Starting phenix.real_space_refine on Fri Mar 15 08:49:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kve_23048/03_2024/7kve_23048.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kve_23048/03_2024/7kve_23048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kve_23048/03_2024/7kve_23048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kve_23048/03_2024/7kve_23048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kve_23048/03_2024/7kve_23048.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kve_23048/03_2024/7kve_23048.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.067 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: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 7074 2.51 5 N 1905 2.21 5 O 2108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 18": "NH1" <-> "NH2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B ARG 316": "NH1" <-> "NH2" Residue "B ARG 317": "NH1" <-> "NH2" Residue "B ARG 321": "NH1" <-> "NH2" Residue "B ARG 348": "NH1" <-> "NH2" Residue "B ARG 396": "NH1" <-> "NH2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B ARG 445": "NH1" <-> "NH2" Residue "B ARG 475": "NH1" <-> "NH2" Residue "B ARG 501": "NH1" <-> "NH2" Residue "B ARG 505": "NH1" <-> "NH2" Residue "B ARG 506": "NH1" <-> "NH2" Residue "B ARG 510": "NH1" <-> "NH2" Residue "B ARG 547": "NH1" <-> "NH2" Residue "B PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 608": "NH1" <-> "NH2" Residue "B ARG 619": "NH1" <-> "NH2" Residue "B ARG 643": "NH1" <-> "NH2" Residue "B ARG 652": "NH1" <-> "NH2" Residue "B GLU 662": "OE1" <-> "OE2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "B ARG 701": "NH1" <-> "NH2" Residue "B ARG 709": "NH1" <-> "NH2" Residue "B ARG 712": "NH1" <-> "NH2" Residue "B ARG 1545": "NH1" <-> "NH2" Residue "B ARG 1551": "NH1" <-> "NH2" Residue "B ARG 1571": "NH1" <-> "NH2" Residue "B GLU 1572": "OE1" <-> "OE2" Residue "B GLU 1576": "OE1" <-> "OE2" Residue "B ARG 1603": "NH1" <-> "NH2" Residue "B ARG 1606": "NH1" <-> "NH2" Residue "B ARG 1631": "NH1" <-> "NH2" Residue "B GLU 1691": "OE1" <-> "OE2" Residue "B ARG 1698": "NH1" <-> "NH2" Residue "B GLU 1750": "OE1" <-> "OE2" Residue "B ARG 1761": "NH1" <-> "NH2" Residue "B ARG 1765": "NH1" <-> "NH2" Residue "B ARG 1799": "NH1" <-> "NH2" Residue "B ARG 1865": "NH1" <-> "NH2" Residue "B ARG 1877": "NH1" <-> "NH2" Residue "B ARG 1880": "NH1" <-> "NH2" Residue "B ARG 1907": "NH1" <-> "NH2" Residue "B GLU 1923": "OE1" <-> "OE2" Residue "B ARG 1985": "NH1" <-> "NH2" Residue "B TYR 2012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2019": "NH1" <-> "NH2" Residue "B GLU 2034": "OE1" <-> "OE2" Residue "B ARG 2072": "NH1" <-> "NH2" Residue "B ARG 2080": "NH1" <-> "NH2" Residue "B ARG 2140": "NH1" <-> "NH2" Residue "B ARG 2171": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11142 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 11142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1374, 11142 Classifications: {'peptide': 1374} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 66, 'TRANS': 1305} Chain breaks: 1 Time building chain proxies: 6.35, per 1000 atoms: 0.57 Number of scatterers: 11142 At special positions: 0 Unit cell: (100.1, 106.7, 141.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 2108 8.00 N 1905 7.00 C 7074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 165 " distance=2.04 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 472 " - pdb=" SG CYS B 498 " 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=2.04 Simple disulfide: pdb=" SG CYS B2038 " - pdb=" SG CYS B2193 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.22 Conformation dependent library (CDL) restraints added in 2.2 seconds 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2588 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 21 sheets defined 6.8% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'B' and resid 23 through 28 removed outlier: 4.475A pdb=" N LEU B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.904A pdb=" N LYS B 46 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 344 through 352 removed outlier: 3.948A pdb=" N ARG B 348 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 490 Processing helix chain 'B' and resid 526 through 528 No H-bonds generated for 'chain 'B' and resid 526 through 528' Processing helix chain 'B' and resid 549 through 556 removed outlier: 3.779A pdb=" N ASN B 556 " --> pdb=" O PHE B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 1608 through 1612 removed outlier: 4.352A pdb=" N HIS B1612 " --> pdb=" O TYR B1609 " (cutoff:3.500A) Processing helix chain 'B' and resid 1650 through 1654 removed outlier: 3.612A pdb=" N GLU B1654 " --> pdb=" O LYS B1651 " (cutoff:3.500A) Processing helix chain 'B' and resid 1665 through 1669 removed outlier: 3.606A pdb=" N GLU B1668 " --> pdb=" O TRP B1665 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASP B1669 " --> pdb=" O PHE B1666 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1665 through 1669' Processing helix chain 'B' and resid 1685 through 1689 Processing helix chain 'B' and resid 1707 through 1713 removed outlier: 3.863A pdb=" N ILE B1712 " --> pdb=" O PRO B1708 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS B1713 " --> pdb=" O GLU B1709 " (cutoff:3.500A) Processing helix chain 'B' and resid 1768 through 1772 removed outlier: 4.038A pdb=" N LYS B1772 " --> pdb=" O