Starting phenix.real_space_refine on Sat Jul 20 16:04:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tn9_41411/07_2024/8tn9_41411.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tn9_41411/07_2024/8tn9_41411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tn9_41411/07_2024/8tn9_41411.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tn9_41411/07_2024/8tn9_41411.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tn9_41411/07_2024/8tn9_41411.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tn9_41411/07_2024/8tn9_41411.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 7078 2.51 5 N 1891 2.21 5 O 2122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 549": "OD1" <-> "OD2" Residue "A GLU 662": "OE1" <-> "OE2" Residue "A TYR 1785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2069": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11145 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1368, 11089 Classifications: {'peptide': 1368} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 68, 'TRANS': 1299} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.43, per 1000 atoms: 0.58 Number of scatterers: 11145 At special positions: 0 Unit cell: (115.5, 124.3, 93.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2122 8.00 N 1891 7.00 C 7078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 472 " - pdb=" SG CYS A 498 " distance=2.03 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 656 " distance=2.03 Simple disulfide: pdb=" SG CYS A1697 " - pdb=" SG CYS A1723 " distance=2.03 Simple disulfide: pdb=" SG CYS A1879 " - pdb=" SG CYS A2033 " distance=2.03 Simple disulfide: pdb=" SG CYS A2038 " - pdb=" SG CYS A2193 " distance=2.03 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 Links applied NAG-ASN " NAG A2201 " - " ASN A 269 " " NAG A2202 " - " ASN A1982 " " NAG A2203 " - " ASN A1675 " " NAG A2204 " - " ASN A 211 " Time building additional restraints: 3.81 Conformation dependent library (CDL) restraints added in 2.0 seconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2578 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 21 sheets defined 7.0% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 149 through 156 removed outlier: 3.855A pdb=" N PHE A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 195 removed outlier: 3.530A pdb=" N LYS A 194 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 195 " --> pdb=" O GLU A 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 191 through 195' Processing helix chain 'A' and resid 284 through 290 removed outlier: 3.761A pdb=" N ALA A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.880A pdb=" N THR A 305 " --> pdb=" O PRO A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 488 Processing helix chain 'A' and resid 524 through 528 Processing helix chain 'A' and resid 530 through 536 removed outlier: 3.710A pdb=" N ASN A 536 " --> pdb=" O GLU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'A' and resid 565 through 569 removed outlier: 3.566A pdb=" N ILE A 569 " --> pdb=" O PRO A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1544 removed outlier: 3.892A pdb=" N TRP A1542 " --> pdb=" O ASN A1538 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A1543 " --> pdb=" O ILE A1539 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1689 Processing helix chain 'A' and resid 1707 through 1712 Processing helix chain 'A' and resid 1860 through 1865 Processing helix chain 'A' and resid 1891 through 1893 No H-bonds generated for 'chain 'A' and resid 1891 through 1893' Processing helix chain 'A' and resid 1905 through 1910 removed outlier: 3.654A pdb=" N ARG A1910 " --> pdb=" O ARG A1907 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 removed outlier: 3.604A pdb=" N ILE A 70 " --> pdb=" O TRP A 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65 removed outlier: 6.864A pdb=" N ALA A 64 " --> pdb=" O CYS A 165 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 210 Processing sheet with id=AA4, first strand: chain 'A' and resid 214 through 219 removed outlier: 7.769A pdb=" N ASP A 297 " --> pdb=" O PRO A 215 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE A 217 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 248 through 250 Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 325 Processing sheet with id=AA7, first strand: chain 'A' and resid 328 through 330 removed outlier: 3.640A pdb=" N MET A 367 " --> pdb=" O GLU A 329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 