Starting phenix.real_space_refine on Thu Feb 5 01:36:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i2h_52585/02_2026/9i2h_52585.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i2h_52585/02_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_52585/02_2026/9i2h_52585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i2h_52585/02_2026/9i2h_52585.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i2h_52585/02_2026/9i2h_52585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i2h_52585/02_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-2.0-5952/lib/python3.9/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, 27 Unusual residues: {' CA': 1, ' NA': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.38, per 1000 atoms: 0.24 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: 1.41 Conformation dependent library (CDL) restraints added in 337.1 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: 0.52 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: 2.49 Time building geometry restraints manager: 1.67 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 2.700 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 2.240 ... (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: 6.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 14.110 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: 0.010 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: 22.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 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 covalent geometry : bond 0.00378 (14253) covalent geometry : angle 0.63362 (19273) SS BOND : bond 0.00212 ( 19) SS BOND : angle 0.69149 ( 38) hydrogen bonds : bond 0.29584 ( 247) hydrogen bonds : angle 12.29485 ( 582) Misc. bond : bond 0.00114 ( 2) link_ALPHA1-3 : bond 0.00967 ( 3) link_ALPHA1-3 : angle 1.75390 ( 9) link_ALPHA1-6 : bond 0.00569 ( 5) link_ALPHA1-6 : angle 2.14270 ( 15) link_BETA1-4 : bond 0.00696 ( 6) link_BETA1-4 : angle 3.98471 ( 18) link_BETA1-6 : bond 0.00295 ( 2) link_BETA1-6 : angle 3.62806 ( 6) link_NAG-ASN : bond 0.00671 ( 4) link_NAG-ASN : angle 5.56141 ( 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 : 0.389 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: 0.1166 time to fit residues: 50.9185 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 : 0.879 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: H 178 GLN A 2 GLN 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 ** B1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.113287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.087702 restraints weight = 40787.948| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 5.13 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14294 Z= 0.158 Angle : 0.720 13.515 19371 Z= 0.351 Chirality : 0.048 0.206 2088 Planarity : 0.004 0.044 2457 Dihedral : 10.519 105.517 2321 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.19 % Favored : 93.75 % Rotamer: Outliers : 3.74 % Allowed : 14.29 % Favored : 81.98 % 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: -2.37 (0.20), residues: 1681 helix: -1.56 (0.42), residues: 139 sheet: -1.81 (0.23), residues: 451 loop : -1.49 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 348 TYR 0.016 0.001 TYR B2125 PHE 0.022 0.002 PHE A 574 TRP 0.019 0.002 TRP B1904 HIS 0.006 0.001 HIS B1955 Details of bonding type rmsd covalent geometry : bond 0.00343 (14253) covalent geometry : angle 0.68375 (19273) SS BOND : bond 0.00518 ( 19) SS BOND : angle 1.23296 ( 38) hydrogen bonds : bond 0.04668 ( 247) hydrogen bonds : angle 8.67100 ( 582) Misc. bond : bond 0.00039 ( 2) link_ALPHA1-3 : bond 0.01179 ( 3) link_ALPHA1-3 : angle 2.24463 ( 9) link_ALPHA1-6 : bond 0.00597 ( 5) link_ALPHA1-6 : angle 2.09280 ( 15) link_BETA1-4 : bond 0.00692 ( 6) link_BETA1-4 : angle 4.09184 ( 18) link_BETA1-6 : bond 0.00089 ( 2) link_BETA1-6 : angle 4.15916 ( 6) link_NAG-ASN : bond 0.00889 ( 4) link_NAG-ASN : angle 6.19282 ( 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 256 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 200 time to evaluate : 0.482 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: H 116 MET cc_start: 0.9096 (tpp) cc_final: 0.8629 (tpp) REVERT: H 134 ASP cc_start: 0.8746 (p0) cc_final: 0.8460 (p0) REVERT: H 157 MET cc_start: 0.8918 (ttp) cc_final: 0.8598 (ttp) REVERT: L 98 GLN cc_start: 0.8469 (mt0) cc_final: 0.7998 (tt0) REVERT: L 136 THR cc_start: 0.8309 (p) cc_final: 0.7775 (p) REVERT: A 270 MET cc_start: 0.6135 (OUTLIER) cc_final: 0.5240 (tpt) REVERT: A 387 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.5488 (tp30) REVERT: A 396 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6918 (mtm110) REVERT: A 594 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7936 (mp) REVERT: B 1685 THR cc_start: 0.8198 (p) cc_final: 0.7984 (p) REVERT: B 1734 MET cc_start: 0.8501 (mmt) cc_final: 0.8036 (mmt) REVERT: B 1869 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8826 (pt0) REVERT: B 1904 TRP cc_start: 0.7811 (m-90) cc_final: 0.7565 (m-90) REVERT: B 1988 MET cc_start: 0.8353 (tpp) cc_final: 0.7938 (tpp) REVERT: