Starting phenix.real_space_refine on Tue Aug 4 23:06:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13fo_77048/08_2026/13fo_77048.cif Found real_map, /net/cci-nas-00/data/ceres_data/13fo_77048/08_2026/13fo_77048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/13fo_77048/08_2026/13fo_77048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13fo_77048/08_2026/13fo_77048.map" model { file = "/net/cci-nas-00/data/ceres_data/13fo_77048/08_2026/13fo_77048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13fo_77048/08_2026/13fo_77048.cif" } resolution = 3.2 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 73 5.49 5 S 16 5.16 5 C 4305 2.51 5 N 1219 2.21 5 O 1560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 7173 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1617 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 194} Chain: "D" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2510 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 308} Chain: "T" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1560 Classifications: {'RNA': 73} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 10, 'rna3p_pur': 31, 'rna3p_pyr': 25} Link IDs: {'rna2p': 17, 'rna3p': 55} Chain: "X" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1486 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 11, 'TRANS': 179} Time building chain proxies: 1.82, per 1000 atoms: 0.25 Number of scatterers: 7173 At special positions: 0 Unit cell: (74.394, 86.793, 138.042, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 73 15.00 O 1560 8.00 N 1219 7.00 C 4305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 366.8 milliseconds 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1340 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 6 sheets defined 45.2% alpha, 19.8% beta 27 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'B' and resid 32 through 48 removed outlier: 3.777A pdb=" N ILE B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Proline residue: B 38 - end of helix Processing helix chain 'B' and resid 51 through 55 Processing helix chain 'B' and resid 66 through 81 Processing helix chain 'B' and resid 93 through 101 removed outlier: 3.747A pdb=" N CYS B 101 " --> pdb=" O THR B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 163 through 177 Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'D' and resid 34 through 38 removed outlier: 4.309A pdb=" N LYS D 38 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 66 Proline residue: D 56 - end of helix Processing helix chain 'D' and resid 82 through 98 Processing helix chain 'D' and resid 108 through 121 Processing helix chain 'D' and resid 159 through 172 removed outlier: 3.703A pdb=" N ALA D 163 " --> pdb=" O SER D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 188 removed outlier: 4.358A pdb=" N LYS D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 223 Processing helix chain 'D' and resid 227 through 255 removed outlier: 3.821A pdb=" N VAL D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 267 Processing helix chain 'D' and resid 268 through 283 removed outlier: 3.763A pdb=" N ARG D 272 " --> pdb=" O ASN D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 294 removed outlier: 3.500A pdb=" N CYS D 294 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 311 removed outlier: 4.138A pdb=" N VAL D 301 " --> pdb=" O ASN D 297 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) Processing helix chain 'X' and resid 32 through 48 Proline residue: X 38 - end of helix Processing helix chain 'X' and resid 51 through 55 Processing helix chain 'X' and resid 66 through 82 Processing helix chain 'X' and resid 92 through 101 removed outlier: 3.719A pdb=" N CYS X 101 " --> pdb=" O THR X 97 " (cutoff:3.500A) Processing helix chain 'X' and resid 141 through 150 removed outlier: 4.033A pdb=" N THR X 147 " --> pdb=" O LEU X 143 " (cutoff:3.500A) Processing helix chain 'X' and resid 163 through 177 Processing sheet with id=AA1, first strand: chain 'B' and resid 90 through 92 removed outlier: 7.488A pdb=" N LEU B 91 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL B 60 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 61 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 12 " --> pdb=" O TYR B 27 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL X 57 " --> pdb=" O ASN X 2 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU X 91 " --> pdb=" O VAL X 58 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL X 60 " --> pdb=" O LEU X 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 111 through 114 removed outlier: 5.827A pdb=" N ARG B 112 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR B 119 