396 through 397 Processing sheet with id=AA9, first strand: chain 'A' and resid 558 through 561 removed outlier: 7.191A pdb=" N ASP A 513 " --> pdb=" O GLN A 581 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N HIS A 583 " --> pdb=" O ASP A 513 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLU A 515 " --> pdb=" O HIS A 583 " (cutoff:3.500A) removed outlier: 9.672A pdb=" N CYS A 585 " --> pdb=" O GLU A 515 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N GLN A 517 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 612 through 615 Processing sheet with id=AB2, first strand: chain 'A' and resid 1588 through 1595 removed outlier: 4.129A pdb=" N TYR A1555 " --> pdb=" O TYR A1595 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ARG A1552 " --> pdb=" O GLN A1629 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ARG A1631 " --> pdb=" O ARG A1552 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR A1554 " --> pdb=" O ARG A1631 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LYS A1633 " --> pdb=" O TYR A1554 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE A1556 " --> pdb=" O LYS A1633 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER A1676 " --> pdb=" O ASN A1634 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1620 through 1623 removed outlier: 6.249A pdb=" N ILE A1620 " --> pdb=" O LEU A1721 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N CYS A1723 " --> pdb=" O ILE A1620 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA A1622 " --> pdb=" O CYS A1723 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1739 through 1744 removed outlier: 6.224A pdb=" N ARG A1739 " --> pdb=" O ARG A1799 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N HIS A1801 " --> pdb=" O ARG A1739 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE A1741 " --> pdb=" O HIS A1801 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU A1803 " --> pdb=" O PHE A1741 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A1743 " --> pdb=" O LEU A1803 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1746 through 1747 removed outlier: 3.714A pdb=" N MET A1746 " --> pdb=" O ALA A1779 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A1779 " --> pdb=" O MET A1746 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1791 through 1793 removed outlier: 6.847A pdb=" N MET A1792 " --> pdb=" O MET A1875 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1881 through 1882 removed outlier: 6.859A pdb=" N GLN A2031 " --> pdb=" O THR A1946 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N ILE A1944 " --> pdb=" O PRO A2006 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N THR A1946 " --> pdb=" O PHE A2004 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1895 through 1897 removed outlier: 6.361A pdb=" N GLU A1964 " --> pdb=" O THR A2018 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA A2020 " --> pdb=" O THR A1962 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR A1962 " --> pdb=" O ALA A2020 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1920 through 1921 Processing sheet with id=AC1, first strand: chain 'A' and resid 2055 through 2056 removed outlier: 12.417A pdb=" N LEU A2095 " --> pdb=" O LYS A2178 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N LYS A2178 " --> pdb=" O LEU A2095 " (cutoff:3.500A) removed outlier: 12.529A pdb=" N ILE A2097 " --> pdb=" O ILE A2176 " (cutoff:3.500A) removed outlier: 11.721A pdb=" N ILE A2176 " --> pdb=" O ILE A2097 " (cutoff:3.500A) removed outlier: 12.044A pdb=" N LEU A2099 " --> pdb=" O ARG A2174 " (cutoff:3.500A) removed outlier: 11.258A pdb=" N ARG A2174 " --> pdb=" O LEU A2099 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N LYS A2101 " --> pdb=" O PHE A2172 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N PHE A2172 " --> pdb=" O LYS A2101 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ALA A2107 " --> pdb=" O PRO A2166 " (cutoff:3.500A) removed outlier: 11.901A pdb=" N ILE A2109 " --> pdb=" O PHE A2164 " (cutoff:3.500A) removed outlier: 11.940A pdb=" N PHE A2164 " --> pdb=" O ILE A2109 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER A2124 " --> pdb=" O LYS A2178 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP A2180 " --> pdb=" O VAL A2122 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL A2122 " --> pdb=" O TRP A2180 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR A2125 " --> pdb=" O PHE A2150 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2137 through 2138 