B 1998 THR cc_start: 0.8695 (m) cc_final: 0.8311 (p) REVERT: B 2021 TYR cc_start: 0.7801 (t80) cc_final: 0.7409 (t80) REVERT: B 2044 MET cc_start: 0.7607 (tpp) cc_final: 0.7144 (tpp) REVERT: B 2113 CYS cc_start: 0.7948 (t) cc_final: 0.6923 (t) REVERT: B 2121 TYR cc_start: 0.8694 (p90) cc_final: 0.7796 (p90) outliers start: 56 outliers final: 36 residues processed: 245 average time/residue: 0.1112 time to fit residues: 39.9437 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 : 0.372 ------------------------------------------------------------------------------- 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 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 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 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: 0.2980 chunk 60 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 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: 4.9990 chunk 155 optimal weight: 0.5980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS ** 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** ** B1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1864 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.113168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.087950 restraints weight = 40746.093| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 5.15 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2157 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= 0.145 Angle : 0.679 13.430 19371 Z= 0.329 Chirality : 0.046 0.222 2088 Planarity : 0.004 0.044 2457 Dihedral : 9.389 102.425 2300 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.34 % Allowed : 16.56 % Favored : 80.11 % 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: -1.41 (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 0.006 0.000 ARG B2072 TYR 0.015 0.001 TYR A 415 PHE 0.017 0.001 PHE A 154 TRP 0.022 0.001 TRP B2068 HIS 0.007 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00320 (14253) covalent geometry : angle 0.64359 (19273) SS BOND : bond 0.00186 ( 19) SS BOND : angle 0.85298 ( 38) hydrogen bonds : bond 0.03947 ( 247) hydrogen bonds : angle 8.03193 ( 582) Misc. bond : bond 0.00045 ( 2) link_ALPHA1-3 : bond 0.01326 ( 3) link_ALPHA1-3 : angle 2.11931 ( 9) link_ALPHA1-6 : bond 0.00579 ( 5) link_ALPHA1-6 : angle 2.03772 ( 15) link_BETA1-4 : bond 0.00665 ( 6) link_BETA1-4 : angle 3.92409 ( 18) link_BETA1-6 : bond 0.00129 ( 2) link_BETA1-6 : angle 4.09816 ( 6) link_NAG-ASN : bond 0.00729 ( 4) link_NAG-ASN : angle 6.09223 ( 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 242 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 192 time to evaluate : 0.539 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 75 GLN cc_start: 0.9209 (tp-100) cc_final: 0.8910 (tm-30) REVERT: H 116 MET cc_start: 0.9119 (tpp) cc_final: 0.8686 (tpp) REVERT: H 134 ASP cc_start: 0.8778 (p0) cc_final: 0.8497 (p0) REVERT: H 228 TYR cc_start: 0.8388 (m-80) cc_final: 0.8063 (m-80) REVERT: L 98 GLN cc_start: 0.8414 (mt0) cc_final: 0.7855 (tt0) REVERT: L 136 THR cc_start: 0.8365 (p) cc_final: 0.7729 (p) REVERT: A 270 MET cc_start: 0.6279 (OUTLIER) cc_final: 0.5453 (tpt) REVERT: A 387 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.5576 (tp30) REVERT: A 396 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7063 (mtm110) REVERT: A 594 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7938 (mp) REVERT: A 605 TYR cc_start: 0.7603 (t80) cc_final: 0.6370 (t80) REVERT: B 1734 MET cc_start: 0.8575 (mmt) cc_final: 0.8067 (mmt) REVERT: B 1869 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8065 (pp30) REVERT: B 1892 ASP cc_start: 0.8605 (m-30) cc_final: 0.8004 (t0) REVERT: B 1998 THR cc_start: 0.8620 (m) cc_final: 0.8220 (p) REVERT: B 2021 TYR cc_start: 0.7829 (t80) cc_final: 0.7446 (t80) REVERT: B 2044 MET cc_start: 0.7579 (tpp) cc_final: 0.7120 (tpp) REVERT: B 2120 MET cc_start: 0.8391 (ptm) cc_final: 0.7951 (tmm) REVERT: B 2121 TYR cc_start: 0.8509 (p90) cc_final: 0.8174 (p90) REVERT: B 2123 LYS cc_start: 0.9205 (mmmm) cc_final: 0.8852 (mmmm) REVERT: B 2183 SER cc_start: 0.7992 (t) cc_final: 0.7139 (t) outliers start: 50 outliers final: 34 residues processed: 230 average time/residue: 0.1094 time to fit residues: 37.3472 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 : 0.558 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 27 optimal weight: 20.0000 chunk 144 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 GLN ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 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** B2181 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.108847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.082758 restraints weight = 41677.143| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 5.29 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 14294 Z= 0.281 Angle : 0.755 14.484 19371 Z= 0.372 Chirality : 0.048 0.250 2088 Planarity : 0.004 0.043 2457 Dihedral : 9.377 95.599 2297 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 4.27 % Allowed : 17.89 % Favored : 77.84 % 