_start: 0.7665 (tpp) cc_final: 0.7132 (tpp) REVERT: B 2121 TYR cc_start: 0.8481 (p90) cc_final: 0.8133 (p90) REVERT: B 2123 LYS cc_start: 0.9220 (mmmm) cc_final: 0.8867 (mmmm) REVERT: B 2183 SER cc_start: 0.7957 (t) cc_final: 0.7025 (m) REVERT: B 2188 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8215 (pt) outliers start: 66 outliers final: 40 residues processed: 238 average time/residue: 0.1028 time to fit residues: 36.2119 Evaluate side-chains 219 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 91 HIS Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 168 CYS Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 420 HIS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 ASN Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 1619 ILE Chi-restraints excluded: chain B residue 1634 ASN Chi-restraints excluded: chain B residue 1771 MET Chi-restraints excluded: chain B residue 1841 PHE Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1878 ASP Chi-restraints excluded: chain B residue 1895 ILE Chi-restraints excluded: chain B residue 1935 ILE Chi-restraints excluded: chain B residue 1954 LYS Chi-restraints excluded: chain B residue 1985 ARG Chi-restraints excluded: chain B residue 2013 ILE Chi-restraints excluded: chain B residue 2122 VAL Chi-restraints excluded: chain B residue 2159 HIS Chi-restraints excluded: chain B residue 2188 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 157 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 84 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 129 ASN L 104 GLN ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2085 GLN ** B2111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.112990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.086781 restraints weight = 40956.421| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 5.50 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14294 Z= 0.134 Angle : 0.673 12.342 19371 Z= 0.322 Chirality : 0.046 0.262 2088 Planarity : 0.004 0.041 2457 Dihedral : 8.901 93.578 2297 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.94 % Allowed : 17.42 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.19 (0.20), residues: 1681 helix: -1.33 (0.43), residues: 139 sheet: -1.54 (0.25), residues: 415 loop : -1.48 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1907 TYR 0.014 0.001 TYR A 145 PHE 0.015 0.001 PHE A 154 TRP 0.021 0.001 TRP B2068 HIS 0.003 0.001 HIS A 601 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (14253) covalent geometry : angle 0.63883 / 0.31 (19273) SS BOND : bond 0.00208 / 0.12 ( 19) SS BOND : angle 1.04505 / 0.63 ( 38) hydrogen bonds : bond 0.03342 / 2.28 ( 247) hydrogen bonds : angle 7.14055 / 4.88 ( 582) Misc. bond : bond 0.00045 / 0.02 ( 2) link_ALPHA1-3 : bond 0.01255 / 0.60 ( 3) link_ALPHA1-3 : angle 2.15923 / 1.13 ( 9) link_ALPHA1-6 : bond 0.00559 / 0.35 ( 5) link_ALPHA1-6 : angle 1.98695 / 1.33 ( 15) link_BETA1-4 : bond 0.00666 / 0.34 ( 6) link_BETA1-4 : angle 3.88587 / 1.97 ( 18) link_BETA1-6 : bond 0.00153 / 0.08 ( 2) link_BETA1-6 : angle 3.90908 / 1.98 ( 6) link_NAG-ASN : bond 0.00801 / 0.38 ( 4) link_NAG-ASN : angle 5.74630 / 3.05 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 183 time to evaluate : 0.414 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: H 116 MET cc_start: 0.9103 (tpp) cc_final: 0.8729 (tpp) REVERT: H 228 TYR cc_start: 0.8353 (m-80) cc_final: 0.7909 (m-80) REVERT: L 98 GLN cc_start: 0.8234 (mt0) cc_final: 0.7750 (tt0) REVERT: L 136 THR cc_start: 0.8397 (p) cc_final: 0.7693 (p) REVERT: A 40 GLU cc_start: 0.5981 (OUTLIER) cc_final: 0.5621 (mt-10) REVERT: A 194 LYS cc_start: 0.8708 (tppt) cc_final: 0.8446 (tppt) REVERT: A 270 MET cc_start: 0.6092 (OUTLIER) cc_final: 0.5463 (tpt) REVERT: A 387 GLU cc_start: 0.6218 (OUTLIER) cc_final: 