removed outlier: 7.256A pdb=" N VAL A2122 " --> pdb=" O TRP A2180 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP A2180 " --> pdb=" O VAL A2122 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER A2124 " --> pdb=" O LYS A2178 " (cutoff:3.500A) removed outlier: 11.940A pdb=" N PHE A2164 " --> pdb=" O ILE A2109 " (cutoff:3.500A) removed outlier: 11.901A pdb=" N ILE A2109 " --> pdb=" O PHE A2164 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ALA A2107 " --> pdb=" O PRO A2166 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N PHE A2172 " --> pdb=" O LYS A2101 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N LYS A2101 " --> pdb=" O PHE A2172 " (cutoff:3.500A) removed outlier: 11.258A pdb=" N ARG A2174 " --> pdb=" O LEU A2099 " (cutoff:3.500A) removed outlier: 12.044A pdb=" N LEU A2099 " --> pdb=" O ARG A2174 " (cutoff:3.500A) removed outlier: 11.721A pdb=" N ILE A2176 " --> pdb=" O ILE A2097 " (cutoff:3.500A) removed outlier: 12.529A pdb=" N ILE A2097 " --> pdb=" O ILE A2176 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N LYS A2178 " --> pdb=" O LEU A2095 " (cutoff:3.500A) removed outlier: 12.417A pdb=" N LEU A2095 " --> pdb=" O LYS A2178 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE A2191 " --> pdb=" O THR A2106 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE A2108 " --> pdb=" O GLU A2189 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLU A2189 " --> pdb=" O ILE A2108 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 2061 through 2062 223 hydrogen bonds defined for protein. 546 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.53 Time building geometry restraints manager: 4.28 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: 3579 1.34 - 1.46: 2531 1.46 - 1.58: 5240 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 11440 Sorted by residual: bond pdb=" N MET A1736 " pdb=" CA MET A1736 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.55e+00 bond pdb=" N PHE A 668 " pdb=" CA PHE A 668 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.29e+00 bond pdb=" N ASP A1737 " pdb=" CA ASP A1737 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.24e-02 6.50e+03 5.99e+00 bond pdb=" N SER A1732 " pdb=" CA SER A1732 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.53e+00 bond pdb=" N MET A1734 " pdb=" CA MET A1734 " ideal model delta sigma weight residual 1.451 1.488 -0.037 1.70e-02 3.46e+03 4.73e+00 ... (remaining 11435 not shown) Histogram of bond angle deviations from ideal: 98.96 - 105.98: 278 105.98 - 113.00: 6065 113.00 - 120.02: 3864 120.02 - 127.04: 5118 127.04 - 134.06: 179 Bond angle restraints: 15504 Sorted by residual: angle pdb=" N ASP A 549 " pdb=" CA ASP A 549 " pdb=" C ASP A 549 " ideal model delta sigma weight residual 109.15 119.14 -9.99 1.67e+00 3.59e-01 3.58e+01 angle pdb=" C ASP A 548 " pdb=" N ASP A 549 " pdb=" CA ASP A 549 " ideal model delta sigma weight residual 122.28 113.15 9.13 1.77e+00 3.19e-01 2.66e+01 angle pdb=" C LYS A 386 " pdb=" N GLU A 387 " pdb=" CA GLU A 387 " ideal model delta sigma weight residual 121.54 129.79 -8.25 1.91e+00 2.74e-01 1.86e+01 angle pdb=" N PHE A 668 " pdb=" CA PHE A 668 " pdb=" C PHE A 668 " ideal model delta sigma weight residual 110.80 102.24 8.56 2.13e+00 2.20e-01 1.61e+01 angle pdb=" CA ASN A1733 " pdb=" C ASN A1733 " pdb=" O ASN A1733 " ideal model delta sigma weight residual 122.64 118.01 4.63 1.25e+00 6.40e-01 1.37e+01 ... (remaining 15499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 6193 17.87 - 35.75: 567 35.75 - 53.62: 118 53.62 - 71.49: 19 71.49 - 89.36: 9 Dihedral angle restraints: 6906 sinusoidal: 2892 harmonic: 4014 Sorted by residual: dihedral pdb=" CB CYS A 575 " pdb=" SG CYS A 575 " pdb=" SG CYS A 656 " pdb=" CB CYS A 656 " ideal model delta sinusoidal sigma weight residual 93.00 36.89 56.11 1 1.00e+01 1.00e-02 4.25e+01 dihedral pdb=" CA ASP A1514 " pdb=" C ASP A1514 " pdb=" N TYR A1515 " pdb=" CA TYR A1515 " ideal model delta harmonic sigma weight residual 180.00 152.87 27.13 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA GLU A 669 " pdb=" C GLU A 669 " pdb=" N PRO A 670 " pdb=" CA PRO A 670 " ideal model delta harmonic sigma weight residual 180.00 153.74 26.26 0 5.00e+00 4.00e-02 2.76e+01 ... (remaining 6903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1202 0.045 - 0.091: 306 0.091 - 0.136: 123 0.136 - 0.182: 11 0.182 - 0.227: 2 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CB ILE A 514 " pdb=" CA ILE A 514 " pdb=" CG1 ILE A 514 " pdb=" CG2 ILE A 514 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA PHE A 668 " pdb=" N PHE A 668 " pdb=" C PHE A 668 " pdb=" CB PHE A 668 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA MET A1734 " pdb=" N MET A1734 " pdb=" C MET A1734 " pdb=" CB MET A1734 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.89e-01 ... (remaining 1641 not shown) Planarity restraints: 1997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A2069 " -0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO A2070 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A2070 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A2070 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 269 " -0.025 2.00e-02 2.50e+03 2.29e-02 6.53e+00 pdb=" CG ASN A 269 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 269 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 269 " 0.024 2.00e-02 2.50e+03 pdb=" C1 NAG A2201 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 548 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.97e+00 pdb=" C ASP A 548 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP A 548 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP A 549 " 0.014 2.00e-02 2.50e+03 ... (remaining 1994 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 124 2.60 - 3.17: 9556 3.17 - 3.75: 16204 3.75 - 4.32: 23600 4.32 - 4.90: 39171 Nonbonded interactions: 88655 Sorted by model distance: nonbonded pdb=" O THR A 31 " pdb=" OG SER A 201 " model vdw 2.022 2.440 nonbonded pdb=" OG SER A1970 " pdb=" O ASN A1972 " model vdw 2.119 2.440 nonbonded pdb=" OH TYR A 453 " pdb=" OH TYR A 455 " model vdw 2.161 2.440 nonbonded pdb=" OE2 GLU A1559 " pdb=" OH TYR A1595 " model vdw 2.166 2.440 nonbonded pdb=" O VAL A 261 " pdb=" OG1 THR A 264 " model vdw 2.192 2.440 ... (remaining 88650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 32.440 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 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 : 0.003 0.037 11440 Z= 0.230 Angle : 0.668 9.986 15504 Z= 0.363 Chirality : 0.047 0.227 1644 Planarity : 0.005 0.080 1993 Dihedral : 14.359 89.364 4307 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 0.25 % Allowed : 0.74 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.35 (0.22), residues: 1364 helix: -2.67 (0.60), residues: 56 sheet: -0.44 (0.29), residues: 361 loop : -2.10 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1754 HIS 0.007 0.001 HIS A2128 PHE 0.016 0.001 PHE A 462 TYR 0.032 0.001 TYR A1510 ARG 0.006 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.6404 (pmm) cc_final: 0.5854 (ptp) REVERT: A 279 ILE cc_start: 0.8823 (tt) cc_final: 0.8368 (tt) REVERT: A 288 LEU cc_start: 0.8146 (tp) cc_final: 0.7939 (tp) REVERT: A 577 ASP cc_start: 0.7509 (t70) cc_final: 0.7127 (t0) REVERT: A 1734 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8211 (mtt) outliers start: 3 outliers final: 1 residues processed: 167 average time/residue: 0.2593 time to fit residues: 61.9889 Evaluate side-chains 136 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1733 ASN Chi-restraints excluded: chain A residue 1734 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.3980 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 123 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 HIS A 526 ASN ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1940 GLN ** A1951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11440 Z= 0.264 Angle : 0.660 17.220 15504 Z= 0.339 Chirality : 0.048 0.298 1644 Planarity : 0.004 0.058 1993 Dihedral : 6.861 56.426 1589 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 1.80 % Allowed : 8.02 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.41 (0.22), residues: 1364 helix: -2.62 (0.62), residues: 54 sheet: -0.75 (0.26), residues: 394 loop : -2.05 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1754 HIS 0.007 0.001 HIS A2128 PHE 0.016 0.002 PHE A1872 TYR 0.023 0.002 TYR A1510 ARG 0.003 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 LYS cc_start: 0.8323 (mtmt) cc_final: 0.7905 (mttp) REVERT: A 203 MET cc_start: 0.6339 (pmm) cc_final: 0.6097 (ptp) REVERT: A 279 ILE cc_start: 0.8825 (tt) cc_final: 0.8619 (tt) REVERT: A 407 PHE cc_start: 0.6706 (m-80) cc_final: 0.6493 (m-80) REVERT: A 448 GLN cc_start: 0.7426 (mm-40) cc_final: 0.7157 (mm-40) REVERT: A 517 GLN cc_start: 0.6268 (mt0) cc_final: 0.5954 (mm-40) REVERT: A 529 TRP cc_start: 0.5539 (t-100) cc_final: 0.4945 (t-100) REVERT: A 577 ASP cc_start: 0.7449 (t70) cc_final: 