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: -2.40 (0.20), residues: 1681 helix: -1.43 (0.42), residues: 134 sheet: -1.84 (0.25), residues: 385 loop : -1.59 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 90 TYR 0.029 0.002 TYR A 415 PHE 0.026 0.002 PHE A 154 TRP 0.019 0.002 TRP B2084 HIS 0.009 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00617 (14253) covalent geometry : angle 0.72160 (19273) SS BOND : bond 0.00400 ( 19) SS BOND : angle 1.01729 ( 38) hydrogen bonds : bond 0.04333 ( 247) hydrogen bonds : angle 7.96823 ( 582) Misc. bond : bond 0.00126 ( 2) link_ALPHA1-3 : bond 0.01287 ( 3) link_ALPHA1-3 : angle 2.22737 ( 9) link_ALPHA1-6 : bond 0.00413 ( 5) link_ALPHA1-6 : angle 2.21734 ( 15) link_BETA1-4 : bond 0.00573 ( 6) link_BETA1-4 : angle 3.95829 ( 18) link_BETA1-6 : bond 0.00571 ( 2) link_BETA1-6 : angle 4.31437 ( 6) link_NAG-ASN : bond 0.00404 ( 4) link_NAG-ASN : angle 6.21265 ( 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 242 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 178 time to evaluate : 0.543 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 45 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8595 (t) REVERT: H 75 GLN cc_start: 0.9396 (tp-100) cc_final: 0.9075 (tm-30) REVERT: H 116 MET cc_start: 0.9143 (tpp) cc_final: 0.8772 (tpp) REVERT: H 134 ASP cc_start: 0.8815 (p0) cc_final: 0.8598 (p0) REVERT: H 228 TYR cc_start: 0.8488 (m-80) cc_final: 0.8033 (m-80) REVERT: L 97 ASP cc_start: 0.7513 (t70) cc_final: 0.6745 (t0) REVERT: L 98 GLN cc_start: 0.8241 (mt0) cc_final: 0.7830 (tt0) REVERT: L 102 ARG cc_start: 0.7022 (tpt170) cc_final: 0.4888 (tpt170) REVERT: L 136 THR cc_start: 0.8259 (p) cc_final: 0.7557 (p) REVERT: A 270 MET cc_start: 0.6254 (OUTLIER) cc_final: 0.5539 (tpt) REVERT: A 387 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.5688 (tp30) REVERT: A 396 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7174 (mtm110) REVERT: A 420 HIS cc_start: 0.7579 (OUTLIER) cc_final: 0.6537 (t-90) REVERT: A 558 MET cc_start: 0.6379 (mmm) cc_final: 0.6157 (mmm) REVERT: A 594 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7924 (mp) REVERT: B 1656 LYS cc_start: 0.8736 (tttm) cc_final: 0.7863 (mtpt) REVERT: B 1734 MET cc_start: 0.8560 (mmt) cc_final: 0.8043 (mmt) REVERT: B 1869 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.7245 (pp30) REVERT: B 1892 ASP cc_start: 0.8687 (m-30) cc_final: 0.8197 (t0) REVERT: B 1900 PHE cc_start: 0.8547 (p90) cc_final: 0.7694 (p90) REVERT: B 1998 THR cc_start: 0.8640 (m) cc_final: 0.8227 (p) REVERT: B 2021 TYR cc_start: 0.7820 (t80) cc_final: 0.7446 (t80) REVERT: B 2044 MET cc_start: 0.7562 (tpp) cc_final: 0.7064 (tpp) REVERT: B 2121 TYR cc_start: 0.8554 (p90) cc_final: 0.8189 (p90) REVERT: B 2123 LYS cc_start: 0.9216 (mmmm) cc_final: 0.8874 (mmmm) REVERT: B 2183 SER cc_start: 0.7964 (t) cc_final: 0.7081 (m) outliers start: 64 outliers final: 40 residues processed: 225 average time/residue: 0.1142 time to fit residues: 37.9757 Evaluate side-chains 213 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 45 THR 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 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 84 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 205 THR 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 266 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 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 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 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 2186 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 GLN ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1670 ASN ** B1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1864 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 = 0.4166 r_free = 0.4166 target = 0.110596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.084828 restraints weight = 41123.086| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 5.16 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14294 Z= 0.170 Angle : 0.699 13.377 19371 Z= 0.339 Chirality : 0.047 0.247 2088 Planarity : 0.004 0.043 2457 Dihedral : 9.058 92.020 2294 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.94 % Allowed : 18.76 % Favored : 77.30 % 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: -2.30 (0.20), residues: 1681 helix: -1.30 (0.43), residues: 133 sheet: -1.73 (0.25), residues: 401 loop : -1.52 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 90 TYR 0.014 0.001 TYR A 144 PHE 0.022 0.002 PHE A 603 TRP 0.018 0.002 TRP B2068 HIS 0.008 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00373 (14253) covalent geometry : angle 0.66437 (19273) SS BOND : bond 0.00268 ( 19) SS BOND : angle 0.91912 ( 38) hydrogen bonds : bond 0.03713 ( 247) hydrogen bonds : angle 7.58067 ( 582) Misc. bond : bond 0.00060 ( 2) link_ALPHA1-3 : bond 0.01300 ( 3) link_ALPHA1-3 : angle 2.12405 ( 9) link_ALPHA1-6 : bond 0.00535 ( 5) link_ALPHA1-6 : angle 2.08515 ( 15) link_BETA1-4 : bond 0.00624 ( 6) link_BETA1-4 : angle 3.94337 ( 18) link_BETA1-6 : bond 0.00331 ( 2) link_BETA1-6 : angle 4.07659 ( 6) link_NAG-ASN : bond 