SER B1769 " (cutoff:3.500A) Processing helix chain 'B' and resid 1860 through 1865 removed outlier: 3.833A 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 sheet with id=AA1, first strand: chain 'B' and resid 36 through 40 removed outlier: 3.670A pdb=" N GLN B 11 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ARG B 4 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N HIS B 73 " --> pdb=" O ARG B 4 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N PHE B 6 " --> pdb=" O HIS B 73 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 70 " --> pdb=" O TRP B 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 62 through 64 removed outlier: 6.768A pdb=" N LEU B 62 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.519A pdb=" N ASN B 76 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG B 118 " --> pdb=" O ASN B 76 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 185 through 189 removed outlier: 6.339A pdb=" N LEU B 185 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N MET B 232 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE B 187 " --> pdb=" O MET B 232 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET B 270 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 268 " --> pdb=" O TRP B 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 217 through 219 removed outlier: 3.521A pdb=" N ILE B 217 " --> pdb=" O TYR B 295 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 370 through 371 removed outlier: 4.167A pdb=" N PHE B 325 " --> pdb=" O TYR B 371 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N TYR B 324 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LYS B 408 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE B 326 " --> pdb=" O LYS B 408 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE B 407 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 394 through 397 Processing sheet with id=AA8, first strand: chain 'B' and resid 515 through 520 removed outlier: 3.695A pdb=" N CYS B 585 " --> pdb=" O ALA B 518 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 522 through 524 Processing sheet with id=AB1, first strand: chain 'B' and resid 612 through 615 removed outlier: 3.815A pdb=" N LEU B 613 " --> pdb=" O ILE B 596 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 594 " --> pdb=" O LEU B 615 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1550 through 1554 removed outlier: 5.491A pdb=" N ASN B1550 " --> pdb=" O VAL B1627 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLN B1629 " --> pdb=" O ASN B1550 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ARG B1552 " --> pdb=" O GLN B1629 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ARG B1631 " --> pdb=" O ARG B1552 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TYR B1554 " --> pdb=" O ARG B1631 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1556 through 1563 removed outlier: 3.907A pdb=" N ALA B1557 " --> pdb=" O ARG B1593 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B1593 " --> pdb=" O ALA B1557 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1697 through 1698 Processing sheet with id=AB5, first strand: chain 'B' and resid 1701 through 1703 Processing sheet with id=AB6, first strand: chain 'B' and resid 1776 through 1780 removed outlier: 3.513A pdb=" N MET B1746 " --> pdb=" O ALA B1779 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1791 through 1792 Processing sheet with id=AB8, first strand: chain 'B' and resid 1834 through 1836 Processing sheet with id=AB9, first strand: chain 'B' and resid 1881 through 1882 removed outlier: 6.390A pdb=" N GLN B2031 " --> pdb=" O THR B1946 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL B1943 " --> pdb=" O ALA B2010 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N GLY B1947 " --> pdb=" O PRO B2006 " (cutoff:3.500A) removed outlier: 11.882A pdb=" N GLN B1949 " --> pdb=" O PHE B2004 " (cutoff:3.500A) removed outlier: 12.332A pdb=" N PHE B2004 " --> pdb=" O GLN B1949 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1895 through 1897 removed outlier: 6.746A pdb=" N GLU B1964 " --> pdb=" O THR B2018 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA B2020 " --> pdb=" O THR B1962 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR B1962 " --> pdb=" O ALA B2020 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 2040 through 2041 removed outlier: 3.788A pdb=" N THR B2040 " --> pdb=" O GLY B2192 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY B2192 " --> pdb=" O THR B2040 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLU B2189 " --> pdb=" O ILE B2108 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE B2108 " --> pdb=" O GLU B2189 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE B2191 " --> pdb=" O THR B2106 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ARG B2171 " --> pdb=" O LEU B2099 " (cutoff:3.500A) removed outlier: 10.342A pdb=" N LYS B2101 " --> pdb=" O ILE B2169 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N ILE B2169 " --> pdb=" O LYS B2101 " (cutoff:3.500A) removed outlier: 9.659A pdb=" N LYS B2103 " --> pdb=" O PRO B2167 " (cutoff:3.500A) removed outlier: 10.470A pdb=" N ILE B2105 " --> pdb=" O ASN B2165 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ASN B2165 " --> pdb=" O ILE B2105 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ALA B2107 " --> pdb=" O PHE B2163 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N