0.7041 (t0) REVERT: A 2097 ILE cc_start: 0.8865 (mm) cc_final: 0.8661 (mt) outliers start: 22 outliers final: 18 residues processed: 159 average time/residue: 0.2368 time to fit residues: 55.9653 Evaluate side-chains 152 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 1548 ASN Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1733 ASN Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1940 GLN Chi-restraints excluded: chain A residue 1986 ASN Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2015 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 9.9990 chunk 38 optimal weight: 0.0040 chunk 102 optimal weight: 0.9990 chunk 84 optimal weight: 0.1980 chunk 34 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1553 ASN A1629 GLN ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1940 GLN ** A1951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11440 Z= 0.165 Angle : 0.616 22.106 15504 Z= 0.310 Chirality : 0.046 0.294 1644 Planarity : 0.004 0.047 1993 Dihedral : 6.244 57.733 1586 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 2.05 % Allowed : 11.70 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.40 (0.21), residues: 1364 helix: -2.40 (0.66), residues: 54 sheet: -0.81 (0.26), residues: 397 loop : -2.02 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1665 HIS 0.004 0.001 HIS A2128 PHE 0.012 0.001 PHE A1872 TYR 0.018 0.001 TYR A1510 ARG 0.004 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LYS cc_start: 0.8222 (mtmt) cc_final: 0.7880 (ptmt) REVERT: A 517 GLN cc_start: 0.6135 (mm110) cc_final: 0.5842 (mm-40) REVERT: A 577 ASP cc_start: 0.7389 (t70) cc_final: 0.6967 (t0) REVERT: A 649 LEU cc_start: 0.8195 (tp) cc_final: 0.7831 (tt) REVERT: A 1679 THR cc_start: 0.7447 (OUTLIER) cc_final: 0.7167 (m) outliers start: 25 outliers final: 18 residues processed: 154 average time/residue: 0.2080 time to fit residues: 47.7381 Evaluate side-chains 151 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1679 THR Chi-restraints excluded: chain A residue 1733 ASN Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1865 ARG Chi-restraints excluded: chain A residue 1940 GLN Chi-restraints excluded: chain A residue 1986 ASN Chi-restraints excluded: chain A residue 2005 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 13 optimal weight: 0.0870 chunk 59 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 0.0570 chunk 131 optimal weight: 3.9990 chunk 117 optimal weight: 0.0070 chunk 35 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 overall best weight: 0.3694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN ** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1940 GLN ** A1951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11440 Z= 0.150 Angle : 0.595 23.044 15504 Z= 0.296 Chirality : 0.045 0.272 1644 Planarity : 0.004 0.039 1993 Dihedral : 5.952 56.956 1586 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.54 % Allowed : 13.42 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.33 (0.21), residues: 1364 helix: -2.31 (0.70), residues: 50 sheet: -0.80 (0.26), residues: 399 loop : -1.96 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 582 HIS 0.004 0.001 HIS A2128 PHE 0.012 0.001 PHE A 523 TYR 0.015 0.001 TYR A1515 ARG 0.003 0.000 ARG A2174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 TYR cc_start: 0.7374 (m-80) cc_final: 0.7135 (m-80) REVERT: A 407 PHE cc_start: 0.6129 (m-80) cc_final: 0.5911 (m-80) REVERT: A 517 GLN cc_start: 0.6290 (mm110) cc_final: 0.6084 (mm-40) REVERT: A 577 ASP cc_start: 0.7361 (t70) cc_final: 0.6931 (t0) REVERT: A 649 LEU cc_start: 0.8214 (tp) cc_final: 0.7859 (tt) REVERT: A 1679 THR cc_start: 0.7543 (OUTLIER) cc_final: 0.7314 (m) outliers start: 31 outliers final: 19 residues processed: 160 average time/residue: 0.2025 time to fit residues: 48.5628 Evaluate side-chains 154 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1679 THR Chi-restraints excluded: chain A residue 1733 ASN Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1940 GLN Chi-restraints excluded: chain A residue 1986 ASN Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2015 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 54 optimal weight: 20.0000 chunk 112 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 67 optimal weight: 0.0870 chunk 117 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS ** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1940 GLN ** A1951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11440 Z= 