0.00739 ( 4) link_NAG-ASN : angle 6.06834 ( 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 235 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 176 time to evaluate : 0.575 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 75 GLN cc_start: 0.9312 (tp-100) cc_final: 0.9001 (tm-30) REVERT: H 116 MET cc_start: 0.9136 (tpp) cc_final: 0.8762 (tpp) REVERT: H 134 ASP cc_start: 0.8811 (p0) cc_final: 0.8592 (p0) REVERT: H 228 TYR cc_start: 0.8419 (m-80) cc_final: 0.7986 (m-80) REVERT: L 98 GLN cc_start: 0.8056 (mt0) cc_final: 0.7701 (tt0) REVERT: L 102 ARG cc_start: 0.6858 (tpt170) cc_final: 0.4660 (tpt170) REVERT: L 136 THR cc_start: 0.8280 (p) cc_final: 0.7546 (p) REVERT: A 270 MET cc_start: 0.6175 (OUTLIER) cc_final: 0.5486 (tpt) REVERT: A 387 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.5578 (tp30) REVERT: A 396 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7211 (mtm110) REVERT: A 420 HIS cc_start: 0.7541 (OUTLIER) cc_final: 0.6465 (t-90) REVERT: A 479 SER cc_start: 0.7308 (OUTLIER) cc_final: 0.6896 (t) REVERT: A 594 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7917 (mp) REVERT: B 1610 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8454 (pt0) REVERT: B 1656 LYS cc_start: 0.8754 (tttm) cc_final: 0.7913 (mtpt) REVERT: B 1734 MET cc_start: 0.8574 (mmt) cc_final: 0.8043 (mmt) REVERT: B 1869 GLN cc_start: 0.9216 (OUTLIER) cc_final: 0.7234 (pp30) REVERT: B 1900 PHE cc_start: 0.8593 (p90) cc_final: 0.7753 (p90) REVERT: B 1998 THR cc_start: 0.8620 (m) cc_final: 0.8206 (p) REVERT: B 2021 TYR cc_start: 0.7866 (t80) cc_final: 0.7500 (t80) REVERT: B 2044 MET cc_start: 0.7707 (tpp) cc_final: 0.7146 (tpp) REVERT: B 2121 TYR cc_start: 0.8531 (p90) cc_final: 0.7961 (p90) REVERT: B 2123 LYS cc_start: 0.9215 (mmmm) cc_final: 0.8801 (mmmm) REVERT: B 2126 THR cc_start: 0.8013 (OUTLIER) cc_final: 0.7625 (m) outliers start: 59 outliers final: 36 residues processed: 225 average time/residue: 0.1174 time to fit residues: 39.3296 Evaluate side-chains 207 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 163 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 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 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 301 CYS 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 92 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 160 optimal weight: 0.1980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 GLN ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.110754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.084984 restraints weight = 40710.481| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 5.18 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14294 Z= 0.158 Angle : 0.700 13.202 19371 Z= 0.336 Chirality : 0.047 0.248 2088 Planarity : 0.004 0.046 2457 Dihedral : 8.821 89.857 2294 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.47 % Allowed : 19.63 % Favored : 76.90 % 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: -2.25 (0.20), residues: 1681 helix: -1.21 (0.44), residues: 133 sheet: -1.69 (0.25), residues: 415 loop : -1.50 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 313 TYR 0.013 0.001 TYR B1961 PHE 0.023 0.002 PHE A 603 TRP 0.018 0.002 TRP B2068 HIS 0.007 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00350 (14253) covalent geometry : angle 0.66597 (19273) SS BOND : bond 0.00248 ( 19) SS BOND : angle 0.86813 ( 38) hydrogen bonds : bond 0.03470 ( 247) hydrogen bonds : angle 7.26879 ( 582) Misc. bond : bond 0.00061 ( 2) link_ALPHA1-3 : bond 0.01286 ( 3) link_ALPHA1-3 : angle 2.18817 ( 9) link_ALPHA1-6 : bond 0.00513 ( 5) link_ALPHA1-6 : angle 2.05769 ( 15) link_BETA1-4 : bond 0.00664 ( 6) link_BETA1-4 : angle 3.91925 ( 18) link_BETA1-6 : bond 0.00221 ( 2) link_BETA1-6 : angle 4.15693 ( 6) link_NAG-ASN : bond 0.00804 ( 4) link_NAG-ASN : angle 5.99092 ( 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 227 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 175 time to evaluate : 0.592 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 75 GLN cc_start: 0.9365 (tp-100) cc_final: 0.9037 (tm-30) REVERT: H 116 MET cc_start: 0.9145 (tpp) cc_final: 0.8772 (tpp) REVERT: H 134 ASP cc_start: 0.8821 (p0) cc_final: 0.8614 (p0) REVERT: H 157 MET cc_start: 0.9052 (ttp) cc_final: 0.7950 (mtm) REVERT: L 90 ARG cc_start: 0.7765 (mmp80) cc_final: 0.7508 (mmp80) REVERT: L 97 ASP cc_start: 0.7440 (t70) cc_final: 0.6668 (t0) REVERT: L 98 GLN cc_start: 0.8019 (mt0) cc_final: 0.7717 (tt0) REVERT: L 136 THR cc_start: 0.8384 (p) cc_final: 0.7677 (p) REVERT: A 270 MET cc_start: 0.6030 (OUTLIER) cc_final: 0.5288 (tpt) REVERT: A 387 GLU cc_start: 0.6043 (OUTLIER) cc_final: 0.5361 (tp30) REVERT: A 420 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.6397 (t-90) REVERT: A 479 SER cc_start: 0.7322 (OUTLIER) cc_final: 0.6704 (p) REVERT: A 594 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7851 (mp) REVERT: B 1656 LYS cc_start: 0.8711 (tttm) cc_final: 0.7887 (mtpt) REVERT: B 1734 MET cc_start: 0.8593 (mmt) cc_final: 0.8083 (mmt) REVERT: B 1869 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.7241 (pp30) REVERT: B 1899 GLU cc_start: 0.8170 (pm20) cc_final: 0.7434 (pm20) REVERT: B 1900 PHE cc_start: 0.8556 (p90) cc_final: 0.7539 (p90) REVERT: B 1998 THR cc_start: 0.8620 (m) cc_final: 0.8213 (p) REVERT: B 2021 TYR cc_start: 0.7881 (t80) cc_final: 0.7520 (t80) REVERT: B 2044 MET cc_start: 0.7666 (tpp) cc_final: 0.7129 (tpp) REVERT: B 2060 LYS cc_start: 0.8681 (mmmt) cc_final: 0.8251 (mmmm) REVERT: B 2103 LYS cc_start: 0.5191 (mtpt) cc_final: 0.4725 (mmmt) REVERT: B 2121 TYR cc_start: 0.8499 (p90) cc_final: 0.8071 (p90) REVERT: B 2123 LYS cc_start: 0.9209 (mmmm) cc_final: 0.8881 (mmmm) REVERT: B 2126 THR cc_start: 0.7821 (OUTLIER) cc_final: 0.7469 (m) outliers start: 52 outliers final: 36 residues processed: 215 average time/residue: 0.1302 time to fit residues: 40.9436 Evaluate side-chains 209 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 166 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 132 LYS 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 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 301 CYS 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 587 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 605 TYR 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 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: 0.8980 chunk 139 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1864 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.109349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.083345 restraints weight = 41206.368| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 5.13 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14294 Z= 0.213 Angle : 0.728 13.288 19371 Z= 0.352 Chirality : 0.047 0.262 2088 Planarity : 0.004 0.044 2457 Dihedral : 8.774 86.402 2290 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.74 % Allowed : 19.89 % Favored : 76.37 % 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: -1.12 (0.45), residues: 133 sheet: -1.75 (0.25), residues: 411 loop : -1.58 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 316 TYR 0.017 0.001 TYR A 144 PHE 0.026 0.002 PHE A 603 TRP 0.018 0.002 TRP B2068 HIS 0.008 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00468 (14253) covalent geometry : angle 0.69562 (19273) SS BOND : bond 0.00312 ( 19) SS BOND : angle 0.88624 ( 38) hydrogen bonds : bond 0.03694 ( 247) hydrogen bonds : angle 7.23222 ( 582) Misc. bond : bond 0.00088 ( 2) link_ALPHA1-3 : bond 0.01317 ( 3) link_ALPHA1-3 : angle 2.24794 ( 9) link_ALPHA1-6 : bond 0.00471 ( 5) link_ALPHA1-6 : angle 2.10397 ( 15) link_BETA1-4 : bond 0.00588 ( 6) link_BETA1-4 : angle 3.90882 ( 18) link_BETA1-6 : bond 0.00301 ( 2) link_BETA1-6 : angle 4.06767 ( 6) link_NAG-ASN : bond 0.00771 ( 4) link_NAG-ASN : angle 5.86814 ( 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 227 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 171 time to evaluate : 0.457 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: H 75 GLN cc_start: 0.9388 (tp-100) cc_final: 0.9049 (tm-30) REVERT: H 116 MET cc_start: 0.9172 (tpp) cc_final: 0.8808 (tpp) REVERT: H 207 TYR cc_start: 0.8440 (m-80) cc_final: 0.7948 (m-80) REVERT: L 97 ASP cc_start: 0.7482 (t70) cc_final: 0.6700 (t0) REVERT: L 98 GLN cc_start: 0.7998 (mt0) cc_final: 0.7751 (tt0) REVERT: L 136 THR cc_start: 0.8255 (p) cc_final: 0.7476 (p) REVERT: A 75 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8234 (ptmm) REVERT: A 158 LEU cc_start: 0.7434 (mt) cc_final: 0.7098 (tt) REVERT: A 270 MET cc_start: 0.6066 (OUTLIER) cc_final: 0.5143 (tpt) REVERT: A 387 GLU cc_start: 0.5984 (OUTLIER) cc_final: 0.5330 (tp30) REVERT: A 420 HIS cc_start: 0.7553 (OUTLIER) cc_final: 0.6570 (t-90) REVERT: A 479 SER cc_start: 0.7357 (OUTLIER) cc_final: 0.6747 (p) REVERT: A 594 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7859 (mp) REVERT: B 1656 LYS cc_start: 0.8716 (tttm) cc_final: 0.7923 (mtpt) REVERT: B 1734 MET cc_start: 0.8593 (mmt) cc_final: 0.8084 (mmt) REVERT: B 1869 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.7248 (pp30) REVERT: B 1899 GLU cc_start: 0.8234 (pm20) cc_final: 0.7445 (pm20) REVERT: B 1900 PHE cc_start: 0.8587 (p90) cc_final: 0.7606 (p90) REVERT: B 1998 THR cc_start: 0.8645 (m) cc_final: 0.8219 (p) REVERT: B 2021 TYR cc_start: 0.7889 (t80) cc_final: 0.7527 (t80) REVERT: B 2044 MET cc_start: 0.7677 (tpp) cc_final: 0.7113 (tpp) REVERT: B 2060 LYS cc_start: 0.8674 (mmmt) cc_final: 0.8202 (mmmm) REVERT: B 2103 LYS cc_start: 0.5280 (mtpt) cc_final: 0.4799 (mmmt) REVERT: B 2121 TYR cc_start: 0.8404 (p90) cc_final: 0.8041 (p90) REVERT: B 2123 LYS cc_start: 0.9194 (mmmm) cc_final: 0.8764 (mmmm) REVERT: B 2126 THR cc_start: 0.8091 (OUTLIER) cc_final: 0.7749 (m) outliers start: 56 outliers final: 38 residues processed: 216 average time/residue: 0.1125 time to fit residues: 36.0685 Evaluate side-chains 212 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 166 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 99 PHE Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 84 ILE 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 206 