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N HIS B 118 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL B 137 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N CYS B 120 " --> pdb=" O PRO B 135 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU B 124 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 111 through 114 removed outlier: 5.827A pdb=" N ARG B 112 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR B 119 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 154 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 24 through 30 removed outlier: 5.888A pdb=" N VAL D 24 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP D 19 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL D 26 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL D 73 " --> pdb=" O ARG D 2 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL D 74 " --> pdb=" O VAL D 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 151 through 154 removed outlier: 6.145A pdb=" N VAL D 151 " --> pdb=" O LYS D 142 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LYS D 142 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE D 261 " --> pdb=" O PHE D 287 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 133 through 138 removed outlier: 5.905A pdb=" N GLU X 134 " --> pdb=" O VAL X 122 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL X 122 " --> pdb=" O GLU X 134 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TYR X 117 " --> pdb=" O ALA X 113 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL X 106 " --> pdb=" O ILE X 154 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU X 156 " --> pdb=" O VAL X 106 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU X 108 " --> pdb=" O LEU X 156 " (cutoff:3.500A) 298 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1921 1.33 - 1.45: 1594 1.45 - 1.57: 3772 1.57 - 1.69: 145 1.69 - 1.81: 26 Bond restraints: 7458 Sorted by residual: bond pdb=" N7 A T 38 " pdb=" C5 A T 38 " ideal model delta sigma weight residual 1.388 1.377 0.011 6.00e-03 2.78e+04 3.43e+00 bond pdb=" C5 A T 23 " pdb=" C6 A T 23 " ideal model delta sigma weight residual 1.406 1.392 0.014 9.00e-03 1.23e+04 2.48e+00 bond pdb=" N7 A T 23 " pdb=" C5 A T 23 " ideal model delta sigma weight residual 1.388 1.379 0.009 6.00e-03 2.78e+04 2.21e+00 bond pdb=" C5 A T 38 " pdb=" C6 A T 38 " ideal model delta sigma weight residual 1.406 1.393 0.013 9.00e-03 1.23e+04 2.11e+00 bond pdb=" C8 A T 23 " pdb=" N7 A T 23 " ideal model delta sigma weight residual 1.311 1.301 0.010 7.00e-03 2.04e+04 2.03e+00 ... (remaining 7453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 10052 1.89 - 3.78: 373 3.78 - 5.67: 27 5.67 - 7.56: 1 7.56 - 9.46: 1 Bond angle restraints: 10454 Sorted by residual: angle pdb=" O5' U T 36 " pdb=" C5' U T 36 " pdb=" C4' U T 36 " ideal model delta sigma weight residual 109.40 113.27 -3.87 8.00e-01 1.56e+00 2.34e+01 angle pdb=" O5' A T 14 " pdb=" C5' A T 14 " pdb=" C4' A T 14 " ideal model delta sigma weight residual 109.40 112.76 -3.36 8.00e-01 1.56e+00 1.76e+01 angle pdb=" O5' A T 37 " pdb=" C5' A T 37 " pdb=" C4' A T 37 " ideal model delta sigma weight residual 109.40 112.76 -3.36 8.00e-01 1.56e+00 1.76e+01 angle pdb=" N GLY D 177 " pdb=" CA GLY D 177 " pdb=" C GLY D 177 " ideal model delta sigma weight residual 110.21 113.98 -3.77 9.10e-01 1.21e+00 1.72e+01 angle pdb=" O5' C T 16 " pdb=" C5' C T 16 " pdb=" C4' C T 16 " ideal model delta sigma weight residual 109.40 112.62 -3.22 8.00e-01 1.56e+00 1.62e+01 ... (remaining 10449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 4424 35.30 - 70.59: 206 70.59 - 105.89: 25 105.89 - 141.19: 0 141.19 - 176.49: 2 Dihedral angle restraints: 4657 sinusoidal: 2571 harmonic: 2086 Sorted by residual: dihedral pdb=" O4' C T 34 " pdb=" C1' C T 34 " pdb=" N1 C T 34 " pdb=" C2 C T 34 " ideal model delta sinusoidal sigma weight residual 232.00 55.51 176.49 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U T 33 " pdb=" C1' U T 33 " pdb=" N1 U T 33 " pdb=" C2 U T 33 " ideal model delta sinusoidal sigma weight residual -128.00 41.47 -169.47 1 1.70e+01 3.46e-03 6.59e+01 dihedral pdb=" CA TYR X 184 " pdb=" C TYR X 184 " pdb=" N GLU X 185 " pdb=" CA GLU X 185 " ideal model delta harmonic sigma weight residual 180.00 151.68 28.32 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 4654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 937 0.047 - 0.093: 213 0.093 - 0.140: 112 0.140 - 0.187: 3 0.187 - 0.233: 1 Chirality restraints: 1266 Sorted by residual: chirality pdb=" C1' G T 59 " pdb=" O4' G T 59 " pdb=" C2' G T 59 " pdb=" N9 G T 59 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA TYR X 184 " pdb=" N TYR X 184 " pdb=" C TYR X 