PHE B2163 " --> pdb=" O ALA B2107 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE B2109 " --> pdb=" O LYS B2161 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LYS B2161 " --> pdb=" O ILE B2109 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER B2124 " --> pdb=" O LYS B2178 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP B2180 " --> pdb=" O VAL B2122 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B2122 " --> pdb=" O TRP B2180 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET B2120 " --> pdb=" O CYS B2113 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N CYS B2113 " --> pdb=" O MET B2120 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 2054 through 2056 removed outlier: 6.999A pdb=" N ARG B2171 " --> pdb=" O LEU B2099 " (cutoff:3.500A) removed outlier: 10.342A pdb=" N LYS B2101 " --> pdb=" O ILE B2169 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N ILE B2169 " --> pdb=" O LYS B2101 " (cutoff:3.500A) removed outlier: 9.659A pdb=" N LYS B2103 " --> pdb=" O PRO B2167 " (cutoff:3.500A) removed outlier: 10.470A pdb=" N ILE B2105 " --> pdb=" O ASN B2165 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ASN B2165 " --> pdb=" O ILE B2105 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ALA B2107 " --> pdb=" O PHE B2163 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N PHE B2163 " --> pdb=" O ALA B2107 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE B2109 " --> pdb=" O LYS B2161 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LYS B2161 " --> pdb=" O ILE B2109 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER B2124 " --> pdb=" O LYS B2178 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP B2180 " --> pdb=" O VAL B2122 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B2122 " --> pdb=" O TRP B2180 " (cutoff:3.500A) 160 hydrogen bonds defined for protein. 384 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: 4.48 Time building geometry restraints manager: 4.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1844 1.29 - 1.42: 3119 1.42 - 1.56: 6380 1.56 - 1.70: 1 1.70 - 1.83: 92 Bond restraints: 11436 Sorted by residual: bond pdb=" C VAL B 654 " pdb=" O VAL B 654 " ideal model delta sigma weight residual 1.231 1.153 0.078 1.29e-02 6.01e+03 3.63e+01 bond pdb=" C CYS B 656 " pdb=" O CYS B 656 " ideal model delta sigma weight residual 1.235 1.188 0.047 1.26e-02 6.30e+03 1.38e+01 bond pdb=" C ASP B 653 " pdb=" N VAL B 654 " ideal model delta sigma weight residual 1.331 1.290 0.041 1.20e-02 6.94e+03 1.19e+01 bond pdb=" C ASN B 541 " pdb=" N PRO B 542 " ideal model delta sigma weight residual 1.331 1.359 -0.027 7.90e-03 1.60e+04 1.18e+01 bond pdb=" CA VAL B 654 " pdb=" C VAL B 654 " ideal model delta sigma weight residual 1.526 1.477 0.049 1.43e-02 4.89e+03 1.16e+01 ... (remaining 11431 not shown) Histogram of bond angle deviations from ideal: 99.92 - 107.30: 500 107.30 - 114.69: 6526 114.69 - 122.07: 5929 122.07 - 129.45: 2423 129.45 - 136.84: 112 Bond angle restraints: 15490 Sorted by residual: angle pdb=" N VAL B 654 " pdb=" CA VAL B 654 " pdb=" CB VAL B 654 " ideal model delta sigma weight residual 112.60 100.51 12.09 1.29e+00 6.01e-01 8.78e+01 angle pdb=" N PHE B2059 " pdb=" CA PHE B2059 " pdb=" C PHE B2059 " ideal model delta sigma weight residual 112.72 103.01 9.71 1.36e+00 5.41e-01 5.10e+01 angle pdb=" N VAL B1706 " pdb=" CA VAL B1706 " pdb=" C VAL B1706 " ideal model delta sigma weight residual 112.12 107.30 4.82 8.40e-01 1.42e+00 3.29e+01 angle pdb=" N ASP B 401 " pdb=" CA ASP B 401 " pdb=" C ASP B 401 " ideal model delta sigma weight residual 112.57 106.64 5.93 1.13e+00 7.83e-01 2.75e+01 angle pdb=" C ASN B2036 " pdb=" N GLY B2037 " pdb=" CA GLY B2037 " ideal model delta sigma weight residual 121.51 129.34 -7.83 1.52e+00 4.33e-01 2.65e+01 ... (remaining 15485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6070 17.94 - 35.88: 666 35.88 - 53.82: 92 53.82 - 71.76: 20 71.76 - 89.70: 8 Dihedral angle restraints: 6856 sinusoidal: 2828 harmonic: 4028 Sorted by residual: dihedral pdb=" CB CYS B 139 " pdb=" SG CYS B 139 " pdb=" SG CYS B 165 " pdb=" CB CYS B 165 " ideal model delta sinusoidal sigma weight residual 93.00 20.33 72.67 1 1.00e+01 1.00e-02 6.74e+01 dihedral pdb=" N VAL B 654 " pdb=" C VAL B 654 " pdb=" CA VAL B 654 " pdb=" CB VAL B 654 " ideal model delta harmonic sigma weight residual 123.40 108.17 15.23 0 2.50e+00 1.60e-01 3.71e+01 dihedral pdb=" CA ARG B 90 " pdb=" C ARG B 90 " pdb=" N TYR B 91 " pdb=" CA TYR B 91 " ideal model delta harmonic sigma weight residual -180.00 -155.50 -24.50 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 6853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1519 0.100 - 0.199: 101 0.199 - 0.299: 3 0.299 - 0.398: 3 0.398 - 0.498: 1 Chirality restraints: 1627 Sorted by residual: chirality pdb=" CB VAL B 654 " pdb=" CA VAL B 654 " pdb=" CG1 VAL B 654 " pdb=" CG2 VAL B 654 " both_signs ideal model delta sigma weight residual False -2.63 -2.13 -0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" CA ASP B 660 " pdb=" N ASP B 660 " pdb=" C ASP B 660 " pdb=" CB ASP B 660 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA VAL B 654 " pdb=" N VAL B 654 " pdb=" C VAL B 654 " pdb=" CB VAL B 654 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 1624 not shown) Planarity restraints: 1999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B2033 " -0.021 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C CYS B2033 " 0.071 2.00e-02 2.50e+03 pdb=" O CYS B2033 " -0.026 2.00e-02 2.50e+03 pdb=" N GLU B2034 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 669 " 0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO B 670 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 670 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 670 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B2023 " -0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO B2024 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B2024 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B2024 " -0.028 5.00e-02 4.00e+02 ... (remaining 1996 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1223 2.74 - 3.28: 11124 3.28 - 3.82: 17231 3.82 - 4.36: 20716 4.36 - 4.90: 36116 Nonbonded interactions: 86410 Sorted by model distance: nonbonded pdb=" OD1 ASP B 191 " pdb=" OG SER B 193 " model vdw 2.204 2.440 nonbonded pdb=" OH TYR B1609 " pdb=" OD2 ASP B2005 " model vdw 2.204 2.440 nonbonded pdb=" O SER B 349 " pdb=" NE2 GLN B 358 " model vdw 2.204 2.520 nonbonded pdb=" OH TYR B1554 " pdb=" O ARG B1621 " model vdw 2.212 2.440 nonbonded pdb=" OH TYR B 605 " pdb=" OE2 GLU B 621 " model vdw 2.214 2.440 ... (remaining 86405 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.980 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 33.320 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 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 : 0.005 0.078 11436 Z= 0.319 Angle : 0.817 12.087 15490 Z= 0.482 Chirality : 0.053 0.498 1627 Planarity : 0.005 0.091 1999 Dihedral : 14.673 89.697 4250 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.36 % Allowed : 18.25 % Favored : 81.39 % Rotamer: Outliers : 0.57 % Allowed : 8.65 % Favored : 90.78 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.88 (0.17), residues: 1370 helix: -4.25 (0.41), residues: 45 sheet: -3.39 (0.23), residues: 373 loop : -4.44 (0.14), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B1700 HIS 0.005 0.001 HIS B 242 PHE 0.016 0.001 PHE B2071 TYR 0.021 0.002 TYR B 363 ARG 0.008 0.001 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 153 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 136 ASP cc_start: 0.7739 (m-30) cc_final: 0.7530 (m-30) REVERT: B 244 ASN cc_start: 0.8815 (m-40) cc_final: 0.8450 (m110) REVERT: B 424 PHE cc_start: 0.6930 (m-80) cc_final: 0.6696 (m-80) REVERT: B 445 ARG cc_start: 0.6960 (pmt170) cc_final: 0.6568 (ptt-90) REVERT: B 610 GLU cc_start: 0.7053 (mp0) cc_final: 0.6436 (mp0) REVERT: B 621 GLU cc_start: 0.6896 (tt0) cc_final: 0.6687 (tt0) REVERT: B 650 LYS cc_start: 0.7591 (mptt) cc_final: 0.7251 (mmtm) REVERT: B 1703 TYR cc_start: 0.6750 (p90) cc_final: 0.6523 (p90) REVERT: B 1738 MET cc_start: 0.7127 (ttt) cc_final: 0.6684 (ttt) REVERT: B 1776 GLU cc_start: 0.7933 (tt0) cc_final: 0.7723 (tt0) REVERT: B 1868 MET cc_start: 0.7417 (mtt) cc_final: 0.7128 (mtt) REVERT: B 1878 ASP cc_start: 0.8013 (m-30) cc_final: 0.7598 (p0) outliers start: 7 outliers final: 1 residues processed: 158 average time/residue: 0.2675 time to fit residues: 58.3765 Evaluate side-chains 120 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2036 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 65 optimal weight: 0.0570 chunk 79 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 134 HIS B 252 HIS B 307 ASN B 315 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN B 562 ASN B 583 HIS B 597 HIS B 609 HIS B 639 ASN B 700 ASN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1645 HIS B1670 ASN B1713 HIS B1778 HIS ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1819 GLN ** B1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1828 GLN B1830 GLN B1936 GLN B2002 ASN B2003 GLN B2093 GLN B2128 HIS B2162 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11436 Z= 0.245 Angle : 0.676 9.296 15490 Z= 0.352 Chirality : 0.047 0.155 1627 Planarity : 0.005 0.092 1999 Dihedral : 6.284 34.243 1510 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.91 % Favored : 84.09 % Rotamer: Outliers : 2.04 % Allowed : 14.12 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.24 (0.18), residues: 1370 helix: -3.47 (0.51), residues: 50 sheet: -2.83 (0.26), residues: 360 loop : -4.05 (0.15), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1700 HIS 0.004 0.001 HIS B 134 PHE 0.015 0.001 PHE B2172 TYR 0.028 0.002 TYR B1903 ARG 0.003 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: B 418 TYR cc_start: 0.8181 (t80) cc_final: 0.7965 (t80) REVERT: B 424 PHE cc_start: 0.6963 (m-80) cc_final: 0.6717 (m-80) REVERT: B 445 ARG cc_start: 0.6929 (pmt170) cc_final: 0.6571 (ptt-90) REVERT: B 621 GLU cc_start: 0.6616 (tt0) cc_final: 0.6408 (tt0) REVERT: B 650 LYS cc_start: 0.7669 (mptt) cc_final: 0.7462 (mmtp) REVERT: B 1703 TYR cc_start: 0.6820 (p90) cc_final: 0.6618 (p90) REVERT: B 1738 MET cc_start: 0.7043 (ttt) cc_final: 0.6608 (ttt) REVERT: B 1850 LYS cc_start: 0.7856 (mtpp) cc_final: 0.7160 (mttp) REVERT: B 1868 MET cc_start: 0.7267 (mtt) cc_final: 0.6974 (mtt) outliers start: 25 outliers final: 15 residues processed: 142 average time/residue: 0.2216 time to fit residues: 46.4199 Evaluate side-chains 128 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1798 VAL Chi-restraints excluded: chain B residue 1843 THR Chi-restraints excluded: chain B