0.5457 (tp30) REVERT: A 396 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7234 (mtm110) REVERT: A 558 MET cc_start: 0.6049 (mmm) cc_final: 0.5828 (mmm) REVERT: A 577 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8086 (m-30) REVERT: A 594 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7743 (mt) REVERT: B 1656 LYS cc_start: 0.8697 (tttm) cc_final: 0.7832 (mtpt) REVERT: B 1734 MET cc_start: 0.8544 (mmt) cc_final: 0.8054 (mmt) REVERT: B 1869 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.7238 (pp30) REVERT: B 1900 PHE cc_start: 0.8601 (p90) cc_final: 0.7691 (p90) REVERT: B 1998 THR cc_start: 0.8608 (m) cc_final: 0.8226 (p) REVERT: B 2021 TYR cc_start: 0.7882 (t80) cc_final: 0.7490 (t80) REVERT: B 2044 MET cc_start: 0.7673 (tpp) cc_final: 0.7168 (tpp) REVERT: B 2103 LYS cc_start: 0.4912 (mtpt) cc_final: 0.4583 (mmmt) REVERT: B 2121 TYR cc_start: 0.8501 (p90) cc_final: 0.7966 (p90) REVERT: B 2123 LYS cc_start: 0.9217 (mmmm) cc_final: 0.8811 (mmmm) REVERT: B 2126 THR cc_start: 0.7698 (OUTLIER) cc_final: 0.7325 (m) REVERT: B 2188 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8316 (pp) outliers start: 59 outliers final: 37 residues processed: 225 average time/residue: 0.0994 time to fit residues: 33.1423 Evaluate side-chains 216 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 91 HIS Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 168 CYS Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 420 HIS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 ASN Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 1619 ILE Chi-restraints excluded: chain B residue 1634 ASN Chi-restraints excluded: chain B residue 1841 PHE Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1895 ILE Chi-restraints excluded: chain B residue 1935 ILE Chi-restraints excluded: chain B residue 1954 LYS Chi-restraints excluded: chain B residue 1985 ARG Chi-restraints excluded: chain B residue 2122 VAL Chi-restraints excluded: chain B residue 2126 THR Chi-restraints excluded: chain B residue 2159 HIS Chi-restraints excluded: chain B residue 2188 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 92 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 114 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 0.0770 chunk 160 optimal weight: 3.9990 overall best weight: 1.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 178 GLN L 104 GLN ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1975 ASN B2003 GLN ** B2082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.110430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.084462 restraints weight = 41075.554| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 5.27 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14294 Z= 0.201 Angle : 0.717 12.654 19371 Z= 0.346 Chirality : 0.047 0.261 2088 Planarity : 0.004 0.042 2457 Dihedral : 8.912 91.691 2297 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.87 % Allowed : 18.42 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.23 (0.20), residues: 1681 helix: -1.22 (0.44), residues: 133 sheet: -1.67 (0.24), residues: 421 loop : -1.48 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 313 TYR 0.027 0.002 TYR A 415 PHE 0.023 0.002 PHE A 603 TRP 0.031 0.002 TRP B2068 HIS 0.013 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (14253) covalent geometry : angle 0.68477 / 0.34 (19273) SS BOND : bond 0.00260 / 0.15 ( 19) SS BOND : angle 1.20656 / 0.74 ( 38) hydrogen bonds : bond 0.03610 / 2.46 ( 247) hydrogen bonds : angle 7.11346 / 4.90 ( 582) Misc. bond : bond 0.00082 / 0.04 ( 2) link_ALPHA1-3 : bond 0.01244 / 0.59 ( 3) link_ALPHA1-3 : angle 2.15376 / 1.12 ( 9) link_ALPHA1-6 : bond 0.00456 / 0.29 ( 5) link_ALPHA1-6 : angle 2.05630 / 1.36 ( 15) link_BETA1-4 : bond 0.00581 / 0.32 ( 6) link_BETA1-4 : angle 3.83749 / 1.96 ( 18) link_BETA1-6 : bond 0.00239 / 0.11 ( 2) link_BETA1-6 : angle 3.94986 / 2.08 ( 6) link_NAG-ASN : bond 0.00736 / 0.35 ( 4) link_NAG-ASN : angle 5.72879 / 3.