Starting phenix.real_space_refine on Wed Aug 5 16:11:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/12jv_76497/08_2026/12jv_76497.cif Found real_map, /net/cci-nas-00/data/ceres_data/12jv_76497/08_2026/12jv_76497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/12jv_76497/08_2026/12jv_76497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/12jv_76497/08_2026/12jv_76497.map" model { file = "/net/cci-nas-00/data/ceres_data/12jv_76497/08_2026/12jv_76497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/12jv_76497/08_2026/12jv_76497.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 Cu 2 5.60 5 S 56 5.16 5 C 6523 2.51 5 N 1719 2.21 5 O 1844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10145 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1247, 10100 Classifications: {'peptide': 1247} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1184} Chain breaks: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Unusual residues: {' CA': 1, ' CU': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2127 SG CYS A 310 41.204 56.154 95.117 1.00115.72 S Time building chain proxies: 1.91, per 1000 atoms: 0.19 Number of scatterers: 10145 At special positions: 0 Unit cell: (81.664, 94.656, 138.272, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cu 2 28.99 Ca 1 19.99 S 56 16.00 O 1844 8.00 N 1719 7.00 C 6523 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 248 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 528 " - pdb=" SG CYS A 554 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 711 " distance=2.03 Simple disulfide: pdb=" SG CYS A1832 " - pdb=" SG CYS A1858 " distance=2.03 Simple disulfide: pdb=" SG CYS A1899 " - pdb=" SG CYS A1903 " distance=2.03 Simple disulfide: pdb=" SG CYS A2021 " - pdb=" SG CYS A2169 " distance=2.03 Simple disulfide: pdb=" SG CYS A2174 " - pdb=" SG CYS A2326 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A2401 " - " ASN A2118 " " NAG A2402 " - " ASN A1810 " " NAG A2403 " - " ASN A 239 " Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 228.7 milliseconds 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2338 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 20 sheets defined 8.5% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.910A pdb=" N GLU A 124 " --> pdb=" O ARG A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 170 removed outlier: 3.856A pdb=" N ASN A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 203 through 208 removed outlier: 4.245A pdb=" N TRP A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 497 through 501 Processing helix chain 'A' and resid 538 through 544 Processing helix chain 'A' and resid 586 through 594 Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 694 through 699 removed outlier: 3.854A pdb=" N ARG A 698 " --> pdb=" O ASN A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 1721 through 1725 removed outlier: 3.736A pdb=" N SER A1724 " --> pdb=" O ARG A1721 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1824 Processing helix chain 'A' and resid 1842 through 1849 Processing helix chain 'A' and resid 1890 through 1897 Processing helix chain 'A' and resid 1908 through 1915 removed outlier: 3.581A pdb=" N PHE A1912 " --> pdb=" O GLU A1908 " (cutoff:3.500A) Processing helix chain 'A' and resid 2002 through 2007 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 8 through 13 Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 78 removed outlier: 3.728A pdb=" N VAL A 178 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 89 removed outlier: 3.609A pdb=" N LEU A 88 " --> pdb=" O HIS A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 196 through 197 removed outlier: 7.200A pdb=" N LEU A 197 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 267 through 269 Processing sheet with id=AA7, first strand: chain 'A' and resid 381 through 384 removed outlier: 6.319A pdb=" N TRP A 382 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ILE A 464 " --> pdb=" O TRP A 382 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N HIS A 384 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LYS A 466 " --> pdb=" O HIS A 384 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 390 through 393 removed outlier: 4.142A pdb=" N GLU A 391 " --> pdb=" O LYS A 425 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS A 425 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 453 through 456 removed outlier: 6.712A pdb=" N LEU A 453 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N CYS A 554 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLY A 455 " --> pdb=" O CYS A 554 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY A 549 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR A 533 " --> pdb=" O GLY A 549 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 534 " --> pdb=" O TYR A 476 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 614 through 615 removed outlier: 3.671A pdb=" N LEU A 640 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 642 " --> pdb=" O PHE A 576 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TRP A 637 " --> pdb=" O VAL A 678 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 658 through 660 Processing sheet with id=AB3, first strand: chain 'A' and resid 689 through 690 Processing sheet with id=AB4, first strand: chain 'A' and resid 1733 through 1738 removed outlier: 4.111A pdb=" N PHE A1699 " --> pdb=" O PHE A1738 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE A1700 " --> pdb=" O ARG A1776 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP A1769 " --> pdb=" O VAL A1819 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A1771 " --> pdb=" O TRP A1817 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A1775 " --> pdb=" O LYS A1813 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1832 through 1833 Processing sheet with id=AB6, first strand: chain 'A' and resid 1837 through 1838 Processing sheet with id=AB7, first strand: chain 'A' and resid 1919 through 1920 removed outlier: 3.654A pdb=" N LEU A1944 " --> pdb=" O GLU A1984 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU A1984 " --> pdb=" O LEU A1944 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR A1971 " --> pdb=" O VAL A1965 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1933 through 1935 removed outlier: 4.391A pdb=" N ARG A1997 " --> pdb=" O SER A1959 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2037 through 2039 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2071 through 2085 current: chain 'A' and resid 2113 through 2114 Processing sheet with id=AC1, first strand: chain 'A' and resid 2089 through 2090 Processing sheet with id=AC2, first strand: chain 'A' and resid 2190 through 2191 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2230 through 2246 current: chain 'A' and resid 2272 through 2273 138 hydrogen bonds defined for protein. 