Starting phenix.real_space_refine on Thu Mar 14 15:55:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hv8_0287/03_2024/6hv8_0287.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hv8_0287/03_2024/6hv8_0287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hv8_0287/03_2024/6hv8_0287.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hv8_0287/03_2024/6hv8_0287.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hv8_0287/03_2024/6hv8_0287.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hv8_0287/03_2024/6hv8_0287.pdb" } resolution = 4.4 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= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 47 5.16 5 C 5904 2.51 5 N 1546 2.21 5 O 1707 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 228": "NH1" <-> "NH2" Residue "B ARG 378": "NH1" <-> "NH2" Residue "B ARG 552": "NH1" <-> "NH2" Residue "B PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1436": "NH1" <-> "NH2" Residue "A PHE 1502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1572": "NH1" <-> "NH2" Residue "A ARG 1605": "NH1" <-> "NH2" Residue "A ARG 1664": "NH1" <-> "NH2" Residue "A ARG 1678": "NH1" <-> "NH2" Residue "A ARG 1833": "NH1" <-> "NH2" Residue "A PHE 1915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2132": "NH1" <-> "NH2" Residue "A ARG 2151": "NH1" <-> "NH2" Residue "A ARG 2163": "NH1" <-> "NH2" Residue "A ARG 2166": "NH1" <-> "NH2" Residue "A ARG 2172": "NH1" <-> "NH2" Residue "A ARG 2191": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9206 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3256 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 385} Chain breaks: 7 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 5950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 5950 Unusual residues: {' ZN': 2} Inner-chain residues flagged as termini: ['pdbres="THR A2221 "'] Classifications: {'peptide': 774, 'undetermined': 2} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 92} Link IDs: {'CIS': 4, 'PTRANS': 28, 'TRANS': 741, None: 2} Not linked: pdbres="THR A2221 " pdbres=" ZN A2301 " Not linked: pdbres=" ZN A2301 " pdbres=" ZN A2302 " Chain breaks: 9 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 379 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 330 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 8, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 224 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8329 SG CYS A2108 47.570 64.393 68.209 1.00113.75 S ATOM 8356 SG CYS A2111 49.383 63.715 69.708 1.00115.28 S ATOM 8465 SG CYS A2130 47.298 62.494 71.544 1.00102.72 S ATOM 8489 SG CYS A2133 47.478 66.426 71.323 1.00106.59 S ATOM 8752 SG CYS A2164 45.718 16.530 52.451 1.00196.52 S ATOM 8775 SG CYS A2167 48.593 16.597 50.823 1.00212.37 S ATOM 8876 SG CYS A2179 47.763 15.465 49.902 1.00190.38 S ATOM 8889 SG CYS A2181 48.054 13.753 50.603 1.00197.38 S Time building chain proxies: 5.13, per 1000 atoms: 0.56 Number of scatterers: 9206 At special positions: 0 Unit cell: (90.47, 112.27, 117.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 47 16.00 O 1707 8.00 N 1546 7.00 C 5904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.48 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" SG CYS A2108 " pdb="ZN ZN A2301 " - pdb=" SG CYS A2111 " pdb="ZN ZN A2301 " - pdb=" SG CYS A2133 " pdb="ZN ZN A2301 " - pdb=" SG CYS A2130 " pdb=" ZN A2302 " pdb="ZN ZN A2302 " - pdb=" SG CYS A2181 " pdb="ZN ZN A2302 " - pdb=" SG CYS A2164 " pdb="ZN ZN A2302 " - pdb=" SG CYS A2167 " pdb="ZN ZN A2302 " - pdb=" SG CYS A2179 " Number of angles added : 12 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2280 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 33.9% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'B' and resid 210 through 232 removed outlier: 3.573A pdb=" N LYS B 214 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE B 218 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 276 removed outlier: 3.658A pdb=" N LEU B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 358 Processing helix chain 'B' and resid 384 through 394 removed outlier: 4.201A pdb=" N HIS B 388 " --> pdb=" O LYS B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 427 removed outlier: 4.116A pdb=" N ASP B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP B 427 " --> pdb=" O LYS B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 471 Processing helix chain 'B' and resid 509 through 512 Processing helix chain 'B' and resid 513 through 520 Processing helix chain 'B' and resid 546 through 551 removed outlier: 3.920A pdb=" N LYS B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 610 Processing helix chain 'B' and resid 626 through 631 removed outlier: 3.931A pdb=" N LEU B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1369 Processing helix chain 'A' and resid 1532 through 1546 removed outlier: 4.049A pdb=" N LYS A1538 " --> pdb=" O GLN A1534 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY A1541 " --> pdb=" O GLU A1537 " (cutoff:3.500A) Processing helix chain 'A' and resid 1567 through 1584 removed outlier: 3.896A pdb=" N LEU A1573 " --> pdb=" O LEU A1569 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A1580 " --> pdb=" O GLU A1576 " (cutoff:3.500A) Processing