184 " pdb=" CB TYR X 184 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" C2' A T 21 " pdb=" C3' A T 21 " pdb=" O2' A T 21 " pdb=" C1' A T 21 " both_signs ideal model delta sigma weight residual False -2.62 -2.77 0.15 2.00e-01 2.50e+01 5.67e-01 ... (remaining 1263 not shown) Planarity restraints: 1063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G T 59 " 0.032 2.00e-02 2.50e+03 1.40e-02 5.89e+00 pdb=" N9 G T 59 " -0.033 2.00e-02 2.50e+03 pdb=" C8 G T 59 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G T 59 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G T 59 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G T 59 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G T 59 " 0.013 2.00e-02 2.50e+03 pdb=" N1 G T 59 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G T 59 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G T 59 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G T 59 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G T 59 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 288 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.28e+00 pdb=" N PRO D 289 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 289 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 289 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 163 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO B 164 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " -0.023 5.00e-02 4.00e+02 ... (remaining 1060 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 3897 3.00 - 3.48: 7723 3.48 - 3.95: 12469 3.95 - 4.43: 13921 4.43 - 4.90: 20603 Nonbonded interactions: 58613 Sorted by model distance: nonbonded pdb=" O5' A T 17 " pdb=" O4' A T 17 " model vdw 2.529 2.432 nonbonded pdb=" O ILE D 98 " pdb=" OG SER D 99 " model vdw 2.550 3.040 nonbonded pdb=" O4' U T 29 " pdb=" C6 U T 29 " model vdw 2.551 2.672 nonbonded pdb=" O4' C T 25 " pdb=" C6 C T 25 " model vdw 2.562 2.672 nonbonded pdb=" O GLU D 101 " pdb=" CA LYS D 102 " model vdw 2.567 2.776 ... (remaining 58608 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 0 through 190) selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.400 Set stop_for_unknowns flag: 0.010 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.940 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 : 0.004 0.028 7458 Z= 0.224 Angle : 0.723 9.455 10454 Z= 0.503 Chirality : 0.050 0.233 1266 Planarity : 0.005 0.057 1063 Dihedral : 17.729 176.486 3317 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.17 (0.33), residues: 718 helix: 1.54 (0.30), residues: 297 sheet: -0.08 (0.45), residues: 157 loop : -1.42 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 249 TYR 0.014 0.002 TYR D 226 PHE 0.012 0.002 PHE B 175 TRP 0.011 0.001 TRP B 200 HIS 0.004 0.001 HIS X 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.22 ( 7458) covalent geometry : angle 0.72283 / 0.50 (10454) hydrogen bonds : bond 0.10696 / 7.36 ( 366) hydrogen bonds : angle 5.11226 / 3.62 ( 966) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 ARG cc_start: 0.8032 (mmt90) cc_final: 0.7814 (mmt180) REVERT: B 21 ASP cc_start: 0.8252 (m-30) cc_final: 0.7744 (m-30) REVERT: B 23 PHE cc_start: 0.7829 (m-80) cc_final: 0.7521 (m-80) REVERT: B 56 ASP cc_start: 0.8147 (m-30) cc_final: 0.7890 (m-30) REVERT: B 170 GLU cc_start: 0.7654 (tp30) cc_final: 0.7364 (tp30) REVERT: B 192 GLN cc_start: 0.8893 (mt0) cc_final: 0.8681 (mt0) REVERT: D 19 ASP cc_start: 0.8215 (t70) cc_final: 0.8011 (t70) REVERT: D 313 MET cc_start: 0.7995 (pmm) cc_final: 0.7760 (pmm) REVERT: X 7 ASP cc_start: 0.7730 (t70) cc_final: 0.7521 (t0) REVERT: X 21 ASP cc_start: 0.7654 (m-30) cc_final: 0.6474 (p0) REVERT: X 46 ASP cc_start: 0.8481 (m-30) cc_final: 0.7862 (m-30) REVERT: X 96 MET cc_start: 0.7517 (mmm) cc_final: 0.7285 (mmm) REVERT: X 104 ASP cc_start: 0.8954 (p0) cc_final: 0.8740 (p0) REVERT: X 118 HIS cc_start: 0.6842 (p-80) cc_final: 0.6511 (p-80) REVERT: X 139 SER cc_start: 0.7198 (m) cc_final: 0.6843 (p) REVERT: X 145 GLU cc_start: 0.9321 (tp30) cc_final: 0.8938 (tp30) REVERT: X 169 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8021 (mt-10) REVERT: X 176 ARG cc_start: 0.9129 (mtt180) cc_final: 0.8737 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1065 time to fit residues: 23.6745 Evaluate side-chains 98 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.0770 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 130 ASN X 182 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.089986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.069211 restraints weight = 21763.186| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 4.23 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7458 