321 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: 1.58 Time building geometry restraints manager: 0.92 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: 3204 1.34 - 1.46: 2395 1.46 - 1.58: 4738 1.58 - 1.70: 0 1.70 - 1.82: 93 Bond restraints: 10430 Sorted by residual: bond pdb=" CA ARG A1900 " pdb=" CB ARG A1900 " ideal model delta sigma weight residual 1.523 1.547 -0.024 1.94e-02 2.66e+03 1.54e+00 bond pdb=" CG1 ILE A1925 " pdb=" CD1 ILE A1925 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.31e+00 bond pdb=" C SER A1714 " pdb=" N PRO A1715 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.21e+00 bond pdb=" CB ARG A1900 " pdb=" CG ARG A1900 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.18e+00 bond pdb=" C SER A2204 " pdb=" N PRO A2205 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.11e+00 ... (remaining 10425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 13929 2.34 - 4.68: 196 4.68 - 7.02: 15 7.02 - 9.36: 1 9.36 - 11.70: 1 Bond angle restraints: 14142 Sorted by residual: angle pdb=" C HIS A2054 " pdb=" CA HIS A2054 " pdb=" CB HIS A2054 " ideal model delta sigma weight residual 115.89 110.71 5.18 1.32e+00 5.74e-01 1.54e+01 angle pdb=" CA LEU A 71 " pdb=" CB LEU A 71 " pdb=" CG LEU A 71 " ideal model delta sigma weight residual 116.30 128.00 -11.70 3.50e+00 8.16e-02 1.12e+01 angle pdb=" N CYS A 248 " pdb=" CA CYS A 248 " pdb=" C CYS A 248 " ideal model delta sigma weight residual 108.34 112.55 -4.21 1.31e+00 5.83e-01 1.03e+01 angle pdb=" N GLN A 190 " pdb=" CA GLN A 190 " pdb=" CB GLN A 190 " ideal model delta sigma weight residual 113.65 109.04 4.61 1.47e+00 4.63e-01 9.81e+00 angle pdb=" CA ARG A1900 " pdb=" CB ARG A1900 " pdb=" CG ARG A1900 " ideal model delta sigma weight residual 114.10 119.98 -5.88 2.00e+00 2.50e-01 8.66e+00 ... (remaining 14137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 5612 17.80 - 35.60: 462 35.60 - 53.40: 90 53.40 - 71.20: 20 71.20 - 89.00: 14 Dihedral angle restraints: 6198 sinusoidal: 2560 harmonic: 3638 Sorted by residual: dihedral pdb=" CB CYS A2021 " pdb=" SG CYS A2021 " pdb=" SG CYS A2169 " pdb=" CB CYS A2169 " ideal model delta sinusoidal sigma weight residual 93.00 160.50 -67.50 1 1.00e+01 1.00e-02 5.93e+01 dihedral pdb=" CB CYS A 630 " pdb=" SG CYS A 630 " pdb=" SG CYS A 711 " pdb=" CB CYS A 711 " ideal model delta sinusoidal sigma weight residual 93.00 33.73 59.27 1 1.00e+01 1.00e-02 4.69e+01 dihedral pdb=" CA ILE A1925 " pdb=" C ILE A1925 " pdb=" N MET A1926 " pdb=" CA MET A1926 " ideal model delta harmonic sigma weight residual 180.00 149.24 30.76 0 5.00e+00 4.00e-02 3.78e+01 ... (remaining 6195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1360 0.078 - 0.156: 155 0.156 - 0.234: 1 0.234 - 0.311: 0 0.311 - 0.389: 1 Chirality restraints: 1517 Sorted by residual: chirality pdb=" C1 NAG A2401 " pdb=" ND2 ASN A2118 " pdb=" C2 NAG A2401 " pdb=" O5 NAG A2401 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CB ILE A2032 " pdb=" CA ILE A2032 " pdb=" CG1 ILE A2032 " pdb=" CG2 ILE A2032 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB THR A 83 " pdb=" CA THR A 83 " pdb=" OG1 THR A 83 " pdb=" CG2 THR A 83 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.26e-01 ... (remaining 1514 not shown) Planarity restraints: 1797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 202 " 0.018 2.00e-02 2.50e+03 1.50e-02 3.96e+00 pdb=" CG PHE A 202 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 202 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 202 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 202 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 202 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 202 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 684 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.13e+00 pdb=" N PRO A 685 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 685 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 685 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A1727 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO A1728 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A1728 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1728 " 0.021 5.00e-02 4.00e+02 ... (remaining 1794 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 60 2.66 - 3.22: 9677 3.22 - 3.78: 15241 3.78 - 4.34: 21381 4.34 - 4.90: 33773 Nonbonded interactions: 80132 Sorted by model distance: nonbonded pdb=" ND1 HIS A 315 " pdb="CU CU A2406 " model vdw 2.101 2.320 nonbonded pdb=" CE1 HIS A 232 " pdb="CU CU A2406 " model vdw 2.233 2.460 nonbonded pdb=" CD2 HIS A 267 " pdb="CU CU A2406 " model vdw 2.275 2.460 nonbonded pdb=" O GLU A 122 " pdb="CA CA A2404 " model vdw 2.325 2.510 nonbonded pdb=" CD2 HIS A2005 " pdb="CU CU A2405 " model vdw 2.336 2.460 ... (remaining 80127 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: 5.640 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.120 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 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:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 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 0.045 10441 Z= 0.126 Angle : 0.662 11.697 14167 Z= 0.337 Chirality : 0.046 0.389 1517 Planarity : 0.004 0.044 1794 Dihedral : 13.825 89.002 3836 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.24), residues: 1233 helix: -1.98 (0.54), residues: 65 sheet: -0.95 (0.36), residues: 256 loop : -1.63 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1696 TYR 0.019 0.001 TYR A1709 PHE 0.034 0.002 PHE A 202 TRP 0.014 0.001 TRP A 208 HIS 0.006 0.001 HIS A2152 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (10430) covalent geometry : angle 0.65390 / 0.33 (14142) SS BOND : bond 0.00122 / 0.09 ( 8) SS BOND : angle 1.08142 / 0.68 ( 16) hydrogen bonds : bond 0.24273 / 17.10 ( 138) hydrogen bonds : angle 10.99720 / 7.29 ( 321) link_NAG-ASN : bond 0.00743 / 0.23 ( 3) link_NAG-ASN : angle 3.92270 / 2.29 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.437 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: A 572 ASN cc_start: 0.8155 (m-40) cc_final: 0.7912 (m-40) REVERT: A 573 VAL cc_start: 0.8798 (t) cc_final: 0.8417 (m) REVERT: A 638 TYR cc_start: 0.7384 (m-80) cc_final: 0.7055 (m-80) REVERT: A 671 PHE cc_start: 0.6880 (m-10) cc_final: 0.6390 (m-10) REVERT: A 1772 MET cc_start: 