helix chain 'A' and resid 1597 through 1603 removed outlier: 4.186A pdb=" N LEU A1601 " --> pdb=" O ILE A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1631 removed outlier: 4.121A pdb=" N THR A1630 " --> pdb=" O ASN A1626 " (cutoff:3.500A) Processing helix chain 'A' and resid 1631 through 1636 Processing helix chain 'A' and resid 1636 through 1641 removed outlier: 3.778A pdb=" N LEU A1640 " --> pdb=" O VAL A1636 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A1641 " --> pdb=" O ASN A1637 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1636 through 1641' Processing helix chain 'A' and resid 1641 through 1654 Processing helix chain 'A' and resid 1668 through 1678 removed outlier: 3.570A pdb=" N ILE A1672 " --> pdb=" O MET A1668 " (cutoff:3.500A) Processing helix chain 'A' and resid 1738 through 1744 removed outlier: 3.558A pdb=" N ASN A1742 " --> pdb=" O ASN A1738 " (cutoff:3.500A) Processing helix chain 'A' and resid 1787 through 1800 removed outlier: 3.702A pdb=" N ASP A1800 " --> pdb=" O LYS A1796 " (cutoff:3.500A) Processing helix chain 'A' and resid 1807 through 1814 removed outlier: 4.212A pdb=" N ASN A1814 " --> pdb=" O ASP A1810 " (cutoff:3.500A) Processing helix chain 'A' and resid 1815 through 1820 Processing helix chain 'A' and resid 1831 through 1852 removed outlier: 3.849A pdb=" N HIS A1835 " --> pdb=" O LEU A1831 " (cutoff:3.500A) Processing helix chain 'A' and resid 1881 through 1892 removed outlier: 3.500A pdb=" N MET A1885 " --> pdb=" O TYR A1881 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A1890 " --> pdb=" O MET A1886 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A1891 " --> pdb=" O LYS A1887 " (cutoff:3.500A) Processing helix chain 'A' and resid 1938 through 1943 Processing helix chain 'A' and resid 1949 through 1956 removed outlier: 3.816A pdb=" N PHE A1953 " --> pdb=" O TYR A1949 " (cutoff:3.500A) Processing helix chain 'A' and resid 1957 through 1971 removed outlier: 3.644A pdb=" N TYR A1971 " --> pdb=" O THR A1967 " (cutoff:3.500A) Processing helix chain 'A' and resid 1998 through 2003 Processing helix chain 'A' and resid 2005 through 2019 Proline residue: A2011 - end of helix removed outlier: 3.575A pdb=" N LYS A2014 " --> pdb=" O LYS A2010 " (cutoff:3.500A) Processing helix chain 'A' and resid 2044 through 2058 Proline residue: A2050 - end of helix Processing helix chain 'A' and resid 2067 through 2072 Processing helix chain 'A' and resid 2140 through 2158 Processing helix chain 'A' and resid 2190 through 2208 removed outlier: 4.325A pdb=" N ILE A2194 " --> pdb=" O PRO A2190 " (cutoff:3.500A) Processing helix chain 'A' and resid 2210 through 2221 removed outlier: 3.536A pdb=" N THR A2221 " --> pdb=" O ILE A2217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 171 through 173 removed outlier: 4.507A pdb=" N ARG B 531 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE B 539 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR B 534 " --> pdb=" O GLN B 537 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU B 538 " --> pdb=" O THR B 638 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL B 640 " --> pdb=" O GLU B 538 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL B 540 " --> pdb=" O VAL B 640 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N CYS B 642 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE B 542 " --> pdb=" O CYS B 642 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 181 through 184 removed outlier: 4.063A pdb=" N SER B 182 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 282 through 287 Processing sheet with id=AA4, first strand: chain 'B' and resid 296 through 300 removed outlier: 4.302A pdb=" N TRP B 296 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP B 300 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY B 303 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 339 " --> pdb=" O GLU B 306 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 480 through 483 removed outlier: 3.684A pdb=" N PHE B 399 " --> pdb=" O TYR B 675 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR B 675 " --> pdb=" O PHE B 399 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 649 through 651 Processing sheet with id=AA7, first strand: chain 'A' and resid 1321 through 1327 removed outlier: 6.879A pdb=" N PHE A1339 " --> pdb=" O GLU A1323 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU A1325 " --> pdb=" O GLU A1337 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLU A1337 " --> pdb=" O LEU A1325 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1501 through 1502 removed outlier: 5.641A pdb=" N GLY A1485 " --> pdb=" O LEU A1591 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2102 through 2106 removed outlier: 7.028A pdb=" N ILE A2117 " --> pdb=" O PRO A2104 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2162 through 2163 268 hydrogen bonds defined for protein. 