Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 07:06:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hv8_0287/04_2023/6hv8_0287.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hv8_0287/04_2023/6hv8_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_0287/04_2023/6hv8_0287.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hv8_0287/04_2023/6hv8_0287.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hv8_0287/04_2023/6hv8_0287.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hv8_0287/04_2023/6hv8_0287.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 5.48, per 1000 atoms: 0.60 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: 5.19 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: 0.47 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: 2.54 Time building geometry restraints manager: 5.52 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.260 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 30.880 Find NCS groups from input model: 0.270 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.870 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.218 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 outliers start: 13 outliers final: 2 residues processed: 336 average time/residue: 0.2247 time to fit residues: 102.3552 Evaluate side-chains 218 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 216 time to evaluate : 1.170 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0915 time to fit residues: 1.9351 ------------------------------------------------------------------------------- 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: 10.0000 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 A1422 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 9379 Z= 0.227 Angle : 0.814 9.571 12718 Z= 0.415 Chirality : 0.049 0.217 1486 Planarity : 0.006 0.052 1606 Dihedral : 5.680 34.387 1240 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.90 % Favored : 85.02 % Rotamer Outliers : 0.20 % 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: -3.97 (0.23), residues: 1148 helix: -1.02 (0.26), residues: 340 sheet: -3.04 (0.50), residues: 99 loop : -3.64 (0.21), residues: 709 *********************** 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 264 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 262 time to evaluate : 1.102 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 outliers start: 2 outliers final: 1 residues processed: 263 average time/residue: 0.2549 time to fit residues: 90.0843 Evaluate side-chains 203 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 202 time to evaluate : 1.171 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0968 time to fit residues: 1.7186 ------------------------------------------------------------------------------- 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: 5.9990 chunk 33 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 0.0770 chunk 29 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 36 optimal weight: 0.0470 chunk 86 optimal weight: 4.9990 overall best weight: 2.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN B 628 HIS A1364 GLN A1575 GLN ** A1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1609 GLN A1846 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 9379 Z= 0.239 Angle : 0.785 9.548 12718 Z= 0.401 Chirality : 0.047 0.201 1486 Planarity : 0.006 0.103 1606 Dihedral : 5.749 32.885 1240 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.72 % Favored : 83.28 % Rotamer Outliers : 0.20 % 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: -3.64 (0.24), residues: 1148 helix: -0.43 (0.27), residues: 343 sheet: -3.03 (0.48), residues: 110 loop : -3.58 (0.22), residues: 695 *********************** 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 246 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 244 time to evaluate : 1.218 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 outliers start: 2 outliers final: 1 residues processed: 245 average time/residue: 0.2427 time to fit residues: 79.8455 Evaluate side-chains 189 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 1.213 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0857 time to fit residues: 1.8072 ------------------------------------------------------------------------------- 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: 6.9990 chunk 80 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 0.0270 chunk 72 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- 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 A1422 ASN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9379 Z= 0.183 Angle : 0.734 11.520 12718 Z= 0.368 Chirality : 0.046 0.208 1486 Planarity : 0.005 0.064 1606 Dihedral : 5.685 33.814 1240 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer Outliers : 0.00 % 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: -3.33 (0.24), residues: 1148 helix: -0.03 (0.28), residues: 351 sheet: -2.52 (0.55), residues: 91 loop : -3.58 (0.21), residues: 706 *********************** 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 245 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.209 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 outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.2448 time to fit residues: 81.1541 Evaluate side-chains 196 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.159 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6962 ------------------------------------------------------------------------------- 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: 0.9990 chunk 64 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 648 GLN A1326 GLN ** A1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1609 GLN ** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2139 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9379 Z= 0.193 Angle : 0.728 9.545 12718 Z= 0.364 Chirality : 0.046 0.187 1486 Planarity : 0.004 0.039 1606 Dihedral : 5.648 34.716 1240 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.55 % Favored : 85.45 % Rotamer Outliers : 0.00 % 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: -3.17 (0.24), residues: 1148 helix: 0.33 (0.28), residues: 350 sheet: -2.14 (0.58), residues: 83 loop : -3.64 (0.21), residues: 715 *********************** 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 240 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.261 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 outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.2412 time to fit residues: 78.6444 Evaluate side-chains 195 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6926 ------------------------------------------------------------------------------- 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: 6.9990 chunk 102 optimal weight: 0.0060 chunk 22 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 overall best weight: 3.2004 ------------------------------------------------------------------------------- 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 517 ASN B 648 GLN A1326 GLN A1364 GLN A1575 GLN ** A1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1662 ASN A1814 ASN ** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1940 GLN ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2145 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.4803 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= 0.274 Angle : 0.797 10.385 12718 Z= 0.403 Chirality : 0.048 0.206 1486 Planarity : 0.005 0.050 1606 Dihedral : 6.051 38.080 1240 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.03 % Favored : 81.97 % Rotamer Outliers : 0.00 % 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: -3.40 (0.24), residues: 1148 helix: 0.16 (0.27), residues: 363 sheet: -2.97 (0.46), residues: 120 loop : -3.77 (0.21), residues: 665 *********************** 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 228 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.198 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 outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2251 time to fit residues: 70.8699 Evaluate side-chains 188 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.193 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6713 ------------------------------------------------------------------------------- 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: 5.9990 chunk 12 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 83 optimal weight: 0.0980 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 52 optimal weight: 0.0770 overall best weight: 1.6142 ------------------------------------------------------------------------------- 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 A1326 GLN A1575 GLN A1648 HIS ** A1865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2060 HIS A2139 GLN ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.5072 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= 0.210 Angle : 0.771 10.503 12718 Z= 0.385 Chirality : 0.047 0.242 1486 Planarity : 0.004 0.052 1606 Dihedral : 5.996 37.252 1240 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.63 % Favored : 85.37 % Rotamer Outliers : 0.00 % 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: -3.22 (0.24), residues: 1148 helix: 0.38 (0.28), residues: 357 sheet: -2.98 (0.49), residues: 105 loop : -3.64 (0.21), residues: 686 *********************** 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 229 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.172 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 outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2166 time to fit residues: 69.3595 Evaluate side-chains 189 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.200 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6218 ------------------------------------------------------------------------------- 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: 5.9990 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 ** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 9379 Z= 0.239 Angle : 0.795 10.331 12718 Z= 0.398 Chirality : 0.049 0.249 1486 Planarity : 0.004 0.041 1606 Dihedral : 6.031 38.261 1240 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.38 % Favored : 83.62 % Rotamer Outliers : 0.00 % 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: 0.37 (0.28), residues: 362 sheet: -2.50 (0.54), residues: 91 loop : -3.77 (0.21), residues: 695 *********************** 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 220 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.203 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 outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2280 time to fit residues: 69.4056 Evaluate side-chains 183 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.272 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7541 ------------------------------------------------------------------------------- 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: 0.7980 chunk 99 optimal weight: 20.0000 chunk 105 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 A1575 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 9379 Z= 0.251 Angle : 0.805 9.506 12718 Z= 0.407 Chirality : 0.049 0.236 1486 Planarity : 0.004 0.051 1606 Dihedral : 6.197 38.937 1240 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.99 % Favored : 83.01 % Rotamer Outliers : 0.00 % 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: -3.19 (0.24), residues: 1148 helix: 0.41 (0.28), residues: 361 sheet: -2.47 (0.57), residues: 87 loop : -3.74 (0.20), residues: 700 *********************** 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 221 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.196 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 outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2246 time to fit residues: 68.7840 Evaluate side-chains 183 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.142 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5078 ------------------------------------------------------------------------------- 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: 8.9990 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 0.0570 chunk 99 optimal weight: 20.0000 overall best weight: 0.7502 ------------------------------------------------------------------------------- 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 A1326 GLN ** A1865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2044 HIS ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.5553 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= 0.178 Angle : 0.750 10.643 12718 Z= 0.371 Chirality : 0.047 0.217 1486 Planarity : 0.004 0.038 1606 Dihedral : 5.746 37.069 1240 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.59 % Favored : 86.41 % Rotamer Outliers : 0.00 % 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: -2.89 (0.24), residues: 1148 helix: 0.69 (0.28), residues: 363 sheet: -2.39 (0.64), residues: 73 loop : -3.56 (0.21), residues: 712 ********************** 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 223 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.163 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 outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.2396 time to fit residues: 74.3475 Evaluate side-chains 187 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4948 ------------------------------------------------------------------------------- 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: 0.1980 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 26 optimal weight: 0.0050 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 82 optimal weight: 0.0070 chunk 5 optimal weight: 9.9990 overall best weight: 1.0416 ------------------------------------------------------------------------------- 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 A1742 ASN ** A1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.135953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.115890 restraints weight = 29288.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.118228 restraints weight = 21148.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.119908 restraints weight = 16461.580| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.5761 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= 0.188 Angle : 0.751 9.710 12718 Z= 0.374 Chirality : 0.047 0.223 1486 Planarity : 0.004 0.050 1606 Dihedral : 5.685 37.895 1240 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.20 % Favored : 85.80 % Rotamer Outliers : 0.00 % 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: -2.84 (0.24), residues: 1148 helix: 0.69 (0.28), residues: 364 sheet: -2.17 (0.71), residues: 63 loop : -3.52 (0.21), residues: 721 =============================================================================== Job complete usr+sys time: 2138.33 seconds wall clock time: 39 minutes 31.63 seconds (2371.63 seconds total)