Z= 0.159 Angle : 0.624 7.040 10454 Z= 0.329 Chirality : 0.042 0.207 1266 Planarity : 0.005 0.047 1063 Dihedral : 20.219 176.549 1931 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.95 % Allowed : 11.71 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.18 (0.32), residues: 718 helix: 1.65 (0.30), residues: 298 sheet: -0.05 (0.44), residues: 157 loop : -1.58 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 17 TYR 0.028 0.002 TYR D 175 PHE 0.024 0.002 PHE B 150 TRP 0.013 0.003 TRP D 282 HIS 0.003 0.001 HIS X 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 7458) covalent geometry : angle 0.62394 / 0.33 (10454) hydrogen bonds : bond 0.05785 / 4.29 ( 366) hydrogen bonds : angle 4.54122 / 3.30 ( 966) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 PHE cc_start: 0.7713 (m-80) cc_final: 0.7512 (m-80) REVERT: B 82 SER cc_start: 0.9267 (OUTLIER) cc_final: 0.8910 (m) REVERT: D 86 LEU cc_start: 0.8887 (mt) cc_final: 0.8185 (mt) REVERT: D 313 MET cc_start: 0.7988 (pmm) cc_final: 0.7756 (pmm) REVERT: X 7 ASP cc_start: 0.7727 (t70) cc_final: 0.7480 (t0) REVERT: X 21 ASP cc_start: 0.7459 (m-30) cc_final: 0.6525 (p0) REVERT: X 31 LYS cc_start: 0.7852 (tptp) cc_final: 0.7596 (tptp) REVERT: X 43 LYS cc_start: 0.6913 (tmtt) cc_final: 0.6650 (tttt) REVERT: X 46 ASP cc_start: 0.8475 (m-30) cc_final: 0.8224 (m-30) REVERT: X 118 HIS cc_start: 0.6741 (p-80) cc_final: 0.6384 (p-80) REVERT: X 139 SER cc_start: 0.7215 (m) cc_final: 0.6957 (m) REVERT: X 145 GLU cc_start: 0.9354 (tp30) cc_final: 0.8977 (tp30) REVERT: X 163 SER cc_start: 0.9148 (m) cc_final: 0.8726 (t) REVERT: X 169 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7963 (mt-10) REVERT: X 176 ARG cc_start: 0.9121 (mtt180) cc_final: 0.8725 (mmm-85) outliers start: 12 outliers final: 7 residues processed: 119 average time/residue: 0.0949 time to fit residues: 15.0154 Evaluate side-chains 104 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 95 GLU Chi-restraints excluded: chain X residue 122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 52 optimal weight: 20.0000 chunk 16 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 130 ASN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 ASN D 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.089740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.068909 restraints weight = 21014.746| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 4.07 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7458 Z= 0.139 Angle : 0.596 9.921 10454 Z= 0.313 Chirality : 0.041 0.167 1266 Planarity : 0.005 0.043 1063 Dihedral : 20.183 176.621 1931 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.09 % Allowed : 12.85 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.23 (0.32), residues: 718 helix: 1.75 (0.30), residues: 298 sheet: -0.01 (0.45), residues: 157 loop : -1.65 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 17 TYR 0.018 0.002 TYR D 175 PHE 0.021 0.002 PHE D 287 TRP 0.015 0.002 TRP D 282 HIS 0.004 0.001 HIS X 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 7458) covalent geometry : angle 0.59564 / 0.31 (10454) hydrogen bonds : bond 0.05297 / 3.92 ( 366) hydrogen bonds : angle 4.29077 / 3.12 ( 966) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 ARG cc_start: 0.7989 (mmt180) cc_final: 0.7713 (mmm-85) REVERT: B 54 ASP cc_start: 0.9162 (m-30) cc_final: 0.8760 (t0) REVERT: B 82 SER cc_start: 0.9240 (OUTLIER) cc_final: 0.8863 (m) REVERT: B 130 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7725 (m-40) REVERT: D 86 LEU cc_start: 0.8947 (mt) cc_final: 0.8389 (mt) REVERT: D 313 MET cc_start: 0.7969 (pmm) cc_final: 0.7720 (pmm) REVERT: X 7 ASP cc_start: 0.7777 (t70) cc_final: 0.7544 (t0) REVERT: X 21 ASP cc_start: 0.7399 (m-30) cc_final: 0.6540 (p0) REVERT: X 31 LYS cc_start: 0.8030 (tptp) cc_final: 0.7638 (tptp) REVERT: X 43 LYS cc_start: 0.6879 (tmtt) cc_final: 0.6578 (tttt) REVERT: X 118 HIS cc_start: 0.6815 (p-80) cc_final: 0.6528 (p-80) REVERT: X 119 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.6643 (p90) REVERT: X 139 SER cc_start: 0.7769 (m) cc_final: 0.7411 (p) REVERT: X 163 SER cc_start: 0.9151 (m) cc_final: 0.8728 (t) REVERT: X 169 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7961 (mp0) REVERT: X 176 ARG cc_start: 0.9130 (mtt180) cc_final: 0.8731 (mmm-85) outliers start: 19 outliers final: 13 residues processed: 115 average time/residue: 0.0836 time to fit residues: 13.3329 Evaluate side-chains 107 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 236 GLN Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 95 GLU Chi-restraints excluded: chain X residue 119 TYR Chi-restraints excluded: chain X residue 122 VAL Chi-restraints excluded: chain X residue 186 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 37 optimal weight: 0.0170 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 57 optimal weight: 20.0000 chunk 60 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 overall best weight: 1.0420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.090651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.068847 restraints weight = 21825.196| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 4.36 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7458 Z= 0.150 Angle : 0.586 8.011 10454 Z= 0.310 Chirality : 0.041 0.153 1266 Planarity : 0.005 0.049 1063 Dihedral : 20.184 176.540 1931 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.58 % Allowed : 14.80 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.20 (0.32), residues: 718 helix: 1.81 (0.30), residues: 300 sheet: -0.04 (0.44), residues: 159 loop : -1.83 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 173 TYR 0.011 0.001 TYR D 226 PHE 0.019 0.002 PHE X 150 TRP 0.008 0.001 TRP D 282 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 7458) covalent geometry : angle 0.58594 / 0.31 (10454) hydrogen bonds : bond 0.05194 / 3.82 ( 366) hydrogen bonds : angle 4.22983 / 3.07 ( 966) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 ARG cc_start: 0.8035 (mmt180) cc_final: 0.7755 (mmm-85) REVERT: B 82 SER cc_start: 0.9272 (OUTLIER) cc_final: 0.8889 (m) REVERT: D 86 LEU cc_start: 0.8959 (mt) cc_final: 0.8331 (mt) REVERT: D 313 MET cc_start: 0.7922 (pmm) cc_final: 0.7649 (pmm) REVERT: X 11 ARG cc_start: 0.7262 (mtp85) cc_final: 0.6997 (mtp85) REVERT: X 21 ASP cc_start: 0.7365 (m-30) cc_final: 0.6515 (p0) REVERT: X 31 LYS cc_start: 0.8086 (tptp) cc_final: 0.7676 (tptp) REVERT: X 43 LYS cc_start: 0.6959 (tmtt) cc_final: 0.6735 (tttt) REVERT: X 118 HIS cc_start: 0.6791 (p-80) cc_final: 0.6540 (p-80) REVERT: X 119 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.6623 (p90) REVERT: X 139 SER cc_start: 0.7738 (m) cc_final: 0.7254 (p) REVERT: X 163 SER cc_start: 0.9107 (m) cc_final: 0.8680 (t) REVERT: X 169 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7953 (mp0) REVERT: X 176 ARG cc_start: 0.9149 (mtt180) cc_final: 0.8757 (mmm-85) outliers start: 22 outliers final: 15 residues processed: 106 average time/residue: 0.0883 time to fit residues: 12.8368 Evaluate side-chains 101 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 236 GLN Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 95 GLU Chi-restraints excluded: chain X residue 119 TYR Chi-restraints excluded: chain X residue 122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 0.0970 chunk 74 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.089655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.068588 restraints weight = 22004.247| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 4.24 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7458 Z= 0.150 Angle : 0.580 8.856 10454 Z= 0.307 Chirality : 0.041 0.215 1266 Planarity : 0.004 0.050 1063 Dihedral : 20.198 176.062 1931 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.41 % Allowed : 15.45 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.19 (0.32), residues: 718 helix: 1.86 (0.31), residues: 300 sheet: -0.10 (0.43), residues: 159 loop : -1.86 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 173 TYR 0.013 0.002 TYR D 226 PHE 0.015 0.001 PHE X 150 TRP 0.004 0.001 TRP D 282 HIS 0.003 0.001 HIS X 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 7458) covalent geometry : angle 0.58018 / 0.31 (10454) hydrogen bonds : bond 0.05100 / 3.75 ( 366) hydrogen bonds : angle 4.17198 / 3.03 ( 966) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 ARG cc_start: 0.8056 (mmt180) cc_final: 0.7766 (mmm-85) REVERT: B 82 SER cc_start: 0.9268 (OUTLIER) cc_final: 0.8886 (m) REVERT: D 86 LEU cc_start: 0.8995 (mt) cc_final: 0.8387 (mt) REVERT: D 313 MET cc_start: 0.7912 (pmm) cc_final: 0.7620 (pmm) REVERT: X 11 ARG cc_start: 0.7358 (mtp85) cc_final: 0.7155 (mtp85) REVERT: X 21 ASP cc_start: 0.7408 (m-30) cc_final: 0.6553 (p0) REVERT: X 31 LYS cc_start: 0.8185 (tptp) cc_final: 0.7798 (tptp) REVERT: X 43 LYS cc_start: 0.7017 (tmtt) cc_final: 0.6775 (tttt) REVERT: X 118 HIS cc_start: 0.6806 (p-80) cc_final: 0.6552 (p-80) REVERT: X 119 TYR cc_start: 0.7659 (OUTLIER) cc_final: 0.6642 (p90) REVERT: X 139 SER cc_start: 0.7721 (m) cc_final: 0.7135 (p) REVERT: X 163 SER cc_start: 0.9120 (m) cc_final: 0.8706 (t) REVERT: X 169 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7968 (mp0) REVERT: X 176 ARG cc_start: 0.9144 (mtt180) cc_final: 0.8763 (mmm-85) outliers start: 21 outliers final: 17 residues processed: 103 average time/residue: 0.0896 time