771 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: 2.46 Time building geometry restraints manager: 3.78 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: 2898 1.34 - 1.47: 2185 1.47 - 1.59: 4223 1.59 - 1.72: 0 1.72 - 1.84: 73 Bond restraints: 9379 Sorted by residual: bond pdb=" C GLN A1628 " pdb=" N PRO A1629 " ideal model delta sigma weight residual 1.336 1.369 -0.033 9.80e-03 1.04e+04 1.15e+01 bond pdb=" N ILE A1712 " pdb=" CA ILE A1712 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.99e+00 bond pdb=" N MET A1713 " pdb=" CA MET A1713 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.28e-02 6.10e+03 8.53e+00 bond pdb=" N ASN A1714 " pdb=" CA ASN A1714 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.31e+00 bond pdb=" N GLU A1717 " pdb=" CA GLU A1717 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.25e-02 6.40e+03 6.62e+00 ... (remaining 9374 not shown) Histogram of bond angle deviations from ideal: 96.70 - 104.71: 205 104.71 - 112.72: 4876 112.72 - 120.73: 4418 120.73 - 128.74: 3122 128.74 - 136.75: 97 Bond angle restraints: 12718 Sorted by residual: angle pdb=" N PRO A2030 " pdb=" CA PRO A2030 " pdb=" CB PRO A2030 " ideal model delta sigma weight residual 103.23 111.22 -7.99 1.07e+00 8.73e-01 5.58e+01 angle pdb=" N VAL A2047 " pdb=" CA VAL A2047 " pdb=" C VAL A2047 " ideal model delta sigma weight residual 113.39 102.78 10.61 1.47e+00 4.63e-01 5.21e+01 angle pdb=" C TRP A1911 " pdb=" N MET A1912 " pdb=" CA MET A1912 " ideal model delta sigma weight residual 122.08 134.52 -12.44 1.84e+00 2.95e-01 4.57e+01 angle pdb=" N ASN A1657 " pdb=" CA ASN A1657 " pdb=" C ASN A1657 " ideal model delta sigma weight residual 110.80 125.14 -14.34 2.13e+00 2.20e-01 4.53e+01 angle pdb=" C SER A1896 " pdb=" N TYR A1897 " pdb=" CA TYR A1897 " ideal model delta sigma weight residual 121.70 133.40 -11.70 1.80e+00 3.09e-01 4.23e+01 ... (remaining 12713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.77: 5116 12.77 - 25.54: 436 25.54 - 38.32: 100 38.32 - 51.09: 22 51.09 - 63.86: 2 Dihedral angle restraints: 5676 sinusoidal: 2194 harmonic: 3482 Sorted by residual: dihedral pdb=" C ARG B 669 " pdb=" N ARG B 669 " pdb=" CA ARG B 669 " pdb=" CB ARG B 669 " ideal model delta harmonic sigma weight residual -122.60 -137.36 14.76 0 2.50e+00 1.60e-01 3.48e+01 dihedral pdb=" N ARG B 669 " pdb=" C ARG B 669 " pdb=" CA ARG B 669 " pdb=" CB ARG B 669 " ideal model delta harmonic sigma weight residual 122.80 136.65 -13.85 0 2.50e+00 1.60e-01 3.07e+01 dihedral pdb=" C ASN A1714 " pdb=" N ASN A1714 " pdb=" CA ASN A1714 " pdb=" CB ASN A1714 " ideal model delta harmonic sigma weight residual -122.60 -132.83 10.23 0 2.50e+00 1.60e-01 1.67e+01 ... (remaining 5673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1301 0.111 - 0.222: 167 0.222 - 0.332: 15 0.332 - 0.443: 2 0.443 - 0.554: 1 Chirality restraints: 1486 Sorted by residual: chirality pdb=" CA ARG B 669 " pdb=" N ARG B 669 " pdb=" C ARG B 669 " pdb=" CB ARG B 669 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.68e+00 chirality pdb=" CB ILE A1923 " pdb=" CA ILE A1923 " pdb=" CG1 ILE A1923 " pdb=" CG2 ILE A1923 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA ASN A1657 " pdb=" N ASN A1657 " pdb=" C ASN A1657 " pdb=" CB ASN A1657 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 1483 not shown) Planarity restraints: 1606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 300 " 0.053 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO B 301 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 301 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 301 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1689 " -0.018 2.00e-02 2.50e+03 1.91e-02 9.11e+00 pdb=" CG TRP A1689 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A1689 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A1689 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1689 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A1689 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1689 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1689 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1689 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A1689 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 458 " 0.019 2.00e-02 2.50e+03 2.09e-02 7.67e+00 pdb=" CG PHE B 458 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE B 458 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE B 458 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 458 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 458 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 458 " -0.003 2.00e-02 2.50e+03 ... (remaining 1603 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.16: 1 2.16 - 2.84: 2978 2.84 - 3.53: 12425 3.53 - 4.21: 19684 4.21 - 4.90: 31638 Nonbonded interactions: 66726 Sorted by model distance: nonbonded pdb=" N CYS A2167 " pdb="ZN ZN A2302 " model vdw 1.472 2.310 nonbonded pdb=" O VAL A1836 " pdb=" OG1 THR A1840 " model vdw 2.228 2.440 nonbonded pdb=" OH TYR A1317 " pdb=" O SER A1320 " model vdw 2.243 2.440 nonbonded pdb=" OE1 GLN A1435 " pdb=" OH TYR A1670 " model vdw 2.274 2.440 nonbonded pdb=" OH TYR B 672 " pdb=" OE1 GLU B 685 " model vdw 2.277 2.440 ... (remaining 66721 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 group one per residue 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: 0.280 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: 1.880 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.140 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 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 : 0.009 