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 174 time to evaluate : 0.362 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: H 116 MET cc_start: 0.9146 (tpp) cc_final: 0.8771 (tpp) REVERT: H 157 MET cc_start: 0.9026 (ttp) cc_final: 0.7976 (mtm) REVERT: H 207 TYR cc_start: 0.8429 (m-80) cc_final: 0.7981 (m-80) REVERT: L 97 ASP cc_start: 0.7454 (t70) cc_final: 0.6675 (t0) REVERT: L 98 GLN cc_start: 0.8058 (mt0) cc_final: 0.7706 (tt0) REVERT: L 136 THR cc_start: 0.8274 (p) cc_final: 0.7522 (p) REVERT: A 40 GLU cc_start: 0.6135 (OUTLIER) cc_final: 0.5622 (mt-10) REVERT: A 270 MET cc_start: 0.6086 (OUTLIER) cc_final: 0.5254 (tpt) REVERT: A 387 GLU cc_start: 0.5732 (OUTLIER) cc_final: 0.4977 (tp30) REVERT: A 479 SER cc_start: 0.7295 (OUTLIER) cc_final: 0.6664 (p) REVERT: A 577 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8102 (m-30) REVERT: A 594 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7913 (mp) REVERT: B 1656 LYS cc_start: 0.8702 (tttm) cc_final: 0.7894 (mtpt) REVERT: B 1734 MET cc_start: 0.8576 (mmt) cc_final: 0.8078 (mmt) REVERT: B 1869 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.7224 (pp30) REVERT: B 1899 GLU cc_start: 0.8175 (pm20) cc_final: 0.7394 (pm20) REVERT: B 1900 PHE cc_start: 0.8624 (p90) cc_final: 0.7582 (p90) REVERT: B 1998 THR cc_start: 0.8645 (m) cc_final: 0.8240 (p) REVERT: B 2021 TYR cc_start: 0.7886 (t80) cc_final: 0.7501 (t80) REVERT: B 2044 MET cc_start: 0.7699 (tpp) cc_final: 0.7192 (tpp) REVERT: B 2069 GLU cc_start: 0.9044 (mp0) cc_final: 0.8727 (mp0) REVERT: B 2121 TYR cc_start: 0.8499 (p90) cc_final: 0.7989 (p90) REVERT: B 2123 LYS cc_start: 0.9204 (mmmm) cc_final: 0.8845 (mmmm) REVERT: B 2126 THR cc_start: 0.7868 (OUTLIER) cc_final: 0.7523 (m) outliers start: 58 outliers final: 38 residues processed: 219 average time/residue: 0.0963 time to fit residues: 31.3319 Evaluate side-chains 208 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 162 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 91 HIS Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 126 ASP Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 168 CYS Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 420 HIS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 1619 ILE Chi-restraints excluded: chain B residue 1634 ASN Chi-restraints excluded: chain B residue 1841 PHE Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1895 ILE Chi-restraints excluded: chain B residue 1935 ILE Chi-restraints excluded: chain B residue 1954 LYS Chi-restraints excluded: chain B residue 1985 ARG Chi-restraints excluded: chain B residue 2013 ILE Chi-restraints excluded: chain B residue 2122 VAL Chi-restraints excluded: chain B residue 2126 THR Chi-restraints excluded: chain B residue 2159 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 138 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 139 optimal weight: 0.2980 chunk 106 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 135 GLN ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1670 ASN B1729 HIS ** B1857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.111889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.085949 restraints weight = 40874.817| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 5.23 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14294 Z= 0.142 Angle : 0.686 12.080 19371 Z= 0.330 Chirality : 0.046 0.272 2088 Planarity : 0.004 0.045 2457 Dihedral : 8.618 89.159 2293 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.74 % Allowed : 18.62 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.24 (0.20), residues: 1681 helix: -1.35 (0.43), residues: 140 sheet: -1.53 (0.25), residues: 413 loop : -1.53 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 90 TYR 0.030 0.001 TYR A 415 PHE 0.026 0.001 PHE A 603 TRP 0.020 0.001 TRP B2068 HIS 0.011 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (14253) covalent geometry : angle 0.65378 / 0.32 (19273) SS BOND : bond 0.00395 / 0.16 ( 19) SS BOND : angle 1.03279 / 0.65 ( 38) hydrogen bonds : bond 0.03312 / 2.26 ( 247) hydrogen bonds : angle 6.90434 / 4.76 ( 582) Misc. bond : bond 0.00050 / 0.02 ( 2) link_ALPHA1-3 : bond 0.01464 / 0.71 ( 3) link_ALPHA1-3 : angle 2.25110 / 1.19 ( 9) link_ALPHA1-6 : bond 0.00535 / 0.34 ( 5) link_ALPHA1-6 : angle 1.97575 / 1.31 ( 15) link_BETA1-4 : bond 0.00679 / 0.34 ( 6) link_BETA1-4 : angle 3.87708 / 1.93 ( 18) link_BETA1-6 : bond 0.00140 / 0.07 ( 2) link_BETA1-6 : angle 3.81289 / 1.94 ( 6) link_NAG-ASN : bond 0.00770 / 0.36 ( 4) link_NAG-ASN : angle 5.65333 / 3.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 178 time to evaluate : 0.532 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: H 116 MET cc_start: 0.9155 (tpp) cc_final: 0.8807 (tpp) REVERT: H 207 TYR cc_start: 0.8422 (m-80) cc_final: 0.7992 (m-80) REVERT: L 97 ASP cc_start: 0.7455 (t70) cc_final: 0.6687 (t0) REVERT: L 98 GLN cc_start: 0.7962 (mt0) cc_final: 0.7609 (tt0) REVERT: L 136 THR cc_start: 0.8317 (p) cc_final: 0.7570 (p) REVERT: A 40 GLU cc_start: 0.6003 (OUTLIER) cc_final: 0.5720 (mt-10) REVERT: A 270 MET cc_start: 0.5992 (OUTLIER) cc_final: 0.5402 (tpt) REVERT: A 387 GLU cc_start: 0.5844 (OUTLIER) cc_final: 0.5085 (tp30) REVERT: A 479 SER cc_start: 0.7287 (OUTLIER) cc_final: 0.6664 (p) REVERT: A 577 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8050 (m-30) REVERT: B 1610 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8401 (pt0) REVERT: B 1656 LYS cc_start: 0.8707 (tttm) cc_final: 0.7863 (mtpt) REVERT: B 1734 MET cc_start: 0.8565 (mmt) cc_final: 0.8057 (mmt) REVERT: B 1869 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.7220 (pp30) REVERT: B 1899 GLU cc_start: 0.8124 (pm20) cc_final: 0.7275 (pm20) REVERT: B 1900 PHE cc_start: 0.8570 (p90) cc_final: 0.7541 (p90) REVERT: B 1998 THR cc_start: 0.8624 (m) cc_final: 0.8229 (p) REVERT: B 2021 TYR cc_start: 0.7944 (t80) cc_final: 0.7547 (t80) REVERT: B 2042 LEU cc_start: 0.8088 (mt) cc_final: 0.6946 (tp) REVERT: B 2044 MET cc_start: 0.7632 (tpp) cc_final: 0.7133 (tpp) REVERT: B 2069 GLU cc_start: 0.9038 (mp0) cc_final: 0.8812 (mp0) REVERT: B 2121 TYR cc_start: 0.8371 (p90) cc_final: 0.7956 (p90) REVERT: B 2123 LYS cc_start: 0.9202 (mmmm) cc_final: 0.8697 (mmmm) REVERT: B 2126 THR cc_start: 0.7698 (OUTLIER) cc_final: 0.7344 (m) outliers start: 56 outliers final: 37 residues processed: 220 average time/residue: 0.0950 time to fit residues: 31.0447 Evaluate side-chains 214 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 91 HIS Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 168 CYS Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 420 HIS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 ASN Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 1619 ILE Chi-restraints excluded: chain B residue 1624 VAL Chi-restraints excluded: chain B residue 1634 ASN Chi-restraints excluded: chain B residue 1841 PHE Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1895 ILE Chi-restraints excluded: chain B residue 1935 ILE Chi-restraints excluded: chain B residue 1954 LYS Chi-restraints excluded: chain B residue 1985 ARG Chi-restraints excluded: chain B residue 2013 ILE Chi-restraints excluded: chain B residue 2122 VAL Chi-restraints excluded: chain B residue 2126 THR Chi-restraints excluded: chain B residue 2159 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.7980 chunk 159 