residue 1920 TRP Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2165 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 10.0000 chunk 38 optimal weight: 0.0030 chunk 103 optimal weight: 3.9990 chunk 84 optimal weight: 0.0670 chunk 34 optimal weight: 0.2980 chunk 124 optimal weight: 0.5980 chunk 134 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 overall best weight: 0.3128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 HIS ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1670 ASN ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1824 ASN B1936 GLN B1973 GLN B2036 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11436 Z= 0.151 Angle : 0.602 11.771 15490 Z= 0.305 Chirality : 0.045 0.156 1627 Planarity : 0.005 0.087 1999 Dihedral : 5.474 27.330 1508 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.97 % Favored : 88.03 % Rotamer: Outliers : 2.04 % Allowed : 18.20 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.75 (0.19), residues: 1370 helix: -3.29 (0.54), residues: 52 sheet: -2.39 (0.26), residues: 378 loop : -3.75 (0.16), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1834 HIS 0.002 0.000 HIS B 379 PHE 0.018 0.001 PHE B 552 TYR 0.023 0.001 TYR B1903 ARG 0.003 0.000 ARG B 485 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 445 ARG cc_start: 0.6747 (pmt170) cc_final: 0.6419 (ptt-90) REVERT: B 594 LEU cc_start: 0.8621 (mt) cc_final: 0.8407 (mt) REVERT: B 610 GLU cc_start: 0.7323 (mp0) cc_final: 0.6889 (mm-30) REVERT: B 621 GLU cc_start: 0.6563 (tt0) cc_final: 0.6320 (tt0) REVERT: B 1638 ARG cc_start: 0.7521 (ptm-80) cc_final: 0.7313 (mtp-110) REVERT: B 1700 TRP cc_start: 0.7460 (OUTLIER) cc_final: 0.5813 (m-10) REVERT: B 1703 TYR cc_start: 0.6714 (p90) cc_final: 0.6472 (p90) REVERT: B 1738 MET cc_start: 0.6594 (ttt) cc_final: 0.6226 (ttt) REVERT: B 1850 LYS cc_start: 0.7990 (mtpp) cc_final: 0.7326 (mttp) REVERT: B 1868 MET cc_start: 0.7056 (mtt) cc_final: 0.6744 (mtt) REVERT: B 1878 ASP cc_start: 0.7898 (m-30) cc_final: 0.7570 (p0) REVERT: B 1883 MET cc_start: 0.8735 (mmm) cc_final: 0.8319 (mpp) REVERT: B 2067 TYR cc_start: 0.3689 (p90) cc_final: 0.3419 (p90) outliers start: 25 outliers final: 14 residues processed: 149 average time/residue: 0.2368 time to fit residues: 51.4853 Evaluate side-chains 131 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1798 VAL Chi-restraints excluded: chain B residue 1920 TRP Chi-restraints excluded: chain B residue 1982 ASN Chi-restraints excluded: chain B residue 2009 VAL Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2165 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 chunk 65 optimal weight: 0.3980 chunk 118 optimal weight: 0.0060 chunk 35 optimal weight: 8.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1670 ASN ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11436 Z= 0.219 Angle : 0.630 9.780 15490 Z= 0.321 Chirality : 0.046 0.203 1627 Planarity : 0.005 0.090 1999 Dihedral : 5.664 29.417 1508 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.31 % Favored : 85.69 % Rotamer: Outliers : 2.45 % Allowed : 20.24 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.58 (0.19), residues: 1370 helix: -3.23 (0.55), residues: 52 sheet: -2.25 (0.26), residues: 372 loop : -3.64 (0.16), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B2084 HIS 0.003 0.001 HIS B 228 PHE 0.017 0.001 PHE B 552 TYR 0.019 0.002 TYR B1903 ARG 0.005 0.000 ARG B1631 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 121 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: B 418 TYR cc_start: 0.8189 (t80) cc_final: 0.7966 (t80) REVERT: B 445 ARG cc_start: 0.6745 (pmt170) cc_final: 0.6405 (ptt-90) REVERT: B 621 GLU cc_start: 0.6500 (tt0) cc_final: 0.6230 (tt0) REVERT: B 1638 ARG cc_start: 0.7731 (ptm-80) cc_final: 0.7223 (mtp-110) REVERT: B 1700 TRP cc_start: 0.7510 (OUTLIER) cc_final: 0.5779 (m-10) REVERT: B 1703 TYR cc_start: 0.6774 (p90) cc_final: 0.6431 (p90) REVERT: B 1738 MET cc_start: 0.6936 (ttt) cc_final: 0.6509 (ttt) REVERT: B 1850 LYS cc_start: 0.7839 (mtpp) cc_final: 0.7117 (mttp) REVERT: B 1868 MET cc_start: 0.7181 (mtt) cc_final: 0.6868 (mtt) REVERT: B 1878 ASP cc_start: 0.7847 (m-30) cc_final: 0.7453 (p0) REVERT: B 1883 MET cc_start: 0.8777 (mmm) cc_final: 0.8467 (tpp) outliers start: 30 outliers final: 24 residues processed: 144 average time/residue: 0.2145 time to fit residues: 46.0266 Evaluate side-chains 139 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1783 MET Chi-restraints excluded: chain B residue 1798 VAL Chi-restraints excluded: chain B residue 1843 THR Chi-restraints excluded: chain B residue 1856 LEU Chi-restraints excluded: chain B residue 1920 TRP Chi-restraints excluded: chain B residue 1982 ASN Chi-restraints excluded: chain B residue 2009 VAL Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2165 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 113 optimal weight: 0.3980 chunk 91 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 67 optimal weight: 0.0970 chunk 118 optimal weight: 0.0970 chunk 33 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11436 Z= 0.189 Angle : 0.614 9.859 15490 Z= 0.313 Chirality : 0.045 0.173 1627 Planarity : 0.005 0.090 1999 Dihedral : 5.565 28.943 1508 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.21 % Favored : 86.79 % Rotamer: Outliers : 3.51 % Allowed : 20.73 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.43 (0.20), residues: 1370 helix: -3.14 (0.57), residues: 52 sheet: -2.14 (0.26), residues: 376 loop : -3.52 (0.17), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1700 HIS 0.002 0.001 HIS B 682 PHE 0.016 0.001 PHE B1568 TYR 0.018 0.001 TYR B1903 ARG 0.004 0.000 ARG B 648 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 124 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 445 ARG cc_start: 0.6726 (pmt170) cc_final: 0.6394 (ptt-90) REVERT: B 505 ARG cc_start: 0.7087 (ptt-90) cc_final: 0.6221 (tpt-90) REVERT: B 590 GLN cc_start: 0.6536 (OUTLIER) cc_final: 0.6241 (pm20) REVERT: B 605 TYR cc_start: 0.8073 (t80) cc_final: 0.7861 (t80) REVERT: B 621 GLU cc_start: 0.6371 (tt0) cc_final: 0.6122 (tt0) REVERT: B 1638 ARG cc_start: 0.7754 (ptm-80) cc_final: 0.7211 (mtp-110) REVERT: B 1700 TRP cc_start: 0.7470 (OUTLIER) cc_final: 0.5846 (m-10) REVERT: B 1703 TYR cc_start: 0.6756 (p90) cc_final: 0.6421 (p90) REVERT: B 1738 MET cc_start: 0.6804 (ttt) cc_final: 0.6392 (ttt) REVERT: B 1850 LYS cc_start: 0.7850 (mtpp) cc_final: 0.7223 (mttp) REVERT: B 1868 MET cc_start: 0.7186 (mtt) cc_final: 0.6823 (mtt) REVERT: B 1878 ASP cc_start: 0.7876 (m-30) cc_final: 0.7551 (p0) REVERT: B 1883 MET cc_start: 0.8759 (mmm) cc_final: 0.8451 (mpp) outliers start: 43 outliers final: 27 residues processed: 159 average time/residue: 0.1992 time to fit residues: 47.7659 Evaluate side-chains 146 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 117 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1783 MET Chi-restraints excluded: chain B residue 1798 VAL Chi-restraints excluded: chain B residue 1843 THR Chi-restraints excluded: chain B residue 1856 LEU Chi-restraints excluded: chain B residue 1920 TRP Chi-restraints excluded: chain B residue 1982 ASN Chi-restraints excluded: chain B residue 2009 VAL Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2165 ASN Chi-restraints excluded: chain B residue 2173 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 110 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11436 Z= 0.183 Angle : 0.606 9.864 15490 Z= 0.309 Chirality : 0.045 0.196 1627 Planarity : 0.005 0.089 1999 Dihedral : 5.464 27.593 1508 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.65 % Favored : 86.35 % Rotamer: Outliers : 3.18 % Allowed : 21.55 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.20), residues: 1370 helix: -2.69 (0.60), residues: 58 sheet: -1.94 (0.27), residues: 373 loop : -3.47 (0.17), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1934 HIS 0.002 0.001 HIS B 682 PHE 0.017 0.001 PHE B 552 TYR 0.016 0.001 TYR B1903 ARG 0.004 0.000 ARG B 648 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 123 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 363 TYR cc_start: 0.3915 (OUTLIER) cc_final: 0.2563 (t80) REVERT: B 445 ARG cc_start: 0.6725 (pmt170) cc_final: 0.6404 (ptt-90) REVERT: B 505 ARG cc_start: 0.7026 (ptt-90) cc_final: 0.6058 (mmm160) REVERT: B 590 GLN cc_start: 0.6436 (OUTLIER) cc_final: 0.6192 (pm20) REVERT: B 605 TYR cc_start: 0.7997 (t80) cc_final: 0.7713 (t80) REVERT: B 621 GLU cc_start: 0.6372 (tt0) cc_final: 0.6041 (tt0) REVERT: B 1638 ARG cc_start: 0.7727 (ptm-80) cc_final: 0.7235 (mtp-110) REVERT: B 1700 TRP cc_start: 0.7465 (OUTLIER) cc_final: 0.5860 (m-10) REVERT: B 1703 TYR cc_start: 0.6840 (p90) cc_final: 0.6440 (p90) REVERT: B 1738 MET cc_start: 0.7131 (ttt) cc_final: 0.6683 (ttt) REVERT: B 1850 LYS cc_start: 0.7849 (mtpp) cc_final: 0.7160 (mttp) REVERT: B 1868 MET cc_start: 0.7255 (mtt) cc_final: 0.6881 (mtt) REVERT: B 1883 MET cc_start: 0.8745 (mmm) cc_final: 0.8447 (mpp) outliers start: 39 outliers final: 27 residues processed: 155 average time/residue: 0.2088 time to fit residues: 48.8053 Evaluate side-chains 146 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 116 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1798 VAL Chi-restraints excluded: chain B residue 1843 THR Chi-restraints excluded: chain B residue 1846 MET Chi-restraints excluded: chain B residue 1856 LEU Chi-restraints excluded: chain B residue 1920 TRP Chi-restraints excluded: chain B residue 1982 ASN Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2062 SER Chi-restraints excluded: chain B residue 2165 ASN Chi-restraints excluded: chain B residue 2173 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 0.0070 chunk 96 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 82 optimal weight: 0.4980 chunk 80 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1670 ASN ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11436 Z= 0.166 Angle : 0.592 9.807 15490 Z= 0.300 Chirality : 0.045 0.154 1627 Planarity : 0.005 0.088 1999 Dihedral : 5.267 25.245 1508 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.48 % Favored : 87.52 % Rotamer: Outliers : 3.18 % Allowed : 22.04 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.20), residues: 1370 helix: -2.88 (0.59), residues: 52 sheet: -1.76 (0.28), residues: 366 loop : -3.35 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1934 HIS 0.002 0.000 HIS B 682 PHE 0.035 0.001 PHE B 552 TYR 0.027 0.001 TYR B 418 ARG 0.003 0.000 ARG B 648 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 127 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 363 TYR cc_start: 0.3965 (OUTLIER) cc_final: 0.2614 (t80) REVERT: B 445 ARG cc_start: 0.6729 (pmt170) cc_final: 0.6414 (ptt-90) REVERT: B 505 ARG