to fit residues: 12.5685 Evaluate side-chains 106 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 236 GLN Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 95 GLU Chi-restraints excluded: chain X residue 119 TYR Chi-restraints excluded: chain X residue 122 VAL Chi-restraints excluded: chain X residue 186 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.086895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.065901 restraints weight = 22233.124| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 4.20 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 7458 Z= 0.266 Angle : 0.673 9.431 10454 Z= 0.355 Chirality : 0.044 0.154 1266 Planarity : 0.005 0.049 1063 Dihedral : 20.319 175.528 1931 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.90 % Allowed : 17.24 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.03 (0.32), residues: 718 helix: 1.66 (0.31), residues: 301 sheet: -0.23 (0.43), residues: 160 loop : -1.95 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 2 TYR 0.015 0.002 TYR B 123 PHE 0.018 0.002 PHE D 209 TRP 0.004 0.001 TRP B 200 HIS 0.005 0.001 HIS X 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.27 ( 7458) covalent geometry : angle 0.67319 / 0.36 (10454) hydrogen bonds : bond 0.05821 / 4.26 ( 366) hydrogen bonds : angle 4.39299 / 3.17 ( 966) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 ARG cc_start: 0.8232 (mmt180) cc_final: 0.7947 (mmm-85) REVERT: B 23 PHE cc_start: 0.7727 (m-80) cc_final: 0.7492 (m-80) REVERT: B 82 SER cc_start: 0.9281 (OUTLIER) cc_final: 0.8875 (m) REVERT: D 37 GLN cc_start: 0.8336 (tt0) cc_final: 0.7411 (tm-30) REVERT: D 86 LEU cc_start: 0.9040 (mt) cc_final: 0.8427 (mt) REVERT: D 146 ASP cc_start: 0.8474 (m-30) cc_final: 0.8208 (p0) REVERT: D 313 MET cc_start: 0.7856 (pmm) cc_final: 0.7532 (pmm) REVERT: X 7 ASP cc_start: 0.7840 (t0) cc_final: 0.7519 (t0) REVERT: X 21 ASP cc_start: 0.7453 (m-30) cc_final: 0.7161 (m-30) REVERT: X 31 LYS cc_start: 0.8222 (tptp) cc_final: 0.7830 (tptp) REVERT: X 43 LYS cc_start: 0.6932 (tmtt) cc_final: 0.6710 (tttt) REVERT: X 119 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.6778 (p90) REVERT: X 139 SER cc_start: 0.7943 (m) cc_final: 0.7440 (p) REVERT: X 163 SER cc_start: 0.9116 (m) cc_final: 0.8702 (t) REVERT: X 169 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8010 (mp0) REVERT: X 176 ARG cc_start: 0.9132 (mtt180) cc_final: 0.8734 (mmm-85) outliers start: 24 outliers final: 18 residues processed: 102 average time/residue: 0.0976 time to fit residues: 13.2297 Evaluate side-chains 99 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 95 GLU Chi-restraints excluded: chain X residue 119 TYR Chi-restraints excluded: chain X residue 122 VAL Chi-restraints excluded: chain X residue 161 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 16 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 33 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.088798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.066950 restraints weight = 21920.882| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 4.28 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7458 Z= 0.165 Angle : 0.612 10.323 10454 Z= 0.323 Chirality : 0.041 0.173 1266 Planarity : 0.004 0.047 1063 Dihedral : 20.326 174.516 1931 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.58 % Allowed : 18.05 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.01 (0.32), residues: 718 helix: 1.73 (0.31), residues: 301 sheet: -0.19 (0.43), residues: 160 loop : -2.01 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 173 TYR 0.016 0.002 TYR D 175 PHE 0.015 0.002 PHE X 150 TRP 0.002 0.001 TRP D 282 HIS 0.003 0.001 HIS X 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 7458) covalent geometry : angle 0.61248 / 0.32 (10454) hydrogen bonds : bond 0.05249 / 3.87 ( 366) hydrogen bonds : angle 4.22893 / 3.06 ( 966) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 ARG cc_start: 0.8215 (mmt180) cc_final: 0.7935 (mmm-85) REVERT: B 23 PHE cc_start: 0.7698 (m-80) cc_final: 0.7466 (m-80) REVERT: B 82 SER cc_start: 0.9264 (OUTLIER) cc_final: 0.8881 (m) REVERT: D 37 GLN cc_start: 0.8298 (tt0) cc_final: 0.7402 (tm-30) REVERT: D 86 LEU cc_start: 0.9034 (mt) cc_final: 0.8532 (mt) REVERT: D 146 ASP cc_start: 0.8476 (m-30) cc_final: 0.8208 (p0) REVERT: D 236 GLN cc_start: 0.8944 (pt0) cc_final: 0.8574 (pp30) REVERT: D 313 MET cc_start: 0.7761 (pmm) cc_final: 0.7431 (pmm) REVERT: X 7 ASP cc_start: 0.7831 (t0) cc_final: 0.7503 (t0) REVERT: X 21 ASP cc_start: 0.7365 (m-30) cc_final: 0.7080 (m-30) REVERT: X 31 LYS cc_start: 0.8287 (tptp) cc_final: 0.7902 (tptp) REVERT: X 112 ARG cc_start: 0.8537 (tpp80) cc_final: 0.8124 (tpp80) REVERT: X 119 