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 117 optimal weight: 0.0970 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 104 GLN ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.112095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.086119 restraints weight = 40959.778| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 5.30 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14294 Z= 0.136 Angle : 0.697 11.756 19371 Z= 0.333 Chirality : 0.046 0.273 2088 Planarity : 0.004 0.048 2457 Dihedral : 8.410 86.065 2291 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.94 % Allowed : 19.83 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.18 (0.20), residues: 1681 helix: -1.32 (0.43), residues: 140 sheet: -1.48 (0.25), residues: 422 loop : -1.49 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 90 TYR 0.030 0.001 TYR A 415 PHE 0.029 0.001 PHE A 603 TRP 0.025 0.001 TRP B2068 HIS 0.006 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (14253) covalent geometry : angle 0.66583 / 0.33 (19273) SS BOND : bond 0.00234 / 0.13 ( 19) SS BOND : angle 0.99868 / 0.63 ( 38) hydrogen bonds : bond 0.03166 / 2.15 ( 247) hydrogen bonds : angle 6.78278 / 4.69 ( 582) Misc. bond : bond 0.00044 / 0.02 ( 2) link_ALPHA1-3 : bond 0.01435 / 0.70 ( 3) link_ALPHA1-3 : angle 2.26825 / 1.20 ( 9) link_ALPHA1-6 : bond 0.00527 / 0.33 ( 5) link_ALPHA1-6 : angle 1.94606 / 1.29 ( 15) link_BETA1-4 : bond 0.00696 / 0.35 ( 6) link_BETA1-4 : angle 3.82551 / 1.90 ( 18) link_BETA1-6 : bond 0.00158 / 0.08 ( 2) link_BETA1-6 : angle 3.80545 / 1.93 ( 6) link_NAG-ASN : bond 0.00774 / 0.37 ( 4) link_NAG-ASN : angle 5.54379 / 2.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.402 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: H 116 MET cc_start: 0.9149 (tpp) cc_final: 0.8811 (tpp) REVERT: H 157 MET cc_start: 0.8967 (ttp) cc_final: 0.8472 (mtp) REVERT: H 207 TYR cc_start: 0.8402 (m-80) cc_final: 0.7998 (m-80) REVERT: H 228 TYR cc_start: 0.8235 (m-80) cc_final: 0.7756 (m-80) REVERT: L 97 ASP cc_start: 0.7452 (t70) cc_final: 0.6684 (t0) REVERT: L 98 GLN cc_start: 0.7866 (mt0) cc_final: 0.7569 (tt0) REVERT: L 136 THR cc_start: 0.8291 (p) cc_final: 0.7528 (p) REVERT: A 158 LEU cc_start: 0.6924 (mt) cc_final: 0.6708 (tt) REVERT: A 270 MET cc_start: 0.5910 (OUTLIER) cc_final: 0.5462 (tpt) REVERT: A 387 GLU cc_start: 0.5667 (OUTLIER) cc_final: 0.4909 (tp30) REVERT: A 475 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8137 (mmm-85) REVERT: A 479 SER cc_start: 0.7244 (OUTLIER) cc_final: 0.6676 (t) REVERT: A 577 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8058 (m-30) REVERT: B 1656 LYS cc_start: 0.8676 (tttm) cc_final: 0.7862 (mtpt) REVERT: B 1734 MET cc_start: 0.8566 (mmt) cc_final: 0.8086 (mmt) REVERT: B 1869 GLN cc_start: 0.9221 (OUTLIER) cc_final: 0.7249 (pp30) REVERT: B 1899 GLU cc_start: 0.8103 (pm20) cc_final: 0.7228 (pm20) REVERT: B 1900 PHE cc_start: 0.8556 (p90) cc_final: 0.7533 (p90) REVERT: B 1998 THR cc_start: 0.8638 (m) cc_final: 0.8247 (p) REVERT: B 2021 TYR cc_start: 0.7953 (t80) cc_final: 0.7558 (t80) REVERT: B 2042 LEU cc_start: 0.8062 (mt) cc_final: 0.6782 (tp) REVERT: B 2044 MET cc_start: 0.7603 (tpp) cc_final: 0.7094 (tpp) REVERT: B 2060 LYS cc_start: 0.8534 (mmmt) cc_final: 0.8196 (mmmm) REVERT: B 2069 GLU cc_start: 0.9003 (mp0) cc_final: 0.8737 (mp0) REVERT: B 2103 LYS cc_start: 0.5317 (mtpt) cc_final: 0.4780 (mmmt) REVERT: B 2121 TYR cc_start: 0.8298 (p90) cc_final: 0.7998 (p90) REVERT: B 2126 THR cc_start: 0.7699 (OUTLIER) cc_final: 0.7350 (m) outliers start: 44 outliers final: 34 residues processed: 211 average time/residue: 0.1025 time to fit residues: 32.2996 Evaluate side-chains 208 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 91 HIS Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 