0.106 9379 Z= 0.588 Angle : 1.616 16.763 12718 Z= 0.887 Chirality : 0.077 0.554 1486 Planarity : 0.008 0.080 1606 Dihedral : 10.198 63.859 3396 Min Nonbonded Distance : 1.472 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.61 % Allowed : 22.13 % Favored : 77.26 % Rotamer: Outliers : 1.31 % Allowed : 5.63 % Favored : 93.07 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.36 % 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: -4.84 (0.21), residues: 1148 helix: -2.23 (0.23), residues: 321 sheet: -3.81 (0.45), residues: 88 loop : -3.85 (0.20), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.005 TRP A1689 HIS 0.017 0.004 HIS A2168 PHE 0.047 0.005 PHE B 458 TYR 0.040 0.004 TYR A1860 ARG 0.008 0.001 ARG B 543 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 329 time to evaluate : 1.171 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: B 174 ASN cc_start: 0.7106 (OUTLIER) cc_final: 0.6293 (t0) REVERT: B 183 TYR cc_start: 0.5785 (t80) cc_final: 0.5416 (t80) REVERT: B 219 LEU cc_start: 0.9315 (mt) cc_final: 0.9089 (mt) REVERT: B 352 ARG cc_start: 0.6809 (ttp-170) cc_final: 0.6098 (ttp-170) REVERT: B 407 PHE cc_start: 0.8205 (m-80) cc_final: 0.7928 (m-80) REVERT: B 419 LYS cc_start: 0.9053 (mttt) cc_final: 0.8710 (mmmm) REVERT: B 455 SER cc_start: 0.9417 (p) cc_final: 0.8796 (t) REVERT: B 510 SER cc_start: 0.8086 (p) cc_final: 0.7820 (t) REVERT: B 627 ASP cc_start: 0.8587 (t0) cc_final: 0.8231 (t0) REVERT: B 641 LEU cc_start: 0.8943 (mt) cc_final: 0.8119 (mt) REVERT: A 1376 ILE cc_start: 0.8856 (mt) cc_final: 0.8415 (tp) REVERT: A 1573 LEU cc_start: 0.9566 (tt) cc_final: 0.9112 (tp) REVERT: A 1581 LYS cc_start: 0.8938 (ttmt) cc_final: 0.8720 (tttt) REVERT: A 1586 LEU cc_start: 0.8837 (mt) cc_final: 0.8498 (mm) REVERT: A 1592 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8310 (tt) REVERT: A 1800 ASP cc_start: 0.8799 (p0) cc_final: 0.8573 (p0) REVERT: A 1906 TRP cc_start: 0.6221 (m100) cc_final: 0.5850 (m100) REVERT: A 1929 GLU cc_start: 0.9337 (tt0) cc_final: 0.8850 (mp0) REVERT: A 2162 LEU cc_start: 0.8384 (mt) cc_final: 0.7574 (mt) REVERT: A 2196 GLN cc_start: 0.9118 (mt0) cc_final: 0.8903 (tt0) REVERT: A 2197 LYS cc_start: 0.9068 (mttt) cc_final: 0.8647 (mmtt) outliers start: 13 outliers final: 2 residues processed: 336 average time/residue: 0.2178 time to fit residues: 99.4395 Evaluate side-chains 227 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 223 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 30.0000 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 35 optimal weight: 0.0870 chunk 56 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 461 ASN B 505 GLN B 609 GLN A1326 GLN A1364 GLN A1369 GLN A1373 ASN A1413 ASN A1575 GLN ** A1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1609 GLN A1742 ASN A1814 ASN A1837 HIS A2049 ASN ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9379 Z= 0.248 Angle : 0.834 9.697 12718 Z= 0.427 Chirality : 0.049 0.246 1486 Planarity : 0.006 0.053 1606 Dihedral : 5.703 33.651 1240 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 15.77 % Favored : 84.15 % Rotamer: Outliers : 0.10 % Allowed : 3.82 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.03 (0.23), residues: 1148 helix: -1.06 (0.26), residues: 340 sheet: -3.10 (0.48), residues: 102 loop : -3.68 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A1689 HIS 0.007 0.001 HIS A2168 PHE 0.026 0.002 PHE A1915 TYR 0.021 0.002 TYR A2207 ARG 0.004 0.001 ARG B 671 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 261 time to evaluate : 1.034 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: B 214 LYS cc_start: 0.9264 (pttm) cc_final: 0.9012 (pttp) REVERT: B 215 VAL cc_start: 0.9452 (m) cc_final: 0.8586 (m) REVERT: B 219 LEU cc_start: 0.9315 (mt) cc_final: 0.9043 (mt) REVERT: B 386 ARG cc_start: 0.9002 (mtm-85) cc_final: 0.8686 (mmm-85) REVERT: B 407 PHE cc_start: 0.8228 (m-80) cc_final: 0.7773 (m-80) REVERT: B 419 LYS cc_start: 0.9024 (mttt) cc_final: 0.8687 (mmmm) REVERT: B 429 PRO cc_start: 0.8326 (Cg_exo) cc_final: 0.8050 (Cg_endo) REVERT: B 455 SER cc_start: 0.9363 (p) cc_final: 0.8803 (t) REVERT: B 510 SER cc_start: 0.8194 (p) cc_final: 0.7943 (t) REVERT: B 627 ASP cc_start: 0.8169 (t0) cc_final: 0.7945 (t0) REVERT: B 639 MET cc_start: 0.7892 (ttp) cc_final: 0.7561 (ttt) REVERT: B 641 LEU cc_start: 0.8981 (mt) cc_final: 0.8055 (mt) REVERT: B 673 MET cc_start: 0.7905 (tpt) cc_final: 0.7518 (tpp) REVERT: A 1484 ILE cc_start: 0.7503 (tp) cc_final: 0.7291 (tp) REVERT: A 1573 LEU cc_start: 0.9633 (tt) cc_final: 0.9233 (tp) REVERT: A 1579 LYS cc_start: 0.9278 (ttpt) cc_final: 0.9033 (tptp) REVERT: A 1613 VAL cc_start: 0.8668 (t) cc_final: 0.7952 (t) REVERT: A 1679 LYS cc_start: 0.8746 (mmtt) cc_final: 0.8410 (mmmt) REVERT: A 1841 LYS cc_start: 0.7731 (ttpt) cc_final: 0.7293 (ttpt) REVERT: A 1854 LEU cc_start: 0.8798 (mt) cc_final: 0.8589 (mp) REVERT: A 1879 TYR cc_start: 0.8468 (t80) cc_final: 0.8001 (t80) REVERT: A 1929 GLU cc_start: 0.9277 (tt0) cc_final: 0.8830 (mp0) REVERT: A 2197 LYS cc_start: 0.8840 (mttt) cc_final: 0.8628 (mmtt) outliers start: 1 outliers final: 0 residues processed: 262 average time/residue: 0.2358 time to fit residues: 82.8536 Evaluate side-chains 208 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 89 optimal weight: 0.3980 chunk 72 optimal weight: 0.0030 chunk 29 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 overall best weight: 1.