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.6707 (p90) REVERT: X 134 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8190 (mm-30) REVERT: X 139 SER cc_start: 0.8181 (m) cc_final: 0.7574 (p) REVERT: X 163 SER cc_start: 0.9089 (m) cc_final: 0.8655 (t) REVERT: X 169 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7971 (mp0) REVERT: X 176 ARG cc_start: 0.9118 (mtt180) cc_final: 0.8798 (mmm-85) outliers start: 22 outliers final: 19 residues processed: 103 average time/residue: 0.0971 time to fit residues: 13.4080 Evaluate side-chains 103 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain X residue 95 GLU Chi-restraints excluded: chain X residue 119 TYR Chi-restraints excluded: chain X residue 122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.088155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.067038 restraints weight = 22421.614| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 4.30 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7458 Z= 0.160 Angle : 0.598 10.767 10454 Z= 0.316 Chirality : 0.041 0.174 1266 Planarity : 0.005 0.047 1063 Dihedral : 20.326 174.306 1931 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.58 % Allowed : 18.37 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.04 (0.32), residues: 718 helix: 1.79 (0.31), residues: 301 sheet: -0.12 (0.43), residues: 159 loop : -2.07 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 173 TYR 0.014 0.002 TYR D 175 PHE 0.015 0.002 PHE X 150 TRP 0.002 0.000 TRP D 282 HIS 0.004 0.001 HIS X 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 7458) covalent geometry : angle 0.59790 / 0.32 (10454) hydrogen bonds : bond 0.05076 / 3.73 ( 366) hydrogen bonds : angle 4.17803 / 3.02 ( 966) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 6 LEU cc_start: 0.8760 (tt) cc_final: 0.8402 (pp) REVERT: B 11 ARG cc_start: 0.8174 (mmt180) cc_final: 0.7907 (mmm-85) REVERT: B 23 PHE cc_start: 0.7685 (m-80) cc_final: 0.7457 (m-80) REVERT: B 82 SER cc_start: 0.9264 (OUTLIER) cc_final: 0.8878 (m) REVERT: D 37 GLN cc_start: 0.8314 (tt0) cc_final: 0.7458 (tm-30) REVERT: D 86 LEU cc_start: 0.9009 (mt) cc_final: 0.8504 (mt) REVERT: D 146 ASP cc_start: 0.8437 (m-30) cc_final: 0.8161 (p0) REVERT: D 236 GLN cc_start: 0.9071 (pt0) cc_final: 0.8538 (pp30) REVERT: D 313 MET cc_start: 0.7755 (pmm) cc_final: 0.7416 (pmm) REVERT: X 7 ASP cc_start: 0.7777 (t0) cc_final: 0.7511 (t0) REVERT: X 21 ASP cc_start: 0.7354 (m-30) cc_final: 0.7057 (m-30) REVERT: X 31 LYS cc_start: 0.8281 (tptp) cc_final: 0.8072 (tptp) REVERT: X 112 ARG cc_start: 0.8583 (tpp80) cc_final: 0.8190 (tpp80) REVERT: X 119 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.6752 (p90) REVERT: X 134 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8117 (mm-30) REVERT: X 139 SER cc_start: 0.7773 (m) cc_final: 0.7295 (p) REVERT: X 141 GLU cc_start: 0.9060 (pm20) cc_final: 0.8781 (pm20) REVERT: X 163 SER cc_start: 0.9094 (m) cc_final: 0.8694 (t) REVERT: X 169 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7973 (mp0) REVERT: X 176 ARG cc_start: 0.9122 (mtt180) cc_final: 0.8797 (mmm-85) outliers start: 22 outliers final: 18 residues processed: 98 average time/residue: 0.0953 time to fit residues: 12.5769 Evaluate side-chains 104 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 95 GLU Chi-restraints excluded: chain X residue 119 TYR Chi-restraints excluded: chain X residue 122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.088559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.067522 restraints weight = 22071.338| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 4.25 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7458 Z= 0.142 Angle : 0.595 11.515 10454 Z= 0.313 Chirality : 0.041 0.169 1266 Planarity : 0.004 0.047 1063 Dihedral : 20.314 174.192 1931 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.58 % Allowed : 18.54 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.04 (0.33), residues: 718 helix: 1.80 (0.31), residues: 301 sheet: -0.09 (0.44), residues: 157 loop : -2.11 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 173 TYR 0.015 0.002 TYR X 84 PHE 0.015 0.001 PHE X 150 TRP 0.001 0.000 TRP D 282 HIS 0.004 0.001 HIS X 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 7458) covalent geometry : angle 0.59511 / 0.31 (10454) hydrogen bonds : bond 0.04895 / 3.59 ( 366) hydrogen bonds : angle 4.14596 / 3.00 ( 966) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 LEU cc_start: 0.8749 (tt) cc_final: 0.8405 (pp) REVERT: B 11 ARG cc_start: 0.8119 (mmt180) cc_final: 0.7847 (mmm-85) REVERT: B 23 PHE cc_start: 0.7708 (m-80) cc_final: 0.7490 (m-80) REVERT: B 82 SER cc_start: 0.9267 (OUTLIER) cc_final: 0.8891 (m) REVERT: D 