0.6952 (ttm) cc_final: 0.6729 (ttp) REVERT: A 1918 PHE cc_start: 0.5644 (m-10) cc_final: 0.5416 (m-10) REVERT: A 1927 ASP cc_start: 0.5686 (m-30) cc_final: 0.5386 (m-30) REVERT: A 1989 LEU cc_start: 0.8288 (tt) cc_final: 0.7983 (pp) REVERT: A 2050 LEU cc_start: 0.7769 (mt) cc_final: 0.7521 (tt) REVERT: A 2163 ARG cc_start: 0.6301 (mtp180) cc_final: 0.4958 (mtm-85) REVERT: A 2238 MET cc_start: 0.6631 (mmm) cc_final: 0.6315 (mmm) REVERT: A 2240 VAL cc_start: 0.7860 (t) cc_final: 0.7649 (p) REVERT: A 2243 VAL cc_start: 0.6412 (t) cc_final: 0.5755 (m) REVERT: A 2249 LYS cc_start: 0.7728 (tmmt) cc_final: 0.7252 (pttt) REVERT: A 2289 SER cc_start: 0.7647 (p) cc_final: 0.7327 (t) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.1081 time to fit residues: 42.2787 Evaluate side-chains 213 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.0470 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.0170 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 GLN A 694 ASN A 699 ASN ** A1729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2007 HIS A2113 GLN A2155 HIS A2309 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.166504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.146998 restraints weight = 21239.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.151313 restraints weight = 12184.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.154253 restraints weight = 7964.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.156292 restraints weight = 5678.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.157791 restraints weight = 4309.330| |-----------------------------------------------------------------------------| r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6117 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10441 Z= 0.157 Angle : 0.693 10.274 14167 Z= 0.351 Chirality : 0.047 0.392 1517 Planarity : 0.005 0.057 1794 Dihedral : 5.810 59.494 1420 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 1.44 % Allowed : 11.63 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.24), residues: 1233 helix: -2.67 (0.44), residues: 74 sheet: -0.89 (0.33), residues: 282 loop : -1.70 (0.22), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 531 TYR 0.019 0.002 TYR A1709 PHE 0.023 0.002 PHE A 594 TRP 0.013 0.001 TRP A1835 HIS 0.005 0.001 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (10430) covalent geometry : angle 0.68524 / 0.35 (14142) SS BOND : bond 0.00342 / 0.20 ( 8) SS BOND : angle 1.34284 / 0.83 ( 16) hydrogen bonds : bond 0.04164 / 2.73 ( 138) hydrogen bonds : angle 7.97237 / 5.37 ( 321) link_NAG-ASN : bond 0.00800 / 0.24 ( 3) link_NAG-ASN : angle 3.95418 / 2.29 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 224 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 MET cc_start: 0.5971 (mmm) cc_final: 0.4994 (mmm) REVERT: A 323 TYR cc_start: 0.6937 (m-10) cc_final: 0.6724 (m-80) REVERT: A 612 ASN cc_start: 0.8198 (m-40) cc_final: 0.7935 (t0) REVERT: A 613 ILE cc_start: 0.8805 (mt) cc_final: 0.8373 (mm) REVERT: A 618 ASN cc_start: 0.7898 (m110) cc_final: 0.7402 (m-40) REVERT: A 699 ASN cc_start: 0.7905 (t0) cc_final: 0.7259 (t0) REVERT: A 1732 LYS cc_start: 0.8517 (mmtp) cc_final: 0.8209 (mttp) REVERT: A 1875 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6634 (mt-10) REVERT: A 1926 MET cc_start: 0.5344 (mmm) cc_final: 0.4894 (mmm) REVERT: A 1927 ASP cc_start: 0.5452 (m-30) cc_final: 0.4841 (p0) REVERT: A 1989 LEU cc_start: 0.8097 (tt) cc_final: 0.7714 (mp) REVERT: A 2108 ASP cc_start: 0.5527 (p0) cc_final: 0.4825 (p0) REVERT: A 2126 PHE cc_start: 0.6687 (m-80) cc_final: 0.6394 (m-80) REVERT: A 2129 ASN cc_start: 0.5328 (p0) cc_final: 0.5084 (p0) REVERT: A 2139 ILE cc_start: 0.8047 (pt) cc_final: 0.7802 (tt) REVERT: A 2148 TYR cc_start: 0.7156 (m-80) cc_final: 0.6910 (m-80) REVERT: A 2163 ARG cc_start: 0.6110 (mtp180) cc_final: 0.5217 (mtp85) REVERT: A 2199 MET cc_start: 0.4063 (tpp) cc_final: 0.3771 (tpp) REVERT: A 2240 VAL cc_start: 0.7870 (t) cc_final: 0.7635 (p) REVERT: A 2249 LYS cc_start: 0.7776 (tmmt) cc_final: 0.7256 (pttt) REVERT: A 2271 TRP cc_start: 0.4268 (m100) cc_final: 0.4040 (m100) REVERT: A 2289 SER cc_start: 0.7820 (p) cc_final: 0.7472 (t) outliers start: 16 outliers final: 8 residues processed: 229 average time/residue: 0.1120 time to fit residues: 35.1130 Evaluate side-chains 210 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 201 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain A residue 1875 GLU Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2131 ASP Chi-restraints excluded: chain A residue 2145 ILE Chi-restraints excluded: chain A residue 2198 ASN Chi-restraints excluded: chain A residue 2232 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 31 optimal weight: 0.9990 chunk 78 optimal weight: 0.2980 chunk 113 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN A 161 HIS ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 ASN ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2155 HIS A2309 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.161091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.141811 restraints weight = 21372.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.146104 restraints weight = 12333.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.148981 restraints weight = 7993.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.151038 restraints weight = 5668.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.152499 restraints weight = 4269.658| |-----------------------------------------------------------------------------| r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10441 Z= 0.192 Angle : 0.733 10.629 14167 Z= 0.371 Chirality : 0.049 0.407 1517 Planarity : 0.005 0.054 1794 Dihedral : 6.078 58.736 1420 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 2.16 % Allowed : 15.24 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.24), residues: 1233 helix: -2.33 (0.53), residues: 67 sheet: -1.21 (0.32), residues: 296 loop : -1.84 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 421 TYR 0.026 0.002 TYR A 156 PHE 0.027 0.002 PHE A 436 TRP 0.017 0.002 TRP A 106 HIS 0.006 0.001 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (10430) covalent geometry : angle 0.72507 / 0.37 (14142) SS BOND : bond 0.00177 / 0.10 ( 8) SS BOND : angle 1.23797 / 0.76 ( 16) hydrogen bonds : bond 0.03902 / 2.52 ( 138) hydrogen bonds : angle 7.02462 / 4.72 ( 321) link_NAG-ASN : bond 0.00800 / 0.25 ( 3) link_NAG-ASN : angle 4.12766 / 2.41 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.7507 (tttm) cc_final: 0.7252 (tttp) REVERT: A 301 MET cc_start: 0.5868 (mmm) cc_final: 0.4832 (mmm) REVERT: A 426 VAL cc_start: 0.6919 (p) cc_final: 0.6639 (p) REVERT: A 586 TYR cc_start: 0.6390 (m-10) cc_final: 0.6102 (m-80) REVERT: A 613 ILE cc_start: 0.8753 (mt) cc_final: 0.8360 (mm) REVERT: A 699 ASN cc_start: 0.7904 (t0) cc_final: 0.7213 (t0) REVERT: A 1790 ILE cc_start: 0.4835 (OUTLIER) cc_final: 0.4444 (mt) REVERT: A 1926 MET cc_start: 0.5777 (mmm) cc_final: 0.5469 (mmm) REVERT: A 1927 ASP cc_start: 0.5815 (m-30) cc_final: 0.5316 (p0) REVERT: A 1989 LEU cc_start: 0.8161 (tt) cc_final: 0.7709 (mp) REVERT: A 1992 LYS cc_start: 0.7837 (mtpp) cc_final: 0.7409 (mtpp) REVERT: A 2079 MET cc_start: 0.7903 (mmm) cc_final: 0.7679 (mmm) REVERT: A 2108 ASP cc_start: 0.5728 (p0) cc_final: 0.4976 (p0) REVERT: A 2126 PHE cc_start: 0.6678 (m-80) cc_final: 0.6472 (m-80) REVERT: A 2163 ARG cc_start: 0.6413 (mtp180) cc_final: 0.5513 (mtp85) REVERT: A 2199 MET cc_start: 0.4066 (tpp) cc_final: 0.3774 (tpp) REVERT: A 2249 LYS cc_start: 0.7844 (tmmt) cc_final: 0.7224 (pttt) REVERT: A 2289 SER cc_start: 0.7868 (p) cc_final: 0.7545 (t) outliers start: 24 outliers final: 19 residues processed: 226 average time/residue: 0.1084 time to fit residues: 34.0612 Evaluate side-chains 218 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain A residue 1774 THR Chi-restraints excluded: chain A residue 1790 ILE Chi-restraints excluded: chain A residue 1843 LEU Chi-restraints excluded: chain A residue 1851 LEU Chi-restraints excluded: chain A residue 1859 HIS Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2131 ASP Chi-restraints excluded: chain A residue 2145 ILE Chi-restraints excluded: chain A residue 2152 HIS Chi-restraints excluded: chain A residue 2164 MET Chi-restraints excluded: chain A residue 2198 ASN Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2308 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 76 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 113 optimal weight: 0.0970 chunk 30 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 590 ASN ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 ASN ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2155 HIS A2309 HIS ** A2316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.161851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.142707 restraints weight = 21635.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.147001 restraints weight = 12423.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.149936 restraints weight = 8066.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.151964 restraints weight = 5694.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.153425 restraints weight = 4296.282| |-----------------------------------------------------------------------------| r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10441 Z= 0.145 Angle : 0.678 10.205 14167 Z= 0.341 Chirality : 0.047 0.399 1517 Planarity : 0.004 0.052 1794 Dihedral : 5.938 58.301 1420 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 3.07 % Allowed : 16.86 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.24), residues: 1233 helix: -2.57 (0.47), residues: 75 sheet: -1.27 (0.32), residues: 298 loop : -1.85 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 531 TYR 0.021 0.002 TYR A1709 PHE 0.026 0.002 PHE A 594 TRP 0.022 0.002 TRP A 14 HIS 0.004 0.001 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (10430) covalent geometry : angle 0.67001 / 0.34 (14142) SS BOND : bond 0.00587 / 0.20 ( 8) SS BOND : angle 0.97305 / 0.60 ( 16) hydrogen bonds : bond 0.03350 / 2.19 ( 138) hydrogen bonds : angle 6.74132 / 4.50 ( 321) link_NAG-ASN : bond 0.00818 / 0.25 ( 3) link_NAG-ASN : angle 3.94644 / 2.30 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.7529 (tttm) cc_final: 0.7270 (tttp) REVERT: A 98 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7160 (tt) REVERT: A 301 MET cc_start: 0.5833 (mmm) cc_final: 0.4800 (mmm) REVERT: A 324 VAL cc_start: 0.8074 (m) cc_final: 0.7794 (p) REVERT: A 426 VAL cc_start: 0.6970 (p) cc_final: 0.6714 (p) REVERT: A 431 TYR cc_start: 0.5277 (m-10) cc_final: 0.5009 (m-10) REVERT: A 586 TYR cc_start: 0.6300 (m-10) cc_final: 0.6069 (m-10) REVERT: A 613 ILE cc_start: 0.8660 (mt) cc_final: 0.8281 (mm) REVERT: A 699 ASN cc_start: 0.7853 (t0) cc_final: 0.7130 (t0) REVERT: A 1696 ARG cc_start: 0.8545 (mtm-85) cc_final: 0.8299 (mtm110) REVERT: A 1812 THR cc_start: 0.7497 (t) cc_final: 0.7112 (p) REVERT: A 1926 MET cc_start: 0.5756 (mmm) cc_final: 0.5531 (mmm) REVERT: A 1927 ASP cc_start: 0.5797 (m-30) cc_final: 0.5222 (p0) REVERT: A 1989 LEU cc_start: 0.8176 (tt) cc_final: 0.7854 (pp) REVERT: A 1992 LYS cc_start: 0.7812 (mtpp) cc_final: 0.7433 (mtpp) REVERT: A 2079 MET cc_start: 0.7954 (mmm) cc_final: 0.7725 (mmm) REVERT: A 2108 ASP cc_start: 0.5645 (p0) cc_final: 0.4991 (p0) REVERT: A 2163 ARG cc_start: 0.6214 (mtp180) cc_final: 0.5815 (mtp180) REVERT: A 2199 MET cc_start: 0.3499 (tpp) cc_final: 0.3219 (tpp) REVERT: A 2238 MET cc_start: 0.6078 (mmm) cc_final: 0.5585 (mmm) REVERT: A 2240 VAL cc_start: 0.7811 (m) cc_final: 0.7517 (p) REVERT: A 2249 LYS cc_start: 0.7784 (tmmt) cc_final: 0.7156 (pttt) REVERT: A 2289 SER cc_start: 0.7879 (p) cc_final: 0.7554 (t) outliers start: 34 outliers final: 19 residues processed: 216 average time/residue: 0.1035 time to fit residues: 31.6938 Evaluate side-chains 205 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain A residue 1770 ASN Chi-restraints excluded: chain A residue 1774 THR Chi-restraints excluded: chain A residue 1859 HIS Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 2007 HIS Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2131 ASP Chi-restraints excluded: chain A residue 2145 ILE Chi-restraints excluded: chain A residue 2152 HIS Chi-restraints excluded: chain A residue 2198 ASN Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2308 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 109 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 0.0270 chunk 13 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS A 694 ASN ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2155 HIS A2309 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.161223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.142209 restraints weight = 21407.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.146497 restraints weight = 12261.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.149375 restraints weight = 7979.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.151348 restraints weight = 5669.