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 HIS A1364 GLN A1575 GLN ** A1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1609 GLN ** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2139 GLN ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9379 Z= 0.212 Angle : 0.753 9.731 12718 Z= 0.384 Chirality : 0.047 0.201 1486 Planarity : 0.005 0.052 1606 Dihedral : 5.665 32.711 1240 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.11 % Favored : 83.89 % Rotamer: Outliers : 0.10 % Allowed : 4.72 % Favored : 95.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.62 (0.23), residues: 1148 helix: -0.36 (0.27), residues: 342 sheet: -2.67 (0.52), residues: 92 loop : -3.68 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1689 HIS 0.005 0.001 HIS A2168 PHE 0.020 0.002 PHE A1828 TYR 0.014 0.002 TYR A2207 ARG 0.003 0.001 ARG A1664 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 1.134 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: B 219 LEU cc_start: 0.9319 (mt) cc_final: 0.9017 (mt) REVERT: B 407 PHE cc_start: 0.8093 (m-80) cc_final: 0.7773 (m-80) REVERT: B 419 LYS cc_start: 0.9056 (mttt) cc_final: 0.8734 (mmmm) REVERT: B 455 SER cc_start: 0.9341 (p) cc_final: 0.8780 (t) REVERT: B 641 LEU cc_start: 0.8965 (mt) cc_final: 0.8736 (mt) REVERT: A 1353 ILE cc_start: 0.7820 (mm) cc_final: 0.7404 (tp) REVERT: A 1470 MET cc_start: 0.7161 (mtt) cc_final: 0.6864 (mtt) REVERT: A 1484 ILE cc_start: 0.7663 (tp) cc_final: 0.7240 (tp) REVERT: A 1573 LEU cc_start: 0.9650 (tt) cc_final: 0.9370 (tp) REVERT: A 1679 LYS cc_start: 0.8704 (mmtt) cc_final: 0.8371 (mmmt) REVERT: A 1879 TYR cc_start: 0.8581 (t80) cc_final: 0.8097 (t80) REVERT: A 1910 ILE cc_start: 0.7812 (mt) cc_final: 0.7590 (mt) REVERT: A 1929 GLU cc_start: 0.9325 (tt0) cc_final: 0.8850 (mp0) REVERT: A 2118 ASP cc_start: 0.7356 (t0) cc_final: 0.7020 (t0) REVERT: A 2173 ASP cc_start: 0.8383 (p0) cc_final: 0.8153 (p0) REVERT: A 2197 LYS cc_start: 0.8986 (mttt) cc_final: 0.8713 (mmtt) outliers start: 1 outliers final: 0 residues processed: 255 average time/residue: 0.2194 time to fit residues: 75.4274 Evaluate side-chains 207 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 0.0070 chunk 11 optimal weight: 8.9990 chunk 51 optimal weight: 0.0270 chunk 72 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 HIS B 648 GLN A1326 GLN A1575 GLN ** A1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1609 GLN A1662 ASN ** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9379 Z= 0.169 Angle : 0.708 9.697 12718 Z= 0.357 Chirality : 0.046 0.216 1486 Planarity : 0.004 0.040 1606 Dihedral : 5.502 33.312 1240 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.55 % Favored : 85.45 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.23 (0.24), residues: 1148 helix: 0.09 (0.28), residues: 345 sheet: -2.16 (0.58), residues: 83 loop : -3.55 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 624 HIS 0.003 0.001 HIS A1352 PHE 0.018 0.002 PHE A1915 TYR 0.016 0.001 TYR A1905 ARG 0.007 0.001 ARG A1664 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.113 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: B 170 PHE cc_start: 0.8082 (t80) cc_final: 0.7766 (p90) REVERT: B 219 LEU cc_start: 0.9233 (mt) cc_final: 0.8975 (mt) REVERT: B 228 ARG cc_start: 0.8588 (mtp180) cc_final: 0.8284 (ptp-110) REVERT: B 289 ASN cc_start: 0.8921 (m110) cc_final: 0.7452 (t0) REVERT: B 410 ASP cc_start: 0.8662 (m-30) cc_final: 0.7395 (t0) REVERT: B 419 LYS cc_start: 0.8958 (mttt) cc_final: 0.8675 (mmmm) REVERT: B 422 GLN cc_start: 0.8937 (tt0) cc_final: 0.8425 (mm-40) REVERT: B 455 SER cc_start: 0.9298 (p) cc_final: 0.8753 (t) REVERT: A 1353 ILE cc_start: 0.7655 (mm) cc_final: 0.7228 (tp) REVERT: A 1573 LEU cc_start: 0.9810 (tt) cc_final: 0.9443 (tp) REVERT: A 1613 VAL cc_start: 0.8704 (t) cc_final: 0.8479 (t) REVERT: A 1879 TYR cc_start: 0.8472 (t80) cc_final: 0.8108 (t80) REVERT: A 1910 ILE cc_start: 0.7717 (mt) cc_final: 0.7453 (mt) REVERT: A 1929 GLU cc_start: 0.9138 (tt0) cc_final: 0.8730 (mp0) REVERT: A 2118 ASP cc_start: 0.7432 (t0) cc_final: 0.6987 (t0) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.2410 time to fit residues: 80.8822 Evaluate side-chains 199 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 78 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN B 648 GLN ** A1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1662 ASN A1814 ASN ** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2139 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9379 Z= 0.223 Angle : 0.753 11.516 12718 Z= 0.376 Chirality : 0.047 0.191 1486 Planarity : 0.004 0.049 1606 Dihedral : 5.694 35.153 1240 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.77 % Favored : 84.23 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.36 % 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: -3.12 (0.24), residues: 1148 helix: 0.39 (0.29), residues: 344 sheet: -2.21 (0.56), residues: 90 loop : -3.59 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1906 HIS 0.006 0.001 HIS A2168 PHE 0.021 0.002 PHE A1718 TYR 