0.198 Angle : 0.617 23.083 15504 Z= 0.308 Chirality : 0.046 0.272 1644 Planarity : 0.004 0.045 1993 Dihedral : 5.884 56.296 1586 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 2.54 % Allowed : 15.14 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.32 (0.21), residues: 1364 helix: -2.37 (0.68), residues: 50 sheet: -0.77 (0.26), residues: 400 loop : -1.96 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1754 HIS 0.005 0.001 HIS A2128 PHE 0.013 0.001 PHE A1872 TYR 0.017 0.001 TYR A1515 ARG 0.003 0.000 ARG A2174 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 133 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 TYR cc_start: 0.7329 (m-80) cc_final: 0.7032 (m-80) REVERT: A 407 PHE cc_start: 0.6307 (m-80) cc_final: 0.6056 (m-80) REVERT: A 492 ILE cc_start: 0.8310 (tp) cc_final: 0.7946 (tt) REVERT: A 577 ASP cc_start: 0.7457 (t70) cc_final: 0.7020 (t0) REVERT: A 649 LEU cc_start: 0.8243 (tp) cc_final: 0.7872 (tt) REVERT: A 1679 THR cc_start: 0.7615 (OUTLIER) cc_final: 0.7315 (m) REVERT: A 2061 LYS cc_start: 0.8173 (tptp) cc_final: 0.7917 (tptp) outliers start: 31 outliers final: 25 residues processed: 153 average time/residue: 0.2146 time to fit residues: 48.8604 Evaluate side-chains 154 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1679 THR Chi-restraints excluded: chain A residue 1733 ASN Chi-restraints excluded: chain A residue 1746 MET Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1865 ARG Chi-restraints excluded: chain A residue 1940 GLN Chi-restraints excluded: chain A residue 1986 ASN Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2008 ILE Chi-restraints excluded: chain A residue 2015 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1643 HIS A1729 HIS ** A1951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2181 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 11440 Z= 0.607 Angle : 0.861 22.231 15504 Z= 0.441 Chirality : 0.053 0.341 1644 Planarity : 0.006 0.075 1993 Dihedral : 7.001 53.682 1586 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.14 % Favored : 88.78 % Rotamer: Outliers : 3.19 % Allowed : 16.61 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.78 (0.21), residues: 1364 helix: -2.72 (0.63), residues: 48 sheet: -1.15 (0.26), residues: 403 loop : -2.26 (0.18), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 457 HIS 0.010 0.002 HIS A2128 PHE 0.032 0.003 PHE A 462 TYR 0.038 0.003 TYR A1515 ARG 0.007 0.001 ARG A1593 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 129 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8649 (mt) REVERT: A 335 TYR cc_start: 0.7946 (m-80) cc_final: 0.7592 (m-80) REVERT: A 398 GLN cc_start: 0.7207 (tt0) cc_final: 0.6943 (tp40) REVERT: A 492 ILE cc_start: 0.8394 (tp) cc_final: 0.8017 (tt) REVERT: A 517 GLN cc_start: 0.7074 (mm-40) cc_final: 0.6568 (mm110) REVERT: A 577 ASP cc_start: 0.7551 (t70) cc_final: 0.7116 (t0) REVERT: A 603 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: A 649 LEU cc_start: 0.8243 (tp) cc_final: 0.7844 (tt) REVERT: A 2061 LYS cc_start: 0.8118 (tptp) cc_final: 0.7821 (tptp) outliers start: 39 outliers final: 28 residues processed: 160 average time/residue: 0.2153 time to fit residues: 51.1520 Evaluate side-chains 152 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 1625 ASP Chi-restraints excluded: chain A residue 1630 VAL Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1679 THR Chi-restraints excluded: chain A residue 1688 SER Chi-restraints excluded: chain A residue 1733 ASN Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1837 LEU Chi-restraints excluded: chain A residue 1986 ASN Chi-restraints excluded: chain A residue 2008 ILE Chi-restraints excluded: chain A residue 2015 ILE Chi-restraints excluded: chain A residue 2028 LEU Chi-restraints excluded: chain A residue 2039 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1643 HIS A1729 HIS ** A1951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2181 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 11440 Z= 0.213 Angle : 0.705 27.126 15504 Z= 0.348 Chirality : 0.047 0.281 1644 Planarity : 0.004 0.047 1993 Dihedral : 6.518 57.829 1586 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 2.37 % Allowed : 18.49 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.73 (0.21), residues: 1364 helix: -2.91 (0.59), residues: 54 sheet: -1.11 (0.26), residues: 406 loop : -2.20 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 582 HIS 0.005 0.001 HIS A2128 PHE 0.014 0.001 PHE A1872 TYR 