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.152805 restraints weight = 4317.934| |-----------------------------------------------------------------------------| r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10441 Z= 0.163 Angle : 0.706 10.296 14167 Z= 0.353 Chirality : 0.048 0.402 1517 Planarity : 0.004 0.040 1794 Dihedral : 6.027 58.002 1420 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 3.79 % Allowed : 16.95 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.24), residues: 1233 helix: -2.51 (0.50), residues: 75 sheet: -1.23 (0.32), residues: 300 loop : -1.92 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 531 TYR 0.025 0.002 TYR A 454 PHE 0.030 0.002 PHE A 594 TRP 0.038 0.002 TRP A 14 HIS 0.004 0.001 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (10430) covalent geometry : angle 0.69896 / 0.35 (14142) SS BOND : bond 0.00111 / 0.08 ( 8) SS BOND : angle 1.01006 / 0.63 ( 16) hydrogen bonds : bond 0.03397 / 2.25 ( 138) hydrogen bonds : angle 6.59850 / 4.41 ( 321) link_NAG-ASN : bond 0.00842 / 0.27 ( 3) link_NAG-ASN : angle 3.98689 / 2.33 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7149 (tt) REVERT: A 301 MET cc_start: 0.5749 (mmm) cc_final: 0.4772 (mmm) REVERT: A 324 VAL cc_start: 0.8090 (m) cc_final: 0.7799 (p) REVERT: A 426 VAL cc_start: 0.6946 (p) cc_final: 0.6693 (p) REVERT: A 613 ILE cc_start: 0.8693 (mt) cc_final: 0.8307 (mm) REVERT: A 614 MET cc_start: 0.5731 (mmt) cc_final: 0.5498 (mmt) REVERT: A 698 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7972 (ttp-110) REVERT: A 699 ASN cc_start: 0.7863 (t0) cc_final: 0.7109 (t0) REVERT: A 1696 ARG cc_start: 0.8517 (mtm-85) cc_final: 0.8253 (mtm110) REVERT: A 1926 MET cc_start: 0.5846 (mmm) cc_final: 0.5630 (mmm) REVERT: A 1927 ASP cc_start: 0.5929 (m-30) cc_final: 0.5373 (p0) REVERT: A 1989 LEU cc_start: 0.8178 (tt) cc_final: 0.7871 (pp) REVERT: A 1992 LYS cc_start: 0.7817 (mtpp) cc_final: 0.7422 (mtpp) REVERT: A 2104 MET cc_start: 0.2564 (ptm) cc_final: 0.2304 (ptm) REVERT: A 2108 ASP cc_start: 0.5633 (p0) cc_final: 0.4982 (p0) REVERT: A 2163 ARG cc_start: 0.6208 (mtp180) cc_final: 0.5848 (mtt180) REVERT: A 2199 MET cc_start: 0.3521 (tpp) cc_final: 0.3214 (tpp) REVERT: A 2238 MET cc_start: 0.6097 (mmm) cc_final: 0.5625 (mmm) REVERT: A 2240 VAL cc_start: 0.7841 (m) cc_final: 0.7510 (p) REVERT: A 2249 LYS cc_start: 0.7852 (tmmt) cc_final: 0.7203 (pttt) REVERT: A 2289 SER cc_start: 0.7930 (p) cc_final: 0.7613 (t) outliers start: 42 outliers final: 23 residues processed: 233 average time/residue: 0.1119 time to fit residues: 36.2005 Evaluate side-chains 216 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain A residue 1770 ASN Chi-restraints excluded: chain A residue 1774 THR Chi-restraints excluded: chain A residue 1859 HIS Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1912 PHE Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2131 ASP Chi-restraints excluded: chain A residue 2145 ILE Chi-restraints excluded: chain A residue 2152 HIS Chi-restraints excluded: chain A residue 2164 MET Chi-restraints excluded: chain A residue 2198 ASN Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2253 THR Chi-restraints excluded: chain A residue 2308 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 27 optimal weight: 5.9990 chunk 74 optimal weight: 0.0770 chunk 104 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 43 optimal weight: 0.0670 chunk 54 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 ASN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN A 609 GLN ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2155 HIS A2309 HIS A2316 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.161870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.143284 restraints weight = 20965.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.147620 restraints weight = 11780.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.150572 restraints weight = 7494.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.152640 restraints weight = 5198.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.153964 restraints weight = 3843.049| |-----------------------------------------------------------------------------| r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10441 Z= 0.137 Angle : 0.718 11.080 14167 Z= 0.357 Chirality : 0.049 0.394 1517 Planarity : 0.004 0.039 1794 Dihedral : 5.887 57.461 1420 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 3.34 % Allowed : 18.12 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.24), residues: 1233 helix: -2.54 (0.48), residues: 75 sheet: -1.42 (0.32), residues: 295 loop : -1.94 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 471 TYR 0.025 0.002 TYR A1890 PHE 0.027 0.002 PHE A1775 TRP 0.049 0.002 TRP A 14 HIS 0.003 0.001 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (10430) covalent geometry : angle 0.70796 / 0.35 (14142) SS BOND : bond 0.00816 / 0.26 ( 8) SS BOND : angle 2.28853 / 1.28 ( 16) hydrogen bonds : bond 0.03166 / 2.09 ( 138) hydrogen bonds : angle 6.66505 / 4.46 ( 321) link_NAG-ASN : bond 0.00868 / 0.27 ( 3) link_NAG-ASN : angle 3.86086 / 2.25 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7115 (tt) REVERT: A 301 MET cc_start: 0.5679 (mmm) cc_final: 0.4740 (mmm) REVERT: A 324 VAL cc_start: 0.8106 (m) cc_final: 0.7797 (p) REVERT: A 459 ASP cc_start: 0.6006 (m-30) cc_final: 0.4865 (t0) REVERT: A 613 ILE cc_start: 0.8669 (mt) cc_final: 0.8285 (mm) REVERT: A 699 ASN cc_start: 0.7781 (t0) cc_final: 0.7012 (t0) REVERT: A 1696 ARG cc_start: 0.8522 (mtm-85) cc_final: 0.8215 (mtm110) REVERT: A 1766 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6888 (mt-10) REVERT: A 1790 ILE cc_start: 0.4794 (OUTLIER) cc_final: 0.4460 (mt) REVERT: A 1927 ASP cc_start: 0.5948 (m-30) cc_final: 0.5373 (p0) REVERT: A 1989 LEU cc_start: 0.8154 (tt) cc_final: 0.7859 (pp) REVERT: A 1992 LYS cc_start: 0.7811 (mtpp) cc_final: 0.7414 (mtpp) REVERT: A 2108 ASP cc_start: 0.5616 (p0) cc_final: 0.4980 (p0) REVERT: A 2163 ARG cc_start: 0.6176 (mtp180) cc_final: 0.5500 (mtp180) REVERT: A 2199 MET cc_start: 0.3404 (tpp) cc_final: 0.3052 (tpp) REVERT: A 2235 GLN cc_start: 0.7656 (pp30) cc_final: 0.7428 (pp30) REVERT: A 2238 MET cc_start: 0.6113 (mmm) cc_final: 0.5696 (mmm) REVERT: A 2240 VAL cc_start: 0.7852 (m) cc_final: 0.7518 (p) REVERT: A 2249 LYS cc_start: 0.7817 (tmmt) cc_final: 0.7202 (pttt) REVERT: A 2289 SER cc_start: 0.7863 (p) cc_final: 0.7515 (t) outliers start: 37 outliers final: 20 residues processed: 227 average time/residue: 0.1072 time to fit residues: 33.9808 Evaluate side-chains 213 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 1770 ASN Chi-restraints excluded: chain A residue 1790 ILE Chi-restraints excluded: chain A residue 1859 HIS Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1912 PHE Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 2007 HIS Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2131 ASP Chi-restraints excluded: chain A residue 2145 ILE Chi-restraints excluded: chain A residue 2152 HIS Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2253 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 35 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2155 HIS ** A2309 HIS ** 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 = 0.4418 r_free = 0.4418 target = 0.158181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.139051 restraints weight = 21682.