168 CYS Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 420 HIS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 ASN Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 1619 ILE Chi-restraints excluded: chain B residue 1624 VAL Chi-restraints excluded: chain B residue 1634 ASN Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1895 ILE Chi-restraints excluded: chain B residue 1935 ILE Chi-restraints excluded: chain B residue 1954 LYS Chi-restraints excluded: chain B residue 1985 ARG Chi-restraints excluded: chain B residue 2013 ILE Chi-restraints excluded: chain B residue 2122 VAL Chi-restraints excluded: chain B residue 2126 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 101 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 25 optimal weight: 40.0000 chunk 7 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 178 GLN ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.109563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.083864 restraints weight = 42244.717| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 5.38 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14294 Z= 0.214 Angle : 0.741 12.449 19371 Z= 0.359 Chirality : 0.048 0.267 2088 Planarity : 0.004 0.043 2457 Dihedral : 8.401 82.366 2286 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.94 % Allowed : 19.96 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.26 (0.19), residues: 1681 helix: -1.22 (0.44), residues: 140 sheet: -1.62 (0.25), residues: 409 loop : -1.54 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 90 TYR 0.019 0.002 TYR B1989 PHE 0.029 0.002 PHE A 603 TRP 0.029 0.002 TRP B2084 HIS 0.008 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (14253) covalent geometry : angle 0.71110 / 0.35 (19273) SS BOND : bond 0.00314 / 0.18 ( 19) SS BOND : angle 1.00844 / 0.66 ( 38) hydrogen bonds : bond 0.03485 / 2.35 ( 247) hydrogen bonds : angle 6.97080 / 4.84 ( 582) Misc. bond : bond 0.00084 / 0.04 ( 2) link_ALPHA1-3 : bond 0.01541 / 0.75 ( 3) link_ALPHA1-3 : angle 2.34432 / 1.25 ( 9) link_ALPHA1-6 : bond 0.00437 / 0.27 ( 5) link_ALPHA1-6 : angle 2.04261 / 1.35 ( 15) link_BETA1-4 : bond 0.00513 / 0.29 ( 6) link_BETA1-4 : angle 3.81373 / 1.93 ( 18) link_BETA1-6 : bond 0.00094 / 0.04 ( 2) link_BETA1-6 : angle 3.99398 / 2.11 ( 6) link_NAG-ASN : bond 0.00612 / 0.28 ( 4) link_NAG-ASN : angle 5.60910 / 2.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.354 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: H 116 MET cc_start: 0.9192 (tpp) cc_final: 0.8845 (tpp) REVERT: H 157 MET cc_start: 0.8946 (ttp) cc_final: 0.7927 (mtm) REVERT: H 189 ASP cc_start: 0.8434 (t0) cc_final: 0.8114 (t0) REVERT: H 207 TYR cc_start: 0.8373 (m-80) cc_final: 0.7977 (m-80) REVERT: H 228 TYR cc_start: 0.8330 (m-80) cc_final: 0.7900 (m-80) REVERT: L 97 ASP cc_start: 0.7540 (t70) cc_final: 0.6745 (t0) REVERT: L 136 THR cc_start: 0.8202 (p) cc_final: 0.7397 (p) REVERT: A 158 LEU cc_start: 0.7239 (mt) cc_final: 0.6939 (tt) REVERT: A 194 LYS cc_start: 0.8766 (tppt) cc_final: 0.8404 (tppt) REVERT: A 270 MET cc_start: 0.6012 (OUTLIER) cc_final: 0.5104 (tpt) REVERT: A 373 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7789 (p0) REVERT: A 387 GLU cc_start: 0.5736 (OUTLIER) cc_final: 0.4974 (tp30) REVERT: A 420 HIS cc_start: 0.7619 (OUTLIER) cc_final: 0.6481 (t-90) REVERT: A 475 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8167 (mmm-85) REVERT: A 479 SER cc_start: 0.7371 (OUTLIER) cc_final: 0.6962 (t) REVERT: A 506 ARG cc_start: 0.8952 (ttp-170) cc_final: 0.8570 (tpt170) REVERT: A 577 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8136 (m-30) REVERT: B 1656 LYS cc_start: 0.8701 (tttm) cc_final: 0.7920 (mtpt) REVERT: B 1734 MET cc_start: 0.8622 (mmt) cc_final: 0.8134 (mmt) REVERT: B 1869 