0.023 0.001 TYR A1515 ARG 0.005 0.000 ARG A2174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.6698 (OUTLIER) cc_final: 0.5437 (p90) REVERT: A 89 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8499 (mt) REVERT: A 335 TYR cc_start: 0.7596 (m-80) cc_final: 0.7360 (m-80) REVERT: A 492 ILE cc_start: 0.8287 (tp) cc_final: 0.7907 (tt) REVERT: A 577 ASP cc_start: 0.7506 (t70) cc_final: 0.7080 (t0) REVERT: A 649 LEU cc_start: 0.8312 (tp) cc_final: 0.7953 (tt) REVERT: A 1679 THR cc_start: 0.7818 (OUTLIER) cc_final: 0.7416 (m) REVERT: A 2069 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7675 (mm-30) outliers start: 29 outliers final: 21 residues processed: 153 average time/residue: 0.2094 time to fit residues: 48.3009 Evaluate side-chains 148 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1679 THR Chi-restraints excluded: chain A residue 1688 SER Chi-restraints excluded: chain A residue 1733 ASN Chi-restraints excluded: chain A residue 1746 MET Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1841 PHE Chi-restraints excluded: chain A residue 1865 ARG Chi-restraints excluded: chain A residue 1986 ASN Chi-restraints excluded: chain A residue 2008 ILE Chi-restraints excluded: chain A residue 2015 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN A 471 GLN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11440 Z= 0.299 Angle : 0.713 26.497 15504 Z= 0.354 Chirality : 0.048 0.297 1644 Planarity : 0.004 0.046 1993 Dihedral : 6.511 55.471 1586 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 2.29 % Allowed : 19.39 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.70 (0.21), residues: 1364 helix: -2.77 (0.66), residues: 48 sheet: -1.10 (0.26), residues: 405 loop : -2.19 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1754 HIS 0.006 0.001 HIS A2128 PHE 0.020 0.002 PHE A1872 TYR 0.024 0.002 TYR A1515 ARG 0.006 0.000 ARG A2174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 SER cc_start: 0.7524 (t) cc_final: 0.7218 (t) REVERT: A 89 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8538 (mt) REVERT: A 335 TYR cc_start: 0.7698 (m-80) cc_final: 0.7397 (m-80) REVERT: A 385 MET cc_start: 0.6414 (ptm) cc_final: 0.5952 (ptm) REVERT: A 492 ILE cc_start: 0.8385 (tp) cc_final: 0.8028 (tt) REVERT: A 577 ASP cc_start: 0.7537 (t70) cc_final: 0.7108 (t0) REVERT: A 649 LEU cc_start: 0.8327 (tp) cc_final: 0.7956 (tt) REVERT: A 1679 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7655 (m) REVERT: A 1932 LYS cc_start: 0.8561 (tptm) cc_final: 0.8354 (tptp) REVERT: A 2061 LYS cc_start: 0.8082 (tptp) cc_final: 0.7772 (tptp) REVERT: A 2069 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7705 (mm-30) outliers start: 28 outliers final: 23 residues processed: 147 average time/residue: 0.2156 time to fit residues: 47.8132 Evaluate side-chains 147 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 1630 VAL Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1679 THR Chi-restraints excluded: chain A residue 1688 SER Chi-restraints excluded: chain A residue 1733 ASN Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1841 PHE Chi-restraints excluded: chain A residue 1865 ARG Chi-restraints excluded: chain A residue 1986 ASN Chi-restraints excluded: chain A residue 2008 ILE Chi-restraints excluded: chain A residue 2015 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11440 Z= 0.225 Angle : 0.674 26.565 15504 Z= 0.332 Chirality : 0.047 0.286 1644 Planarity : 0.004 0.047 1993 Dihedral : 6.315 56.800 1586 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 2.45 % Allowed : 19.39 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.68 (0.21), residues: 1364 helix: -2.88 (0.61), residues: 54 sheet: -1.03 (0.26), residues: 404 loop : -2.19 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1754 HIS 0.005 0.001 HIS A2128 PHE 0.016 0.001 PHE A1872 TYR 0.020 0.001 TYR A1515 ARG 0.005 0.000 ARG A2174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 131 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 SER cc_start: 0.7476 (t) cc_final: 0.7150 (t) REVERT: A 38 TYR cc_start: 0.6571 (OUTLIER) cc_final: 0.5275 (p90) REVERT: A 89 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8508 (mt) REVERT: A 335 TYR cc_start: 0.7606 (m-80) cc_final: 0.7353 (m-80) REVERT: A 385 MET cc_start: 0.6379 (ptm) cc_final: 0.5948 (ptm) REVERT: A 492 ILE cc_start: 0.8354 (tp) cc_final: 0.7997 (tt) REVERT: A 577 ASP cc_start: 0.7525 (t70) cc_final: 0.7102 (t0) REVERT: A 649 LEU cc_start: 0.8305 (tp) cc_final: 0.7933 (tt) REVERT: A 1679 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7603 (m) REVERT: A 1932 LYS cc_start: 0.8532 (tptm) cc_final: 0.8319 (tptp) REVERT: A 2069 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7695 (mm-30) outliers start: 30 outliers final: 25 residues processed: 154 average time/residue: 0.2038 time to fit residues: 47.7890 Evaluate side-chains 154 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 1630 VAL Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1679 THR Chi-restraints excluded: chain A residue 1688 SER Chi-restraints excluded: chain A residue 1733 ASN Chi-restraints excluded: chain A residue 1746 MET Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1841 PHE Chi-restraints excluded: chain A residue 1865 ARG Chi-restraints excluded: chain A residue 1986 ASN Chi-restraints excluded: chain A residue 2008 ILE Chi-restraints excluded: chain A residue 2015 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 135 optimal weight: 0.3980 chunk 124 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 11 optimal weight: 0.0770 chunk 83 optimal weight: 0.0060 chunk 66 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1670 ASN ** A1951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11440 Z= 0.173 Angle : 0.643 25.786 15504 Z= 0.315 Chirality : 0.046 0.266 1644 Planarity : 0.004 0.047 1993 Dihedral : 6.029 56.830 1586 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 2.29 % Allowed : 19.64 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.59 (0.21), residues: 1364 helix: -2.81 (0.62), residues: 54 sheet: -0.99 (0.26), residues: 406 loop : -2.12 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1754 HIS 0.004 0.001 HIS A2128 PHE 0.013 0.001 PHE A1872 TYR 0.014 0.001 TYR A1515 ARG 0.004 0.000 ARG A2174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 SER cc_start: 0.7254 (t) cc_final: 0.6897 (t) REVERT: A 38 TYR cc_start: 0.6296 (OUTLIER) cc_final: 0.5364 (p90) REVERT: A 89 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8470 (mt) REVERT: A 329 GLU cc_start: 0.7638 (tt0) cc_final: 0.7332 (tt0) REVERT: A 385 MET cc_start: 0.6268 (ptm) cc_final: 0.5854 (ptm) REVERT: A 407 PHE cc_start: 0.8059 (t80) cc_final: 0.7803 (t80) REVERT: A 492 ILE cc_start: 0.8378 (tp) cc_final: 0.8022 (tt) REVERT: A 577 ASP cc_start: 0.7518 (t70) cc_final: 0.7097 (t0) REVERT: A 649 LEU cc_start: 0.8250 (tp) cc_final: 0.7903 (tt) REVERT: A 1679 THR cc_start: 0.7830 (OUTLIER) cc_final: 0.7576 (m) REVERT: A 1932 LYS cc_start: 0.8448 (tptm) cc_final: 0.8217 (tptp) REVERT: A 2069 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7599 (mm-30) outliers start: 28 outliers final: 24 residues processed: 152 average time/residue: 0.2431 time to fit residues: 55.2699 Evaluate side-chains 154 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 1630 VAL Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1679 THR Chi-restraints excluded: chain A residue 1688 SER Chi-restraints excluded: chain A residue 1733 ASN Chi-restraints excluded: chain A residue 1746 MET Chi-restraints excluded: chain A residue 1831 LEU Chi-restraints excluded: chain A residue 1841 PHE Chi-restraints excluded: chain A residue 1865 ARG Chi-restraints excluded: chain A residue 1986 ASN Chi-restraints excluded: chain A residue 2008 ILE Chi-restraints excluded: chain A residue 2015 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 108 optimal weight: 0.0020 chunk 45 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 13 optimal weight: 0.0010 chunk 19 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.158931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.128772 restraints weight = 16320.517| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.59 r_work: 0.3627 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11440 Z= 0.152 Angle : 0.624 23.980 15504 Z= 0.306 Chirality : 0.046 0.259 1644 Planarity : 0.004 0.047 1993 Dihedral : 5.811 57.254 1586 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 2.21 % Allowed : 19.97 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.46 (0.22), residues: 1364 helix: -2.69 (0.64), residues: 54 sheet: -0.91 (0.26), residues: 409 loop : -2.02 (0.19), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1754 HIS 0.004 0.001 HIS A2159 PHE 0.012 0.001 PHE A1872 TYR 0.015 0.001 TYR A1515 ARG 0.005 0.000 ARG A2174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2521.22 seconds wall clock time: 46 minutes 4.62 seconds (2764.62 seconds total)