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.143177 restraints weight = 12612.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.146005 restraints weight = 8314.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.147926 restraints weight = 5959.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.149371 restraints weight = 4578.915| |-----------------------------------------------------------------------------| r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10441 Z= 0.202 Angle : 0.782 11.335 14167 Z= 0.392 Chirality : 0.050 0.412 1517 Planarity : 0.005 0.049 1794 Dihedral : 6.339 58.759 1420 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.35 % Favored : 88.65 % Rotamer: Outliers : 3.43 % Allowed : 19.21 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.23), residues: 1233 helix: -2.60 (0.47), residues: 82 sheet: -1.58 (0.32), residues: 295 loop : -2.04 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 531 TYR 0.032 0.002 TYR A1890 PHE 0.032 0.002 PHE A 436 TRP 0.043 0.002 TRP A 14 HIS 0.006 0.001 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (10430) covalent geometry : angle 0.77342 / 0.39 (14142) SS BOND : bond 0.01390 / 0.43 ( 8) SS BOND : angle 1.92651 / 1.06 ( 16) hydrogen bonds : bond 0.03734 / 2.46 ( 138) hydrogen bonds : angle 6.77811 / 4.55 ( 321) link_NAG-ASN : bond 0.00780 / 0.24 ( 3) link_NAG-ASN : angle 4.14349 / 2.42 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 14 TRP cc_start: 0.5438 (t60) cc_final: 0.2764 (t60) REVERT: A 98 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.6954 (tt) REVERT: A 301 MET cc_start: 0.5717 (mmm) cc_final: 0.4685 (mmm) REVERT: A 320 MET cc_start: 0.6135 (OUTLIER) cc_final: 0.5595 (pmm) REVERT: A 324 VAL cc_start: 0.8054 (m) cc_final: 0.7795 (p) REVERT: A 612 ASN cc_start: 0.8211 (m-40) cc_final: 0.7967 (t0) REVERT: A 613 ILE cc_start: 0.8675 (mt) cc_final: 0.8299 (mm) REVERT: A 699 ASN cc_start: 0.7760 (t0) cc_final: 0.6951 (t0) REVERT: A 1696 ARG cc_start: 0.8476 (mtm-85) cc_final: 0.8206 (mtm110) REVERT: A 1762 TYR cc_start: 0.7466 (m-10) cc_final: 0.6909 (m-10) REVERT: A 1790 ILE cc_start: 0.5104 (OUTLIER) cc_final: 0.4593 (mt) REVERT: A 1907 MET cc_start: 0.4805 (tmm) cc_final: 0.4564 (tmm) REVERT: A 1927 ASP cc_start: 0.5819 (m-30) cc_final: 0.5307 (p0) REVERT: A 1989 LEU cc_start: 0.8107 (tt) cc_final: 0.7887 (pp) REVERT: A 1992 LYS cc_start: 0.7761 (mtpp) cc_final: 0.7322 (mtpp) REVERT: A 1999 GLU cc_start: 0.4738 (pt0) cc_final: 0.4514 (mt-10) REVERT: A 2079 MET cc_start: 0.7805 (mmm) cc_final: 0.7566 (mmm) REVERT: A 2104 MET cc_start: 0.1827 (OUTLIER) cc_final: 0.1272 (ptm) REVERT: A 2108 ASP cc_start: 0.5471 (p0) cc_final: 0.4875 (p0) REVERT: A 2112 TRP cc_start: 0.7393 (m100) cc_final: 0.7064 (m100) REVERT: A 2163 ARG cc_start: 0.6109 (mtp180) cc_final: 0.5863 (mtt180) REVERT: A 2199 MET cc_start: 0.3665 (tpp) cc_final: 0.3200 (tpp) REVERT: A 2235 GLN cc_start: 0.7679 (pp30) cc_final: 0.7423 (pp30) REVERT: A 2238 MET cc_start: 0.6059 (mmm) cc_final: 0.5709 (mmm) REVERT: A 2240 VAL cc_start: 0.7749 (m) cc_final: 0.7421 (p) REVERT: A 2249 LYS cc_start: 0.7855 (tmmt) cc_final: 0.7299 (pttt) REVERT: A 2289 SER cc_start: 0.8009 (p) cc_final: 0.7688 (t) outliers start: 38 outliers final: 25 residues processed: 216 average time/residue: 0.1118 time to fit residues: 33.5933 Evaluate side-chains 216 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 698 ARG Chi-restraints excluded: chain A residue 1770 ASN Chi-restraints excluded: chain A residue 1790 ILE Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1912 PHE Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1995 ILE Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2104 MET Chi-restraints excluded: chain A residue 2131 ASP Chi-restraints excluded: chain A residue 2145 ILE Chi-restraints excluded: chain A residue 2152 HIS Chi-restraints excluded: chain A residue 2219 TRP Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2308 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 70 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 103 optimal weight: 0.0570 chunk 113 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 54 optimal weight: 0.2980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2155 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.159739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.140892 restraints weight = 20802.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.145081 restraints weight = 11935.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.147951 restraints weight = 7727.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.149937 restraints weight = 5450.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.151380 restraints weight = 4101.036| |-----------------------------------------------------------------------------| r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6285 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10441 Z= 0.152 Angle : 0.758 10.716 14167 Z= 0.374 Chirality : 0.050 0.409 1517 Planarity : 0.004 0.042 1794 Dihedral : 6.138 58.206 1420 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 2.89 % Allowed : 20.38 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.23), residues: 1233 helix: -2.72 (0.46), residues: 80 sheet: -1.66 (0.32), residues: 286 loop : -2.04 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 531 TYR 0.033 0.002 TYR A1890 PHE 0.022 0.002 PHE A 594 TRP 0.027 0.002 TRP A 14 HIS 0.006 0.001 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (10430) covalent geometry : angle 0.74957 / 0.37 (14142) SS BOND : bond 0.00187 / 0.12 ( 8) SS BOND : angle 1.67540 / 0.95 ( 16) hydrogen bonds : bond 0.03277 / 2.14 ( 138) hydrogen bonds : angle 6.80898 / 4.59 ( 321) link_NAG-ASN : bond 0.00838 / 0.25 ( 3) link_NAG-ASN : angle 4.13761 / 2.41 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 