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.7245 (pp30) REVERT: B 1899 GLU cc_start: 0.8191 (pm20) cc_final: 0.7372 (pm20) REVERT: B 1900 PHE cc_start: 0.8579 (p90) cc_final: 0.7604 (p90) REVERT: B 1998 THR cc_start: 0.8629 (m) cc_final: 0.8214 (p) REVERT: B 2042 LEU cc_start: 0.8157 (mt) cc_final: 0.7051 (tp) REVERT: B 2044 MET cc_start: 0.7603 (tpp) cc_final: 0.7095 (tpp) REVERT: B 2060 LYS cc_start: 0.8526 (mmmt) cc_final: 0.8106 (mmmm) REVERT: B 2069 GLU cc_start: 0.9013 (mp0) cc_final: 0.8726 (mp0) REVERT: B 2123 LYS cc_start: 0.9189 (mmmm) cc_final: 0.8988 (mmtm) outliers start: 44 outliers final: 32 residues processed: 211 average time/residue: 0.0990 time to fit residues: 31.3163 Evaluate side-chains 210 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 91 HIS Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 168 CYS Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 420 HIS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 1619 ILE Chi-restraints excluded: chain B residue 1624 VAL Chi-restraints excluded: chain B residue 1634 ASN Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1895 ILE Chi-restraints excluded: chain B residue 1935 ILE Chi-restraints excluded: chain B residue 1954 LYS Chi-restraints excluded: chain B residue 2013 ILE Chi-restraints excluded: chain B residue 2122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 41 optimal weight: 0.0270 chunk 43 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 75 GLN A 228 HIS ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.110905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.085257 restraints weight = 41818.116| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 5.37 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14294 Z= 0.155 Angle : 0.728 11.810 19371 Z= 0.350 Chirality : 0.047 0.276 2088 Planarity : 0.004 0.046 2457 Dihedral : 8.241 76.735 2286 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.74 % Allowed : 20.49 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.22 (0.19), residues: 1681 helix: -1.07 (0.44), residues: 134 sheet: -1.59 (0.25), residues: 412 loop : -1.52 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 90 TYR 0.022 0.001 TYR B2125 PHE 0.029 0.002 PHE A 603 TRP 0.026 0.002 TRP B2068 HIS 0.016 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (14253) covalent geometry : angle 0.69824 / 0.34 (19273) SS BOND : bond 0.00234 / 0.13 ( 19) SS BOND : angle 0.98221 / 0.65 ( 38) hydrogen bonds : bond 0.03246 / 2.23 ( 247) hydrogen bonds : angle 6.88559 / 4.76 ( 582) Misc. bond : bond 0.00048 / 0.02 ( 2) link_ALPHA1-3 : bond 0.01573 / 0.77 ( 3) link_ALPHA1-3 : angle 2.35664 / 1.26 ( 9) link_ALPHA1-6 : bond 0.00512 / 0.32 ( 5) link_ALPHA1-6 : angle 1.94877 / 1.29 ( 15) link_BETA1-4 : bond 0.00688 / 0.35 ( 6) link_BETA1-4 : angle 3.86061 / 1.92 ( 18) link_BETA1-6 : bond 0.00134 / 0.06 ( 2) link_BETA1-6 : angle 3.82794 / 1.96 ( 6) link_NAG-ASN : bond 0.00752 / 0.36 ( 4) link_NAG-ASN : angle 5.48426 / 2.90 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 0.530 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: H 116 MET cc_start: 0.9174 (tpp) cc_final: 0.8821 (tpp) REVERT: H 157 MET cc_start: 0.8914 (ttp) cc_final: 0.7879 (mtm) REVERT: H 189 ASP cc_start: 0.8384 (t0) cc_final: 0.8091 (t0) REVERT: H 207 TYR cc_start: 0.8368 (m-80) cc_final: 0.7978 (m-80) REVERT: H 228 TYR cc_start: 0.8322 (m-80) cc_final: 0.7935 (m-80) REVERT: L 97 ASP cc_start: 0.7389 (t70) cc_final: 0.6589 (t0) REVERT: L 136 THR cc_start: 0.8255 (p) cc_final: 0.7477 (p) REVERT: A 270 MET cc_start: 0.6024 (OUTLIER) cc_final: 0.5409 (tpt) REVERT: A 373 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7760 (p0) REVERT: A 387 GLU cc_start: 0.5646 (OUTLIER) cc_final: 0.4901 (tp30) REVERT: A 420 