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 272 VAL 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 572 LEU 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 A residue 605 TYR Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain B residue 1619 ILE 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 2089 ASN Chi-restraints excluded: chain B residue 2122 VAL Chi-restraints excluded: chain B residue 2126 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 109 optimal weight: 0.1980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** B2082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.110627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.085243 restraints weight = 40925.850| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 5.18 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3049 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= 0.155 Angle : 0.714 12.723 19371 Z= 0.342 Chirality : 0.047 0.295 2088 Planarity : 0.004 0.047 2457 Dihedral : 8.515 82.609 2288 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.40 % Allowed : 20.36 % Favored : 76.23 % 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: -1.11 (0.44), residues: 132 sheet: -1.59 (0.25), residues: 420 loop : -1.53 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 90 TYR 0.013 0.001 TYR B1961 PHE 0.029 0.001 PHE A 603 TRP 0.020 0.002 TRP B2068 HIS 0.005 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00344 (14253) covalent geometry : angle 0.68074 (19273) SS BOND : bond 0.00297 ( 19) SS BOND : angle 1.00204 ( 38) hydrogen bonds : bond 0.03365 ( 247) hydrogen bonds : angle 7.14386 ( 582) Misc. bond : bond 0.00058 ( 2) link_ALPHA1-3 : bond 0.01501 ( 3) link_ALPHA1-3 : angle 2.30913 ( 9) link_ALPHA1-6 : bond 0.00527 ( 5) link_ALPHA1-6 : angle 2.02292 ( 15) link_BETA1-4 : bond 0.00691 ( 6) link_BETA1-4 : angle 3.98744 ( 18) link_BETA1-6 : bond 0.00151 ( 2) link_BETA1-6 : angle 3.93952 ( 6) link_NAG-ASN : bond 0.00887 ( 4) link_NAG-ASN : angle 5.80739 ( 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 225 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 174 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 75 GLN cc_start: 0.9398 (tp-100) cc_final: 0.9085 (tm-30) REVERT: H 116 MET cc_start: 0.9164 (tpp) cc_final: 0.8802 (tpp) REVERT: H 157 MET cc_start: 0.8884 (ttp) cc_final: 0.8394 (mtp) REVERT: H 189 ASP cc_start: 0.8548 (t0) cc_final: 0.8281 (t0) REVERT: H 207 TYR cc_start: 0.8404 (m-80) cc_final: 0.7955 (m-80) REVERT: H 228 TYR cc_start: 0.8286 (m-80) cc_final: 0.7815 (m-80) REVERT: L 97 ASP cc_start: 0.7454 (t70) cc_final: 0.6660 (t0) REVERT: L 98 GLN cc_start: 0.7921 (mt0) cc_final: 0.7680 (tt0) REVERT: L 136 THR cc_start: 0.8294 (p) cc_final: 0.7530 (p) REVERT: A 270 MET cc_start: 0.6062 (OUTLIER) cc_final: 0.5400 (tpt) REVERT: A 387 GLU cc_start: 0.6009 (OUTLIER) cc_final: 0.5246 (tp30) REVERT: A 420 HIS cc_start: 0.7538 (OUTLIER) cc_final: 0.6526 (t-90) REVERT: A 475 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8076 (mmm-85) REVERT: A 479 SER cc_start: 0.7344 (OUTLIER) cc_final: 0.6736 (p) REVERT: A 594 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7843 (mp) REVERT: B 1656 LYS cc_start: 0.8656 (tttm) cc_final: 0.7915 (mtpt) REVERT: B 1734 MET cc_start: 0.8611 (mmt) cc_final: 0.8117 (mmt) REVERT: B 1869 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.7246 (pp30) REVERT: B 1899 GLU cc_start: 0.8113 (pm20) cc_final: 0.7301 (pm20) REVERT: B 1900 PHE cc_start: 0.8570 (p90) cc_final: 0.7620 (p90) REVERT: B 1907 ARG cc_start: 0.8744 (ttp80) cc_final: 0.8219 (mmm160) REVERT: B 1998 THR cc_start: 0.8590 (m) cc_final: 0.8171 (p) REVERT: B 2021 TYR cc_start: 0.7890 (t80) cc_final: 0.7536 (t80) REVERT: B 2044 MET cc_start: 0.7653 (tpp) cc_final: 0.7122 (tpp) REVERT: B 2060 LYS cc_start: 0.8638 (mmmt) cc_final: 0.8164 (mmmm) REVERT: B 2103 LYS cc_start: 0.5205 (mtpt) cc_final: 0.4874 (mmmm) REVERT: B 2121 TYR cc_start: 0.8364 (p90) cc_final: 0.8138 (p90) REVERT: B 2126 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7500 (m) outliers start: 51 outliers final: 36 residues processed: 217 average time/residue: 0.1255 time to fit residues: 39.8093 Evaluate side-chains 213 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 132 LYS 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 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 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 525 GLU 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 A residue 605 TYR Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain B residue 1619 ILE 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 2089 ASN 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: 0.7980 chunk 142 optimal weight: 0.5980 chunk 146 optimal weight: 4.9990 chunk 25 optimal weight: 40.0000 chunk 7 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 HIS ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1864 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 = 0.4186 r_free = 0.4186 target = 0.110523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.084939 restraints weight = 