TRP cc_start: 0.5050 (t60) cc_final: 0.2453 (t60) REVERT: A 98 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7075 (tt) REVERT: A 301 MET cc_start: 0.5709 (mmm) cc_final: 0.4711 (mmm) REVERT: A 324 VAL cc_start: 0.8088 (m) cc_final: 0.7809 (p) REVERT: A 539 MET cc_start: 0.8245 (ppp) cc_final: 0.7601 (ppp) REVERT: A 613 ILE cc_start: 0.8619 (mt) cc_final: 0.8368 (tt) REVERT: A 680 MET cc_start: 0.6083 (mmm) cc_final: 0.5802 (mmm) REVERT: A 699 ASN cc_start: 0.7701 (t0) cc_final: 0.7479 (t0) REVERT: A 1696 ARG cc_start: 0.8479 (mtm-85) cc_final: 0.8147 (mtm110) REVERT: A 1762 TYR cc_start: 0.7410 (m-10) cc_final: 0.6909 (m-10) REVERT: A 1790 ILE cc_start: 0.4989 (OUTLIER) cc_final: 0.4475 (mt) REVERT: A 1806 PHE cc_start: 0.7125 (t80) cc_final: 0.6840 (t80) REVERT: A 1813 LYS cc_start: 0.8480 (mmtt) cc_final: 0.7697 (tptp) REVERT: A 1872 THR cc_start: 0.6037 (OUTLIER) cc_final: 0.5734 (m) REVERT: A 1907 MET cc_start: 0.4825 (tmm) cc_final: 0.4574 (tmm) REVERT: A 1927 ASP cc_start: 0.5725 (m-30) cc_final: 0.5224 (p0) REVERT: A 1989 LEU cc_start: 0.8130 (tt) cc_final: 0.7849 (pp) REVERT: A 2079 MET cc_start: 0.7910 (mmm) cc_final: 0.7665 (mmm) REVERT: A 2104 MET cc_start: 0.1856 (OUTLIER) cc_final: 0.1256 (ptm) REVERT: A 2108 ASP cc_start: 0.5506 (p0) cc_final: 0.4922 (p0) REVERT: A 2112 TRP cc_start: 0.7377 (m100) cc_final: 0.7085 (m100) REVERT: A 2163 ARG cc_start: 0.6022 (mtp180) cc_final: 0.5755 (mtp180) REVERT: A 2199 MET cc_start: 0.3538 (tpp) cc_final: 0.3079 (tpp) REVERT: A 2235 GLN cc_start: 0.7674 (pp30) cc_final: 0.7454 (pp30) REVERT: A 2238 MET cc_start: 0.6113 (mmm) cc_final: 0.5749 (mmm) REVERT: A 2240 VAL cc_start: 0.7785 (m) cc_final: 0.7461 (p) REVERT: A 2249 LYS cc_start: 0.7843 (tmmt) cc_final: 0.7295 (pttt) REVERT: A 2289 SER cc_start: 0.7988 (p) cc_final: 0.7627 (t) outliers start: 32 outliers final: 23 residues processed: 215 average time/residue: 0.1037 time to fit residues: 31.2547 Evaluate side-chains 211 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 1770 ASN Chi-restraints excluded: chain A residue 1790 ILE Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1912 PHE Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1995 ILE Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2053 LEU Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2104 MET Chi-restraints excluded: chain A residue 2131 ASP Chi-restraints excluded: chain A residue 2145 ILE Chi-restraints excluded: chain A residue 2152 HIS Chi-restraints excluded: chain A residue 2219 TRP Chi-restraints excluded: chain A residue 2232 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 106 optimal weight: 0.5980 chunk 39 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 52 optimal weight: 0.0050 chunk 36 optimal weight: 0.0470 chunk 83 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 overall best weight: 0.3692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2155 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.161085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.142367 restraints weight = 20945.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.146570 restraints weight = 11994.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.149413 restraints weight = 7762.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.151424 restraints weight = 5472.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.152863 restraints weight = 4104.544| |-----------------------------------------------------------------------------| r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10441 Z= 0.136 Angle : 0.747 10.715 14167 Z= 0.367 Chirality : 0.049 0.404 1517 Planarity : 0.004 0.041 1794 Dihedral : 6.045 57.635 1420 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 3.25 % Allowed : 20.92 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.23), residues: 1233 helix: -2.64 (0.48), residues: 80 sheet: -1.86 (0.30), residues: 295 loop : -1.98 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 489 TYR 0.033 0.002 TYR A1890 PHE 0.018 0.001 PHE A 594 TRP 0.024 0.002 TRP A 14 HIS 0.005 0.001 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (10430) covalent geometry : angle 0.73805 / 0.36 (14142) SS BOND : bond 0.00315 / 0.15 ( 8) SS BOND : angle 1.63152 / 0.92 ( 16) hydrogen bonds : bond 0.03236 / 2.08 ( 138) hydrogen bonds : angle 6.67199 / 4.40 ( 321) link_NAG-ASN : bond 0.00852 / 0.26 ( 3) link_NAG-ASN : angle 4.11509 / 2.39 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 TRP cc_start: 0.4814 (t60) cc_final: 0.2282 (t60) REVERT: A 98 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7075 (tt) REVERT: A 301 MET cc_start: 0.5741 (mmm) cc_final: 0.4749 (mmm) REVERT: A 324 VAL cc_start: 0.8053 (m) cc_final: 0.7797 (p) REVERT: A 459 ASP cc_start: 0.5890 (m-30) cc_final: 0.4701 (t0) REVERT: A 680 MET cc_start: 0.6230 (mmm) cc_final: 0.5706 (tpt) REVERT: A 699 ASN cc_start: 0.7524 (t0) cc_final: 0.6754 (t0) REVERT: A 1696 ARG cc_start: 0.8423 (mtm-85) cc_final: 0.8205 (mtm-85) REVERT: A 1762 TYR cc_start: 0.7370 (m-10) cc_final: 0.6868 (m-10) REVERT: A 1790 ILE cc_start: 0.4876 (OUTLIER) cc_final: 0.4228 (mt) REVERT: A 1806 PHE cc_start: 0.7120 (t80) cc_final: 0.6874 (t80) REVERT: A 1812 THR cc_start: 0.7192 (t) cc_final: 0.6866 (p) REVERT: A 1813 LYS cc_start: 0.8421 (mmtt) cc_final: 0.7617 (tptp) REVERT: A 1872 THR cc_start: 0.5940 (OUTLIER) cc_final: 0.5663 (m) REVERT: A 1907 MET cc_start: 0.4834 (tmm) cc_final: 0.4529 (tmm) REVERT: A 1927 ASP cc_start: 0.5718 (m-30) cc_final: 0.5315 (p0) REVERT: A 1989 LEU cc_start: 0.8094 (tt) cc_final: 0.7852 (pp) REVERT: A 2079 MET cc_start: 0.7834 (mmm) cc_final: 0.7627 (mmm) REVERT: A 2108 ASP cc_start: 0.5458 (p0) cc_final: 0.4925 (p0) REVERT: A 2111 LYS cc_start: 0.8038 (tptt) cc_final: 0.7818 (tptt) REVERT: A 2163 ARG cc_start: 0.5899 (mtp180) cc_final: 0.5618 (mtp180) REVERT: A 2176 MET cc_start: 0.4040 (mmp) cc_final: 0.3504 (ptp) REVERT: A 2199 MET cc_start: 0.3416 (tpp) cc_final: 0.2999 (tpp) REVERT: A 2238 MET cc_start: 0.5952 (mmm) cc_final: 0.5639 (mmm) REVERT: A 2240 VAL cc_start: 0.7720 (m) cc_final: 0.7415 (p) REVERT: A 2249 LYS cc_start: 0.7766 (tmmt) cc_final: 0.7284 (pttt) REVERT: A 2289 SER cc_start: 0.7989 (p) cc_final: 0.7614 (t) outliers start: 36 outliers final: 24 residues processed: 210 average time/residue: 0.0973 time to fit residues: 28.8312 Evaluate side-chains 209 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 276 PHE Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 1770 ASN Chi-restraints excluded: chain A residue 1790 ILE Chi-restraints excluded: chain A residue 1859 HIS Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1912 PHE Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1995 ILE Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2053 LEU Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2131 ASP Chi-restraints excluded: chain A residue 2145 ILE Chi-restraints excluded: chain A residue 2152 HIS Chi-restraints excluded: chain A residue 2219 TRP Chi-restraints excluded: chain A residue 2232 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 0.0070 chunk 12 optimal weight: 0.6980 chunk 116 optimal weight: 0.1980 chunk 105 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2155 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.161338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.142338 restraints weight = 21190.