cc_start: 0.7086 (ptt-90) cc_final: 0.6203 (tpp80) REVERT: B 590 GLN cc_start: 0.6466 (OUTLIER) cc_final: 0.6201 (pm20) REVERT: B 594 LEU cc_start: 0.8526 (mt) cc_final: 0.8306 (tt) REVERT: B 605 TYR cc_start: 0.8116 (t80) cc_final: 0.7793 (t80) REVERT: B 621 GLU cc_start: 0.6403 (tt0) cc_final: 0.6018 (tt0) REVERT: B 1700 TRP cc_start: 0.7434 (OUTLIER) cc_final: 0.5846 (m-10) REVERT: B 1703 TYR cc_start: 0.6764 (p90) cc_final: 0.6345 (p90) REVERT: B 1716 LEU cc_start: 0.8467 (mt) cc_final: 0.8256 (mp) REVERT: B 1738 MET cc_start: 0.6902 (ttt) cc_final: 0.6509 (ttt) REVERT: B 1850 LYS cc_start: 0.7979 (mtpp) cc_final: 0.7357 (mttp) REVERT: B 1868 MET cc_start: 0.7137 (mtt) cc_final: 0.6778 (mtt) REVERT: B 1878 ASP cc_start: 0.7835 (m-30) cc_final: 0.7557 (p0) REVERT: B 1883 MET cc_start: 0.8754 (mmm) cc_final: 0.8345 (mpp) outliers start: 39 outliers final: 27 residues processed: 157 average time/residue: 0.2095 time to fit residues: 49.7596 Evaluate side-chains 151 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 121 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1657 THR Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1798 VAL Chi-restraints excluded: chain B residue 1843 THR Chi-restraints excluded: chain B residue 1856 LEU Chi-restraints excluded: chain B residue 1920 TRP Chi-restraints excluded: chain B residue 1982 ASN Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2165 ASN Chi-restraints excluded: chain B residue 2173 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 0.7980 chunk 78 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1670 ASN ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1869 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11436 Z= 0.265 Angle : 0.664 9.775 15490 Z= 0.340 Chirality : 0.046 0.149 1627 Planarity : 0.005 0.092 1999 Dihedral : 5.788 31.495 1508 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.62 % Favored : 84.38 % Rotamer: Outliers : 3.51 % Allowed : 22.86 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.20 (0.20), residues: 1370 helix: -2.67 (0.59), residues: 58 sheet: -1.89 (0.27), residues: 375 loop : -3.43 (0.17), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1563 HIS 0.004 0.001 HIS B 228 PHE 0.021 0.001 PHE B 552 TYR 0.017 0.002 TYR B 91 ARG 0.002 0.000 ARG B 648 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 113 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 363 TYR cc_start: 0.4106 (OUTLIER) cc_final: 0.2852 (t80) REVERT: B 424 PHE cc_start: 0.6693 (m-80) cc_final: 0.6398 (m-80) REVERT: B 505 ARG cc_start: 0.6827 (ptt-90) cc_final: 0.6188 (tpp80) REVERT: B 590 GLN cc_start: 0.6543 (OUTLIER) cc_final: 0.6176 (pm20) REVERT: B 605 TYR cc_start: 0.7999 (t80) cc_final: 0.7579 (t80) REVERT: B 621 GLU cc_start: 0.6426 (tt0) cc_final: 0.6019 (tt0) REVERT: B 1700 TRP cc_start: 0.7645 (OUTLIER) cc_final: 0.5957 (m-10) REVERT: B 1738 MET cc_start: 0.6953 (ttt) cc_final: 0.6548 (ttt) REVERT: B 1827 LYS cc_start: 0.7835 (tppt) cc_final: 0.7367 (mmtm) REVERT: B 1850 LYS cc_start: 0.7820 (mtpp) cc_final: 0.7121 (mttp) REVERT: B 1868 MET cc_start: 0.7524 (mtt) cc_final: 0.7182 (mtt) REVERT: B 1881 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7837 (ptt) REVERT: B 1883 MET cc_start: 0.8781 (mmm) cc_final: 0.8539 (tpp) outliers start: 43 outliers final: 31 residues processed: 146 average time/residue: 0.2197 time to fit residues: 48.6265 Evaluate side-chains 146 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 111 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1657 THR Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1798 VAL Chi-restraints excluded: chain B residue 1843 THR Chi-restraints excluded: chain B residue 1846 MET Chi-restraints excluded: chain B residue 1856 LEU Chi-restraints excluded: chain B residue 1881 MET Chi-restraints excluded: chain B residue 1920 TRP Chi-restraints excluded: chain B residue 1982 ASN Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2026 LEU Chi-restraints excluded: chain B residue 2062 SER Chi-restraints excluded: chain B residue 2165 ASN Chi-restraints excluded: chain B residue 2173 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 116 optimal weight: 0.0050 chunk 122 optimal weight: 2.9990 chunk 80 optimal weight: 0.0770 overall best weight: 1.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11436 Z= 0.236 Angle : 0.653 9.777 15490 Z= 0.333 Chirality : 0.046 0.165 1627 Planarity : 0.005 0.091 1999 Dihedral : 5.761 31.962 1508 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.53 % Favored : 85.47 % Rotamer: Outliers : 3.59 % Allowed : 22.94 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.20), residues: 1370 helix: -2.61 (0.60), residues: 58 sheet: -1.89 (0.27), residues: 376 loop : -3.41 (0.17), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 457 HIS 0.004 0.001 HIS B 228 PHE 0.023 0.001 PHE B 552 TYR 0.014 0.002 TYR B1903 ARG 0.003 0.000 ARG B 648 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 114 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 352 LEU cc_start: 0.1572 (OUTLIER) cc_final: 0.1237 (tp) REVERT: B 363 TYR cc_start: 0.3948 (OUTLIER) cc_final: 0.2925 (t80) REVERT: B 424 PHE cc_start: 0.6655 (m-80) cc_final: 0.6385 (m-80) REVERT: B 505 ARG cc_start: 0.6971 (ptt-90) cc_final: 0.6275 (mmp80) REVERT: B 590 GLN cc_start: 0.6519 (OUTLIER) cc_final: 0.6159 (pm20) REVERT: B 605 TYR cc_start: 