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.6483 (t-90) REVERT: A 475 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8112 (mmm-85) REVERT: A 479 SER cc_start: 0.7397 (OUTLIER) cc_final: 0.6982 (t) REVERT: A 482 ASP cc_start: 0.7946 (t0) cc_final: 0.7731 (t70) REVERT: A 577 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8115 (m-30) REVERT: A 605 TYR cc_start: 0.7825 (t80) cc_final: 0.6939 (t80) REVERT: B 1656 LYS cc_start: 0.8639 (tttm) cc_final: 0.7935 (mtpt) REVERT: B 1734 MET cc_start: 0.8599 (mmt) cc_final: 0.8067 (mmt) REVERT: B 1869 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.7280 (pp30) REVERT: B 1899 GLU cc_start: 0.8058 (pm20) cc_final: 0.7175 (pm20) REVERT: B 1900 PHE cc_start: 0.8558 (p90) cc_final: 0.7590 (p90) REVERT: B 1998 THR cc_start: 0.8628 (m) cc_final: 0.8214 (p) REVERT: B 2042 LEU cc_start: 0.8024 (mt) cc_final: 0.6886 (tp) REVERT: B 2044 MET cc_start: 0.7642 (tpp) cc_final: 0.6916 (tpp) REVERT: B 2060 LYS cc_start: 0.8476 (mmmt) cc_final: 0.7978 (mmmm) REVERT: B 2069 GLU cc_start: 0.9008 (mp0) cc_final: 0.8741 (mp0) REVERT: B 2121 TYR cc_start: 0.8339 (p90) cc_final: 0.7918 (p90) outliers start: 41 outliers final: 31 residues processed: 210 average time/residue: 0.1015 time to fit residues: 31.7323 Evaluate side-chains 215 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 91 HIS Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 168 CYS Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 420 HIS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 1619 ILE Chi-restraints excluded: chain B residue 1624 VAL Chi-restraints excluded: chain B residue 1634 ASN Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1895 ILE Chi-restraints excluded: chain B residue 1935 ILE Chi-restraints excluded: chain B residue 1954 LYS Chi-restraints excluded: chain B residue 2013 ILE Chi-restraints excluded: chain B residue 2122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 52 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 154 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 166 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 104 GLN ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.112083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.086541 restraints weight = 41643.022| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 5.43 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14294 Z= 0.129 Angle : 0.712 11.904 19371 Z= 0.344 Chirality : 0.047 0.273 2088 Planarity : 0.004 0.099 2457 Dihedral : 8.060 71.829 2286 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.54 % Allowed : 20.96 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.20 (0.20), residues: 1681 helix: -1.16 (0.43), residues: 139 sheet: -1.53 (0.25), residues: 426 loop : -1.51 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 90 TYR 0.017 0.001 TYR A 477 PHE 0.030 0.001 PHE A 603 TRP 0.028 0.002 TRP B2084 HIS 0.004 0.001 HIS B1815 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (14253) covalent geometry : angle 0.68280 / 0.34 (19273) SS BOND : bond 0.00214 / 0.12 ( 19) SS BOND : angle 0.96397 / 0.61 ( 38) hydrogen bonds : bond 0.03069 / 2.12 ( 247) hydrogen bonds : angle 6.73492 / 4.64 ( 582) Misc. bond : bond 0.00030 / 0.01 ( 2) link_ALPHA1-3 : bond 0.01604 / 0.79 ( 3) link_ALPHA1-3 : angle 2.38837 / 1.29 ( 9) link_ALPHA1-6 : bond 0.00551 / 0.35 ( 5) link_ALPHA1-6 : angle 1.87877 / 1.24 ( 15) link_BETA1-4 : bond 0.00691 / 0.34 ( 6) link_BETA1-4 : angle 3.85629 / 1.91 ( 18) link_BETA1-6 : bond 0.00202 / 0.10 ( 2) link_BETA1-6 : angle 3.80271 / 1.93 ( 6) link_NAG-ASN : bond 0.00797 / 0.38 ( 4) link_NAG-ASN : angle 5.37357 / 2.84 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2910.76 seconds wall clock time: 51 minutes 7.35 seconds (3067.35 seconds total)