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.146530 restraints weight = 12263.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.149389 restraints weight = 8017.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.151387 restraints weight = 5719.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.152841 restraints weight = 4336.580| |-----------------------------------------------------------------------------| r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10441 Z= 0.144 Angle : 0.758 13.320 14167 Z= 0.373 Chirality : 0.049 0.407 1517 Planarity : 0.004 0.045 1794 Dihedral : 6.079 57.976 1420 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 2.71 % Allowed : 21.55 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.23), residues: 1233 helix: -2.53 (0.49), residues: 79 sheet: -1.87 (0.31), residues: 289 loop : -2.01 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 489 TYR 0.035 0.002 TYR A1890 PHE 0.022 0.001 PHE A 594 TRP 0.025 0.002 TRP A 14 HIS 0.006 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (10430) covalent geometry : angle 0.74911 / 0.37 (14142) SS BOND : bond 0.00347 / 0.15 ( 8) SS BOND : angle 1.62582 / 0.93 ( 16) hydrogen bonds : bond 0.03187 / 2.07 ( 138) hydrogen bonds : angle 6.61280 / 4.34 ( 321) link_NAG-ASN : bond 0.00871 / 0.27 ( 3) link_NAG-ASN : angle 4.09447 / 2.38 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 TRP cc_start: 0.4881 (t60) cc_final: 0.2391 (t60) REVERT: A 98 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7062 (tt) REVERT: A 301 MET cc_start: 0.5733 (mmm) cc_final: 0.4767 (mmm) REVERT: A 324 VAL cc_start: 0.8089 (m) cc_final: 0.7800 (p) REVERT: A 459 ASP cc_start: 0.5988 (m-30) cc_final: 0.4790 (t0) REVERT: A 699 ASN cc_start: 0.7577 (t0) cc_final: 0.6826 (t0) REVERT: A 1696 ARG cc_start: 0.8467 (mtm-85) cc_final: 0.8222 (mtm-85) REVERT: A 1762 TYR cc_start: 0.7482 (m-10) cc_final: 0.6948 (m-10) REVERT: A 1790 ILE cc_start: 0.4820 (OUTLIER) cc_final: 0.4177 (mt) REVERT: A 1806 PHE cc_start: 0.7225 (t80) cc_final: 0.6967 (t80) REVERT: A 1812 THR cc_start: 0.7119 (t) cc_final: 0.6741 (p) REVERT: A 1813 LYS cc_start: 0.8493 (mmtt) cc_final: 0.7697 (tptm) REVERT: A 1872 THR cc_start: 0.5905 (OUTLIER) cc_final: 0.5658 (m) REVERT: A 1907 MET cc_start: 0.4968 (tmm) cc_final: 0.4632 (tpt) REVERT: A 1927 ASP cc_start: 0.5920 (m-30) cc_final: 0.5372 (p0) REVERT: A 1989 LEU cc_start: 0.8106 (tt) cc_final: 0.7860 (pp) REVERT: A 2079 MET cc_start: 0.7811 (mmm) cc_final: 0.7595 (mmm) REVERT: A 2108 ASP cc_start: 0.5414 (p0) cc_final: 0.4884 (p0) REVERT: A 2111 LYS cc_start: 0.8067 (tptt) cc_final: 0.7860 (tptt) REVERT: A 2163 ARG cc_start: 0.5929 (mtp180) cc_final: 0.5639 (mtp180) REVERT: A 2176 MET cc_start: 0.4199 (mmp) cc_final: 0.3544 (ptp) REVERT: A 2199 MET cc_start: 0.3453 (tpp) cc_final: 0.3003 (tpp) REVERT: A 2238 MET cc_start: 0.6048 (mmm) cc_final: 0.5710 (mmm) REVERT: A 2240 VAL cc_start: 0.7720 (m) cc_final: 0.7399 (p) REVERT: A 2249 LYS cc_start: 0.7806 (tmmt) cc_final: 0.7283 (pttt) REVERT: A 2289 SER cc_start: 0.8061 (p) cc_final: 0.7670 (t) outliers start: 30 outliers final: 24 residues processed: 204 average time/residue: 0.1019 time to fit residues: 29.1233 Evaluate side-chains 212 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 1770 ASN Chi-restraints excluded: chain A residue 1790 ILE Chi-restraints excluded: chain A residue 1859 HIS Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1912 PHE Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1995 ILE Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2053 LEU Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2131 ASP Chi-restraints excluded: chain A residue 2145 ILE Chi-restraints excluded: chain A residue 2152 HIS Chi-restraints excluded: chain A residue 2219 TRP Chi-restraints excluded: chain A residue 2232 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 16 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 113 optimal weight: 0.2980 chunk 108 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 HIS ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2155 HIS ** A2309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.160137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.141054 restraints weight = 21432.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.145220 restraints weight = 12562.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.148064 restraints weight = 8284.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.150039 restraints weight = 5927.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.151506 restraints weight = 4521.095| |-----------------------------------------------------------------------------| r_work (final): 0.4321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10441 Z= 0.170 Angle : 0.770 12.339 14167 Z= 0.384 Chirality : 0.050 0.413 1517 Planarity : 0.004 0.044 1794 Dihedral : 6.227 58.651 1420 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 2.71 % Allowed : 21.82 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.23), residues: 1233 helix: -2.50 (0.50), residues: 79 sheet: -1.86 (0.30), residues: 292 loop : -2.01 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1997 TYR 0.034 0.002 TYR A1890 PHE 0.025 0.002 PHE A 594 TRP 0.027 0.002 TRP A 14 HIS 0.008 0.001 HIS A2007 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (10430) covalent geometry : angle 0.76204 / 0.38 (14142) SS BOND : bond 0.00396 / 0.16 ( 8) SS BOND : angle 1.49458 / 0.87 ( 16) hydrogen bonds : bond 0.03468 / 2.25 ( 138) hydrogen bonds : angle 6.75973 / 4.43 ( 321) link_NAG-ASN : bond 0.00838 / 0.26 ( 3) link_NAG-ASN : angle 4.17313 / 2.44 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1919.30 seconds wall clock time: 34 minutes 1.17 seconds (2041.17 seconds total)