41344.130| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 5.30 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14294 Z= 0.159 Angle : 0.716 12.148 19371 Z= 0.345 Chirality : 0.047 0.300 2088 Planarity : 0.004 0.045 2457 Dihedral : 8.348 79.112 2286 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.07 % Allowed : 21.56 % Favored : 75.37 % 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: -2.24 (0.20), residues: 1681 helix: -1.17 (0.43), residues: 138 sheet: -1.58 (0.25), residues: 420 loop : -1.53 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 90 TYR 0.020 0.001 TYR A 38 PHE 0.028 0.002 PHE A 603 TRP 0.027 0.002 TRP B2084 HIS 0.006 0.001 HIS H 166 Details of bonding type rmsd covalent geometry : bond 0.00353 (14253) covalent geometry : angle 0.68512 (19273) SS BOND : bond 0.00263 ( 19) SS BOND : angle 0.98219 ( 38) hydrogen bonds : bond 0.03362 ( 247) hydrogen bonds : angle 7.06124 ( 582) Misc. bond : bond 0.00052 ( 2) link_ALPHA1-3 : bond 0.01489 ( 3) link_ALPHA1-3 : angle 2.30936 ( 9) link_ALPHA1-6 : bond 0.00511 ( 5) link_ALPHA1-6 : angle 2.00260 ( 15) link_BETA1-4 : bond 0.00671 ( 6) link_BETA1-4 : angle 3.91895 ( 18) link_BETA1-6 : bond 0.00124 ( 2) link_BETA1-6 : angle 3.85920 ( 6) link_NAG-ASN : bond 0.00825 ( 4) link_NAG-ASN : angle 5.65656 ( 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 217 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 171 time to evaluate : 0.602 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: H 75 GLN cc_start: 0.9410 (tp-100) cc_final: 0.9097 (tm-30) REVERT: H 116 MET cc_start: 0.9163 (tpp) cc_final: 0.8801 (tpp) REVERT: H 157 MET cc_start: 0.8932 (ttp) cc_final: 0.7974 (mtm) REVERT: H 189 ASP cc_start: 0.8512 (t0) cc_final: 0.8255 (t0) REVERT: H 207 TYR cc_start: 0.8380 (m-80) cc_final: 0.7964 (m-80) REVERT: H 228 TYR cc_start: 0.8281 (m-80) cc_final: 0.7846 (m-80) REVERT: L 97 ASP cc_start: 0.7407 (t70) cc_final: 0.6606 (t0) REVERT: L 98 GLN cc_start: 0.7880 (mt0) cc_final: 0.7680 (tt0) REVERT: L 136 THR cc_start: 0.8302 (p) cc_final: 0.7547 (p) REVERT: A 270 MET cc_start: 0.5995 (OUTLIER) cc_final: 0.5332 (tpt) REVERT: A 387 GLU cc_start: 0.6006 (OUTLIER) cc_final: 0.5241 (tp30) REVERT: A 420 HIS cc_start: 0.7513 (OUTLIER) cc_final: 0.6504 (t-90) REVERT: A 475 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8083 (mmm-85) REVERT: A 479 SER cc_start: 0.7366 (OUTLIER) cc_final: 0.6761 (p) REVERT: A 594 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7802 (mp) REVERT: B 1656 LYS cc_start: 0.8614 (tttm) cc_final: 0.7888 (mtpt) REVERT: B 1734 MET cc_start: 0.8644 (mmt) cc_final: 0.8154 (mmt) REVERT: B 1869 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.7267 (pp30) REVERT: B 1899 GLU cc_start: 0.8118 (pm20) cc_final: 0.7288 (pm20) REVERT: B 1900 PHE cc_start: 0.8556 (p90) cc_final: 0.7588 (p90) REVERT: B 1907 ARG cc_start: 0.8719 (ttp80) cc_final: 0.8192 (mmm160) REVERT: B 1998 THR cc_start: 0.8587 (m) cc_final: 0.8168 (p) REVERT: B 2021 TYR cc_start: 0.7923 (t80) cc_final: 0.7571 (t80) REVERT: B 2044 MET cc_start: 0.7664 (tpp) cc_final: 0.7139 (tpp) REVERT: B 2060 LYS cc_start: 0.8629 (mmmt) cc_final: 0.8165 (mmmm) REVERT: B 2103 LYS cc_start: 0.5244 (mtpt) cc_final: 0.4807 (mmmt) REVERT: B 2123 LYS cc_start: 0.9185 (mmmm) cc_final: 0.8876 (mmtm) REVERT: B 2183 SER cc_start: 0.8060 (t) cc_final: 0.7638 (m) outliers start: 46 outliers final: 36 residues processed: 208 average time/residue: 0.1239 time to fit residues: 37.9732 Evaluate side-chains 209 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 166 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 132 LYS 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 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 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 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 A residue 605 TYR Chi-restraints excluded: chain A residue 612 THR 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 2089 ASN 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: 0.0000 chunk 43 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 76 optimal weight: 0.0060 chunk 155 optimal weight: 2.9990 chunk 24 optimal weight: 30.0000 chunk 116 optimal weight: 3.9990 chunk 66 optimal weight: 0.0870 chunk 148 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1864 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.111016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.085672 restraints weight = 41091.190| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 5.20 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3309 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= 0.145 Angle : 0.723 11.790 19371 Z= 0.348 Chirality : 0.047 0.286 2088 Planarity : 0.004 0.046 2457 Dihedral : 8.203 74.851 2286 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.94 % Allowed : 21.96 % Favored : 75.10 % 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 (0.20), residues: 1681 helix: -1.25 (0.43), residues: 140 sheet: -1.54 (0.25), residues: 426 loop : -1.57 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1606 TYR 0.021 