0.8028 (t80) cc_final: 0.7587 (t80) REVERT: B 621 GLU cc_start: 0.6435 (tt0) cc_final: 0.6020 (tt0) REVERT: B 1700 TRP cc_start: 0.7561 (OUTLIER) cc_final: 0.5899 (m-10) REVERT: B 1738 MET cc_start: 0.6971 (ttt) cc_final: 0.6488 (ttt) REVERT: B 1827 LYS cc_start: 0.7740 (tppt) cc_final: 0.7224 (mmtm) REVERT: B 1850 LYS cc_start: 0.7800 (mtpp) cc_final: 0.7093 (mttp) REVERT: B 1868 MET cc_start: 0.7538 (mtt) cc_final: 0.7158 (mtt) REVERT: B 1883 MET cc_start: 0.8784 (mmm) cc_final: 0.8532 (tpp) outliers start: 44 outliers final: 36 residues processed: 150 average time/residue: 0.2217 time to fit residues: 50.2251 Evaluate side-chains 149 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 109 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 1550 ASN Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1657 THR Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1798 VAL Chi-restraints excluded: chain B residue 1843 THR Chi-restraints excluded: chain B residue 1856 LEU Chi-restraints excluded: chain B residue 1920 TRP Chi-restraints excluded: chain B residue 1982 ASN Chi-restraints excluded: chain B residue 2001 GLU Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2026 LEU Chi-restraints excluded: chain B residue 2062 SER Chi-restraints excluded: chain B residue 2156 THR Chi-restraints excluded: chain B residue 2165 ASN Chi-restraints excluded: chain B residue 2173 ILE Chi-restraints excluded: chain B residue 2186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11436 Z= 0.233 Angle : 0.652 9.850 15490 Z= 0.332 Chirality : 0.046 0.151 1627 Planarity : 0.005 0.091 1999 Dihedral : 5.770 32.046 1508 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.40 % Favored : 84.60 % Rotamer: Outliers : 3.35 % Allowed : 23.67 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.20), residues: 1370 helix: -2.57 (0.60), residues: 58 sheet: -1.82 (0.27), residues: 376 loop : -3.40 (0.17), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1563 HIS 0.004 0.001 HIS B 228 PHE 0.024 0.001 PHE B 552 TYR 0.014 0.001 TYR B1903 ARG 0.003 0.000 ARG B 648 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2740 Ramachandran restraints generated. 1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 111 time to evaluate : 1.321 Fit side-chains revert: symmetry clash REVERT: B 352 LEU cc_start: 0.1593 (OUTLIER) cc_final: 0.1350 (tp) REVERT: B 363 TYR cc_start: 0.3993 (OUTLIER) cc_final: 0.2965 (t80) REVERT: B 505 ARG cc_start: 0.6947 (ptt-90) cc_final: 0.5898 (mtt90) REVERT: B 590 GLN cc_start: 0.6516 (OUTLIER) cc_final: 0.6127 (pm20) REVERT: B 605 TYR cc_start: 0.8065 (t80) cc_final: 0.7626 (t80) REVERT: B 621 GLU cc_start: 0.6447 (tt0) cc_final: 0.6036 (tt0) REVERT: B 1700 TRP cc_start: 0.7570 (OUTLIER) cc_final: 0.5872 (m-10) REVERT: B 1738 MET cc_start: 0.7077 (ttt) cc_final: 0.6554 (ttt) REVERT: B 1827 LYS cc_start: 0.7774 (tppt) cc_final: 0.7282 (mmtm) REVERT: B 1850 LYS cc_start: 0.7804 (mtpp) cc_final: 0.7096 (mttp) REVERT: B 1868 MET cc_start: 0.7562 (mtt) cc_final: 0.7182 (mtt) REVERT: B 1881 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7842 (ptt) REVERT: B 1883 MET cc_start: 0.8748 (mmm) cc_final: 0.8490 (tpp) outliers start: 41 outliers final: 34 residues processed: 144 average time/residue: 0.2136 time to fit residues: 47.0482 Evaluate side-chains 148 residues out of total 1225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 109 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 363 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 590 GLN Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 1550 ASN Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1657 THR Chi-restraints excluded: chain B residue 1700 TRP Chi-restraints excluded: chain B residue 1744 LEU Chi-restraints excluded: chain B residue 1798 VAL Chi-restraints excluded: chain B residue 1843 THR Chi-restraints excluded: chain B residue 1856 LEU Chi-restraints excluded: chain B residue 1881 MET Chi-restraints excluded: chain B residue 1920 TRP Chi-restraints excluded: chain B residue 1982 ASN Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2026 LEU Chi-restraints excluded: chain B residue 2062 SER Chi-restraints excluded: chain B residue 2165 ASN Chi-restraints excluded: chain B residue 2173 ILE Chi-restraints excluded: chain B residue 2186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 100 optimal weight: 0.0050 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.141818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.122144 restraints weight = 25785.887| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 3.61 r_work: 0.3784 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11436 Z= 0.173 Angle : 0.614 9.805 15490 Z= 0.310 Chirality : 0.045 0.147 1627 Planarity : 0.005 0.088 1999 Dihedral : 5.420 28.078 1508 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.99 % Favored : 87.01 % Rotamer: Outliers : 3.27 % Allowed : 23.92 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.20), residues: 1370 helix: -2.77 (0.59), residues: 52 sheet: -1.75 (0.27), residues: 376 loop : -3.27 (0.17), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1934 HIS 0.003 0.001 HIS B 228 PHE 0.023 0.001 PHE B 552 TYR 0.036 0.001 TYR B 418 ARG 0.003 0.000 ARG B 648 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2470.32 seconds wall clock time: 45 minutes 18.43 seconds (2718.43 seconds total)