0.017 0.002 TYR B 672 ARG 0.004 0.001 ARG B 352 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.104 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: B 215 VAL cc_start: 0.9180 (m) cc_final: 0.8356 (m) REVERT: B 217 MET cc_start: 0.8478 (ptt) cc_final: 0.8060 (ptt) REVERT: B 219 LEU cc_start: 0.9305 (mt) cc_final: 0.9028 (mt) REVERT: B 289 ASN cc_start: 0.8956 (m110) cc_final: 0.7543 (t0) REVERT: B 407 PHE cc_start: 0.8277 (m-80) cc_final: 0.7928 (m-80) REVERT: B 410 ASP cc_start: 0.8652 (m-30) cc_final: 0.7484 (t0) REVERT: B 419 LYS cc_start: 0.8962 (mttt) cc_final: 0.8710 (mmmm) REVERT: B 628 HIS cc_start: 0.8615 (t70) cc_final: 0.8415 (t70) REVERT: A 1353 ILE cc_start: 0.7756 (mm) cc_final: 0.7363 (tp) REVERT: A 1359 MET cc_start: -0.0763 (mmm) cc_final: -0.1216 (mmt) REVERT: A 1487 LEU cc_start: 0.8980 (tt) cc_final: 0.8712 (tt) REVERT: A 1573 LEU cc_start: 0.9816 (tt) cc_final: 0.9508 (tp) REVERT: A 1679 LYS cc_start: 0.8471 (mmpt) cc_final: 0.8047 (mmmt) REVERT: A 1915 PHE cc_start: 0.6640 (p90) cc_final: 0.6078 (p90) REVERT: A 1929 GLU cc_start: 0.9189 (tt0) cc_final: 0.8771 (mp0) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2299 time to fit residues: 75.7168 Evaluate side-chains 199 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 28 optimal weight: 0.0570 chunk 114 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 52 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN B 611 HIS B 648 GLN ** A1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9379 Z= 0.198 Angle : 0.733 10.206 12718 Z= 0.365 Chirality : 0.046 0.245 1486 Planarity : 0.004 0.042 1606 Dihedral : 5.633 36.255 1240 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.63 % Favored : 85.37 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.05 (0.24), residues: 1148 helix: 0.49 (0.29), residues: 346 sheet: -2.25 (0.56), residues: 96 loop : -3.57 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1798 HIS 0.005 0.001 HIS A2168 PHE 0.020 0.002 PHE B 170 TYR 0.014 0.001 TYR B 672 ARG 0.005 0.001 ARG B 352 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 0.992 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: B 217 MET cc_start: 0.8354 (ptt) cc_final: 0.7878 (ptt) REVERT: B 219 LEU cc_start: 0.9283 (mt) cc_final: 0.9030 (mt) REVERT: B 289 ASN cc_start: 0.8953 (m110) cc_final: 0.7561 (t0) REVERT: B 398 LYS cc_start: 0.8313 (pttp) cc_final: 0.7862 (ttmt) REVERT: B 402 LEU cc_start: 0.9086 (mm) cc_final: 0.8869 (mm) REVERT: B 410 ASP cc_start: 0.8662 (m-30) cc_final: 0.7442 (t0) REVERT: B 414 MET cc_start: 0.8878 (mpp) cc_final: 0.8632 (mpp) REVERT: B 419 LYS cc_start: 0.8891 (mttt) cc_final: 0.8649 (mmmm) REVERT: B 422 GLN cc_start: 0.8980 (tt0) cc_final: 0.8423 (mm-40) REVERT: B 608 ASP cc_start: 0.7977 (m-30) cc_final: 0.7520 (m-30) REVERT: A 1482 MET cc_start: 0.6653 (mmm) cc_final: 0.5672 (mmm) REVERT: A 1487 LEU cc_start: 0.8918 (tt) cc_final: 0.8694 (tt) REVERT: A 1573 LEU cc_start: 0.9810 (tt) cc_final: 0.9483 (tp) REVERT: A 1679 LYS cc_start: 0.8549 (mmpt) cc_final: 0.8077 (mmmt) REVERT: A 1841 LYS cc_start: 0.7749 (tmtt) cc_final: 0.7239 (tmtt) REVERT: A 1854 LEU cc_start: 0.8949 (mt) cc_final: 0.8720 (mp) REVERT: A 1876 GLU cc_start: 0.9225 (tt0) cc_final: 0.8969 (tt0) REVERT: A 1910 ILE cc_start: 0.7529 (mt) cc_final: 0.7263 (mt) REVERT: A 1929 GLU cc_start: 0.9128 (tt0) cc_final: 0.8726 (mp0) REVERT: A 2062 MET cc_start: 0.7061 (pmm) cc_final: 0.6421 (mpp) REVERT: A 2118 ASP cc_start: 0.7342 (t0) cc_final: 0.6952 (t0) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2175 time to fit residues: 72.1361 Evaluate side-chains 197 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 83 optimal weight: 0.2980 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 52 optimal weight: 0.0470 overall best weight: 1.8684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 HIS B 648 GLN ** A1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2060 HIS A2139 GLN A2145 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9379 Z= 0.204 Angle : 0.731 9.750 12718 Z= 0.367 Chirality : 0.047 0.233 1486 Planarity : 0.004 0.045 1606 Dihedral : 5.701 37.030 1240 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.24 % Favored : 84.76 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.36 % 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: -3.04 (0.24), residues: 1148 helix: 0.51 (0.28), residues: 355 sheet: -2.24 (0.56), residues: 98 loop : -3.62 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A1689 HIS 0.005 0.001 HIS A2168 PHE 0.022 0.002 PHE A1718 TYR 0.015 0.001 TYR A1879 ARG 0.005 0.001 ARG B 352 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.124 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: B 217 MET cc_start: 0.8336 (ptt) cc_final: 0.7901 (ptt) REVERT: B 219 LEU cc_start: 0.9351 (mt) cc_final: 0.8915 (mt) REVERT: B 223 TYR cc_start: 0.8651 (m-10) cc_final: 0.8055 (m-10) REVERT: B 226 ASN cc_start: 0.9149 (t0) cc_final: 0.8877 (t0) REVERT: B 230 MET cc_start: 0.9330 (mmp) cc_final: 0.8890 (mmm) REVERT: B 289 ASN cc_start: 0.8985 (m110) cc_final: 0.7644 (t0) REVERT: B 398 LYS cc_start: 0.8205 (pttp) cc_final: 0.7844 (ttmt) REVERT: B 407 PHE cc_start: 0.8316 (m-80) cc_final: 0.7972 (m-80) REVERT: B 410 ASP