0.001 TYR A 38 PHE 0.030 0.002 PHE H 101 TRP 0.027 0.002 TRP B2084 HIS 0.007 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00324 (14253) covalent geometry : angle 0.69245 (19273) SS BOND : bond 0.00223 ( 19) SS BOND : angle 0.94527 ( 38) hydrogen bonds : bond 0.03286 ( 247) hydrogen bonds : angle 6.90934 ( 582) Misc. bond : bond 0.00045 ( 2) link_ALPHA1-3 : bond 0.01590 ( 3) link_ALPHA1-3 : angle 2.37939 ( 9) link_ALPHA1-6 : bond 0.00522 ( 5) link_ALPHA1-6 : angle 1.95666 ( 15) link_BETA1-4 : bond 0.00697 ( 6) link_BETA1-4 : angle 3.91275 ( 18) link_BETA1-6 : bond 0.00138 ( 2) link_BETA1-6 : angle 3.82583 ( 6) link_NAG-ASN : bond 0.00832 ( 4) link_NAG-ASN : angle 5.53975 ( 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 221 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.510 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: H 75 GLN cc_start: 0.9384 (tp-100) cc_final: 0.9073 (tm-30) REVERT: H 116 MET cc_start: 0.9164 (tpp) cc_final: 0.8802 (tpp) REVERT: H 157 MET cc_start: 0.8900 (ttp) cc_final: 0.7931 (mtm) REVERT: H 207 TYR cc_start: 0.8392 (m-80) cc_final: 0.7989 (m-80) REVERT: H 228 TYR cc_start: 0.8328 (m-80) cc_final: 0.7913 (m-80) REVERT: L 97 ASP cc_start: 0.7384 (t70) cc_final: 0.6589 (t0) REVERT: L 136 THR cc_start: 0.8307 (p) cc_final: 0.7559 (p) REVERT: A 270 MET cc_start: 0.6054 (OUTLIER) cc_final: 0.5461 (tpt) REVERT: A 373 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7739 (p0) REVERT: A 387 GLU cc_start: 0.6055 (OUTLIER) cc_final: 0.5272 (tp30) REVERT: A 420 HIS cc_start: 0.7512 (OUTLIER) cc_final: 0.6526 (t-90) REVERT: A 475 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8087 (mmm-85) REVERT: A 479 SER cc_start: 0.7355 (OUTLIER) cc_final: 0.6748 (p) REVERT: A 594 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7772 (mp) REVERT: B 1656 LYS cc_start: 0.8564 (tttm) cc_final: 0.7860 (mtpt) REVERT: B 1734 MET cc_start: 0.8643 (mmt) cc_final: 0.8158 (mmt) REVERT: B 1869 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.7273 (pp30) REVERT: B 1899 GLU cc_start: 0.8063 (pm20) cc_final: 0.7214 (pm20) REVERT: B 1900 PHE cc_start: 0.8537 (p90) cc_final: 0.7580 (p90) REVERT: B 1907 ARG cc_start: 0.8704 (ttp80) cc_final: 0.8186 (mmm160) REVERT: B 1998 THR cc_start: 0.8559 (m) cc_final: 0.8143 (p) REVERT: B 2021 TYR cc_start: 0.7935 (t80) cc_final: 0.7583 (t80) REVERT: B 2044 MET cc_start: 0.7663 (tpp) cc_final: 0.7115 (tpp) REVERT: B 2060 LYS cc_start: 0.8650 (mmmt) cc_final: 0.8286 (mmmm) REVERT: B 2103 LYS cc_start: 0.5327 (mtpt) cc_final: 0.4845 (mmmt) REVERT: B 2121 TYR cc_start: 0.8258 (p90) cc_final: 0.7883 (p90) REVERT: B 2183 SER cc_start: 0.8102 (t) cc_final: 0.7678 (p) outliers start: 44 outliers final: 34 residues processed: 212 average time/residue: 0.1237 time to fit residues: 38.5116 Evaluate side-chains 213 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 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 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 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 A residue 605 TYR Chi-restraints excluded: chain A residue 612 THR 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 2089 ASN 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: 0.9990 chunk 110 optimal weight: 0.5980 chunk 154 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 163 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 166 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 98 GLN ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** 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 = 0.4199 r_free = 0.4199 target = 0.111090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.085545 restraints weight = 41161.965| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 5.21 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14294 Z= 0.150 Angle : 0.719 11.701 19371 Z= 0.347 Chirality : 0.047 0.281 2088 Planarity : 0.004 0.045 2457 Dihedral : 8.111 70.832 2284 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.94 % Allowed : 21.83 % Favored : 75.23 % 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: -2.25 (0.20), residues: 1681 helix: -1.26 (0.43), residues: 140 sheet: -1.54 (0.25), residues: 424 loop : -1.55 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 90 TYR 0.019 0.001 TYR A 38 PHE 0.029 0.001 PHE A 603 TRP 0.037 0.002 TRP B2068 HIS 0.006 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00335 (14253) covalent geometry : angle 0.68909 (19273) SS BOND : bond 0.00229 ( 19) SS BOND : angle 0.92514 ( 38) hydrogen bonds : bond 0.03258 ( 247) hydrogen bonds : angle 6.87957 ( 582) Misc. bond : bond 0.00043 ( 2) link_ALPHA1-3 : bond 0.01627 ( 3) link_ALPHA1-3 : angle 2.40496 ( 9) link_ALPHA1-6 : bond 0.00516 ( 5) link_ALPHA1-6 : angle 1.93883 ( 15) link_BETA1-4 : bond 0.00687 ( 6) link_BETA1-4 : angle 3.90223 ( 18) link_BETA1-6 : bond 0.00123 ( 2) link_BETA1-6 : angle 3.82745 ( 6) link_NAG-ASN : bond 0.00830 ( 4) link_NAG-ASN : angle 5.47805 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3336.22 seconds wall clock time: 58 minutes 28.04 seconds (3508.04 seconds total)