cc_start: 0.8615 (m-30) cc_final: 0.7551 (t0) REVERT: B 419 LYS cc_start: 0.8878 (mttt) cc_final: 0.8627 (mmmm) REVERT: B 422 GLN cc_start: 0.9012 (tt0) cc_final: 0.8426 (mm-40) REVERT: B 429 PRO cc_start: 0.8763 (Cg_endo) cc_final: 0.8562 (Cg_exo) REVERT: A 1470 MET cc_start: 0.6852 (mtt) cc_final: 0.6519 (mtt) REVERT: A 1482 MET cc_start: 0.6776 (mmm) cc_final: 0.5691 (mmm) REVERT: A 1487 LEU cc_start: 0.8929 (tt) cc_final: 0.8665 (tt) REVERT: A 1573 LEU cc_start: 0.9815 (tt) cc_final: 0.9482 (tp) REVERT: A 1578 THR cc_start: 0.8641 (p) cc_final: 0.8024 (p) REVERT: A 1876 GLU cc_start: 0.9228 (tt0) cc_final: 0.9007 (tt0) REVERT: A 1899 ASP cc_start: 0.7053 (t70) cc_final: 0.6791 (t0) REVERT: A 1910 ILE cc_start: 0.7737 (mt) cc_final: 0.7477 (mt) REVERT: A 1929 GLU cc_start: 0.9120 (tt0) cc_final: 0.8725 (mp0) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.2130 time to fit residues: 68.4953 Evaluate side-chains 205 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 77 optimal weight: 0.1980 chunk 56 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 HIS ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN B 628 HIS B 648 GLN ** A1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1662 ASN ** A1729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9379 Z= 0.258 Angle : 0.790 10.113 12718 Z= 0.397 Chirality : 0.048 0.256 1486 Planarity : 0.004 0.046 1606 Dihedral : 5.993 39.005 1240 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.29 % Favored : 83.71 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.36 % 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: -3.18 (0.24), residues: 1148 helix: 0.41 (0.28), residues: 362 sheet: -2.72 (0.53), residues: 99 loop : -3.70 (0.21), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A1689 HIS 0.009 0.002 HIS A2145 PHE 0.025 0.002 PHE A1718 TYR 0.014 0.002 TYR B 672 ARG 0.006 0.001 ARG B 352 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 1.143 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: B 217 MET cc_start: 0.8430 (ptt) cc_final: 0.8050 (ptt) REVERT: B 219 LEU cc_start: 0.9395 (mt) cc_final: 0.8972 (mt) REVERT: B 223 TYR cc_start: 0.8643 (m-10) cc_final: 0.7969 (m-10) REVERT: B 226 ASN cc_start: 0.9183 (t0) cc_final: 0.8922 (t0) REVERT: B 230 MET cc_start: 0.9380 (mmp) cc_final: 0.8898 (mmm) REVERT: B 398 LYS cc_start: 0.8249 (pttp) cc_final: 0.7889 (ttmt) REVERT: B 407 PHE cc_start: 0.8366 (m-80) cc_final: 0.7957 (m-80) REVERT: B 410 ASP cc_start: 0.8713 (m-30) cc_final: 0.7508 (t70) REVERT: B 414 MET cc_start: 0.8793 (mpp) cc_final: 0.8493 (mpp) REVERT: B 419 LYS cc_start: 0.8916 (mttt) cc_final: 0.8632 (mmmm) REVERT: B 422 GLN cc_start: 0.9046 (tt0) cc_final: 0.8434 (mm-40) REVERT: B 429 PRO cc_start: 0.8837 (Cg_endo) cc_final: 0.8599 (Cg_exo) REVERT: A 1337 GLU cc_start: 0.8795 (tp30) cc_final: 0.8378 (tp30) REVERT: A 1353 ILE cc_start: 0.7811 (mm) cc_final: 0.7594 (tp) REVERT: A 1364 GLN cc_start: 0.8377 (tp40) cc_final: 0.8115 (tp40) REVERT: A 1470 MET cc_start: 0.6930 (mtt) cc_final: 0.6578 (mtt) REVERT: A 1482 MET cc_start: 0.6782 (mmm) cc_final: 0.5796 (mmm) REVERT: A 1487 LEU cc_start: 0.8914 (tt) cc_final: 0.8676 (tt) REVERT: A 1578 THR cc_start: 0.8286 (p) cc_final: 0.7923 (p) REVERT: A 1841 LYS cc_start: 0.7874 (tmmt) cc_final: 0.7572 (tttt) REVERT: A 1876 GLU cc_start: 0.9328 (tt0) cc_final: 0.9064 (tt0) REVERT: A 1899 ASP cc_start: 0.7257 (t70) cc_final: 0.6914 (t0) REVERT: A 1910 ILE cc_start: 0.7643 (mt) cc_final: 0.7402 (mt) REVERT: A 1929 GLU cc_start: 0.9151 (tt0) cc_final: 0.8762 (mp0) REVERT: A 2118 ASP cc_start: 0.7374 (t0) cc_final: 0.6902 (t0) REVERT: A 2144 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6966 (tm-30) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.2240 time to fit residues: 72.1045 Evaluate side-chains 196 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9990 chunk 99 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 100 optimal weight: 40.0000 chunk 69 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 GLN ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1940 GLN A2139 GLN ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9379 Z= 0.279 Angle : 0.820 9.733 12718 Z= 0.414 Chirality : 0.049 0.251 1486 Planarity : 0.005 0.047 1606 Dihedral : 6.132 39.408 1240 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.33 % Favored : 82.67 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.36 % 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: -3.21 (0.24), residues: 1148 helix: 0.38 (0.28), residues: 357 sheet: -2.54 (0.56), residues: 89 loop : -3.71 (0.21), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1798 HIS 0.009 0.002 HIS A2145 PHE 0.030 0.002 PHE A1718 TYR 0.024 0.002 TYR B 534 ARG 0.007 0.001 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.141 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: B 212 GLU cc_start: 0.8890 (pm20) cc_final: 0.8598 (pm20) REVERT: B 217 MET cc_start: 0.8483 (ptt) cc_final: 0.8052 (ptt) REVERT: B 219 LEU cc_start: 0.9378 (mt) cc_final: 0.8926 (mt) REVERT: B 223 TYR cc_start: 0.8661 (m-10) cc_final: 0.8056 (m-10) REVERT: B 226 ASN cc_start: 0.9187 (t0) cc_final: 0.8934 (t0) REVERT: B 230 MET cc_start: 0.9393 (mmp) cc_final: 0.8918 (mmm) REVERT: B 289 ASN cc_start: 0.9040 (m110) cc_final: 0.7732 (t0) REVERT: B 398 LYS cc_start: 0.8203 (pttp) cc_final: 0.7864 (ttmt) REVERT: B 407 PHE cc_start: 0.8390 (m-80) cc_final: 0.8019 (m-80) REVERT: B 410 ASP cc_start: 0.8820 (m-30) cc_final: 0.8157 (m-30) REVERT: B 414 MET cc_start: 0.8819 (mpp) cc_final: 0.8546 (mpp) REVERT: B 419 LYS cc_start: 0.8918 (mttt) cc_final: 0.8671 (mmmm) REVERT: B 422 GLN cc_start: 0.9112 (tt0) cc_final: 0.8137 (mm-40) REVERT: B 429 PRO cc_start: 0.8781 (Cg_endo) cc_final: 0.8514 (Cg_exo) REVERT: A 1337 GLU cc_start: 0.9002 (tp30) cc_final: 0.8564 (tp30) REVERT: A 1353 ILE cc_start: 0.7931 (mm) cc_final: 0.7714 (tp) REVERT: A 1364 GLN cc_start: 0.8256 (tp40) cc_final: 0.7983 (tp40) REVERT: A 1470 MET cc_start: 0.6891 (mtt) cc_final: 0.6665 (mtt) REVERT: A 1614 LYS cc_start: 0.3883 (tmtt) cc_final: 0.3066 (tttt) REVERT: A 1841 LYS cc_start: 0.7879 (tmmt) cc_final: 0.7567 (tttt) REVERT: A 1876 GLU cc_start: 0.9342 (tt0) cc_final: 0.9076 (tt0) REVERT: A 1899 ASP cc_start: 0.7225 (t70) cc_final: 0.6876 (t0) REVERT: A 1910 ILE cc_start: 0.7796 (mt) cc_final: 0.7544 (mt) REVERT: A 1929 GLU cc_start: 0.9198 (tt0) cc_final: 0.8785 (mp0) REVERT: A 2144 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6589 (tm-30) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.2058 time to fit residues: 65.8677 Evaluate side-chains 195 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 chunk 77 optimal weight: 0.1980 chunk 117 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 99 optimal weight: 20.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN B 628 HIS B 648 GLN ** A1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2044 HIS ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9379 Z= 0.190 Angle : 0.781 11.098 12718 Z= 0.385 Chirality : 0.047 0.235 1486 Planarity : 0.004 0.043 1606 Dihedral : 5.797 38.030 1240 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.72 % Favored : 85.28 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.99 (0.24), residues: 1148 helix: 0.63 (0.29), residues: 351 sheet: -2.62 (0.65), residues: 69 loop : -3.54 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1689 HIS 0.006 0.001 HIS A2145 PHE 0.031 0.002 PHE A1718 TYR 0.014 0.001 TYR A1879 ARG 0.006 0.001 ARG A1311 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.124 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: B 217 MET cc_start: 0.8305 (ptt) cc_final: 0.7861 (ptt) REVERT: B 219 LEU cc_start: 0.9334 (mt) cc_final: 0.8835 (mt) REVERT: B 223 TYR cc_start: 0.8604 (m-10) cc_final: 0.7975 (m-10) REVERT: B 226 ASN cc_start: 0.9142 (t0) cc_final: 0.8899 (t0) REVERT: B 230 MET cc_start: 0.9337 (mmp) cc_final: 0.8867 (mmm) REVERT: B 289 ASN cc_start: 0.8946 (m110) cc_final: 0.7672 (t0) REVERT: B 398 LYS cc_start: 0.8113 (pttp) cc_final: 0.7733 (ttmt) REVERT: B 410 ASP cc_start: 0.8729 (m-30) cc_final: 0.7546 (t70) REVERT: B 414 MET cc_start: 0.8846 (mpp) cc_final: 0.8645 (mpp) REVERT: B 419 LYS cc_start: 0.8881 (mttt) cc_final: 0.8629 (mmmm) REVERT: B 422 GLN cc_start: 0.9076 (tt0) cc_final: 0.8066 (mm-40) REVERT: B 429 PRO cc_start: 0.8704 (Cg_endo) cc_final: 0.8463 (Cg_exo) REVERT: A 1353 ILE cc_start: 0.7796 (mm) cc_final: 0.7556 (tp) REVERT: A 1364 GLN cc_start: 0.8215 (tp40) cc_final: 0.7994 (tp40) REVERT: A 1482 MET cc_start: 0.6624 (mmm) cc_final: 0.5576 (mmm) REVERT: A 1614 LYS cc_start: 0.3606 (tmtt) cc_final: 0.2647 (tttt) REVERT: A 1798 TRP cc_start: 0.7680 (m-10) cc_final: 0.7410 (m-10) REVERT: A 1876 GLU cc_start: 0.9257 (tt0) cc_final: 0.8983 (tt0) REVERT: A 1899 ASP cc_start: 0.7329 (t70) cc_final: 0.7012 (t0) REVERT: A 1920 LEU cc_start: 0.8074 (pp) cc_final: 0.7766 (pp) REVERT: A 1929 GLU cc_start: 0.9110 (tt0) cc_final: 0.8719 (mp0) REVERT: A 2118 ASP cc_start: 0.7238 (t0) cc_final: 0.6892 (t0) REVERT: A 2144 GLU cc_start: 0.7002 (tm-30) cc_final: 0.6412 (tm-30) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.2184 time to fit residues: 70.2481 Evaluate side-chains 195 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN B 517 ASN B 628 HIS ** A1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2139 GLN ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.130749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.111132 restraints weight = 30064.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.113506 restraints weight = 21295.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.115208 restraints weight = 16405.592| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9379 Z= 0.244 Angle : 0.790 9.656 12718 Z= 0.396 Chirality : 0.048 0.243 1486 Planarity : 0.004 0.044 1606 Dihedral : 5.959 39.470 1240 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.99 % Favored : 83.01 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.36 % 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: -3.11 (0.24), residues: 1148 helix: 0.49 (0.28), residues: 360 sheet: -2.38 (0.56), residues: 92 loop : -3.70 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A1906 HIS 0.008 0.002 HIS A2145 PHE 0.032 0.002 PHE A1718 TYR 0.019 0.002 TYR A1879 ARG 0.006 0.001 ARG B 352 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2207.87 seconds wall clock time: 40 minutes 23.06 seconds (2423.06 seconds total)