37 GLN cc_start: 0.8308 (tt0) cc_final: 0.7440 (tm-30) REVERT: D 64 GLU cc_start: 0.8961 (tp30) cc_final: 0.8722 (tp30) REVERT: D 86 LEU cc_start: 0.9012 (mt) cc_final: 0.8517 (mt) REVERT: D 146 ASP cc_start: 0.8425 (m-30) cc_final: 0.8156 (p0) REVERT: D 236 GLN cc_start: 0.9061 (pt0) cc_final: 0.8546 (pp30) REVERT: D 313 MET cc_start: 0.7760 (pmm) cc_final: 0.7420 (pmm) REVERT: X 7 ASP cc_start: 0.7804 (t0) cc_final: 0.7547 (t0) REVERT: X 21 ASP cc_start: 0.7370 (m-30) cc_final: 0.7083 (m-30) REVERT: X 31 LYS cc_start: 0.8315 (tptp) cc_final: 0.8097 (tptp) REVERT: X 119 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.6797 (p90) REVERT: X 134 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8122 (mm-30) REVERT: X 139 SER cc_start: 0.7915 (m) cc_final: 0.7570 (p) REVERT: X 163 SER cc_start: 0.9087 (m) cc_final: 0.8658 (t) REVERT: X 169 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7963 (mp0) REVERT: X 176 ARG cc_start: 0.9112 (mtt180) cc_final: 0.8786 (mmm-85) outliers start: 22 outliers final: 18 residues processed: 96 average time/residue: 0.0925 time to fit residues: 12.1222 Evaluate side-chains 104 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 95 GLU Chi-restraints excluded: chain X residue 119 TYR Chi-restraints excluded: chain X residue 122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 57 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.090233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.068366 restraints weight = 21619.208| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 4.33 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7458 Z= 0.125 Angle : 0.588 11.655 10454 Z= 0.306 Chirality : 0.040 0.171 1266 Planarity : 0.004 0.046 1063 Dihedral : 20.276 174.775 1931 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.93 % Allowed : 19.19 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.07 (0.33), residues: 718 helix: 1.84 (0.31), residues: 301 sheet: -0.04 (0.44), residues: 157 loop : -2.13 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 173 TYR 0.010 0.001 TYR D 78 PHE 0.015 0.001 PHE X 150 TRP 0.002 0.001 TRP B 200 HIS 0.004 0.001 HIS X 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 7458) covalent geometry : angle 0.58820 / 0.31 (10454) hydrogen bonds : bond 0.04631 / 3.38 ( 366) hydrogen bonds : angle 4.05924 / 2.92 ( 966) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 LEU cc_start: 0.8712 (tt) cc_final: 0.8377 (pp) REVERT: B 11 ARG cc_start: 0.8018 (mmt180) cc_final: 0.7758 (mmm-85) REVERT: B 23 PHE cc_start: 0.7693 (m-80) cc_final: 0.7462 (m-80) REVERT: B 82 SER cc_start: 0.9252 (OUTLIER) cc_final: 0.8903 (m) REVERT: D 37 GLN cc_start: 0.8265 (tt0) cc_final: 0.7432 (tm-30) REVERT: D 86 LEU cc_start: 0.8994 (mt) cc_final: 0.8504 (mt) REVERT: D 236 GLN cc_start: 0.8996 (pt0) cc_final: 0.8496 (pp30) REVERT: D 313 MET cc_start: 0.7701 (pmm) cc_final: 0.7361 (pmm) REVERT: X 7 ASP cc_start: 0.7793 (t0) cc_final: 0.7558 (t0) REVERT: X 21 ASP cc_start: 0.7334 (m-30) cc_final: 0.7052 (m-30) REVERT: X 31 LYS cc_start: 0.8302 (tptp) cc_final: 0.8078 (tptp) REVERT: X 119 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.6691 (p90) REVERT: X 134 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8138 (mm-30) REVERT: X 139 SER cc_start: 0.7911 (m) cc_final: 0.7557 (p) REVERT: X 157 LYS cc_start: 0.8213 (mmmt) cc_final: 0.7938 (mmmt) REVERT: X 163 SER cc_start: 0.9080 (m) cc_final: 0.8673 (t) REVERT: X 169 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7931 (mp0) REVERT: X 176 ARG cc_start: 0.9124 (mtt180) cc_final: 0.8795 (mmm-85) outliers start: 18 outliers final: 14 residues processed: 101 average time/residue: 0.0914 time to fit residues: 12.5239 Evaluate side-chains 103 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 86 ILE Chi-restraints excluded: chain X residue 95 GLU Chi-restraints excluded: chain X residue 119 TYR Chi-restraints excluded: chain X residue 122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.087710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.066662 restraints weight = 21834.552| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 4.23 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7458 Z= 0.185 Angle : 0.640 12.174 10454 Z= 0.331 Chirality : 0.041 0.168 1266 Planarity : 0.005 0.046 1063 Dihedral : 20.295 174.950 1931 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.25 % Allowed : 19.84 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.07 (0.33), residues: 718 helix: 1.76 (0.31), residues: 302 sheet: -0.06 (0.44), residues: 160 loop : -2.04 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 2 TYR 0.016 0.002 TYR D 226 PHE 0.015 0.002 PHE X 150 TRP 0.002 0.001 TRP B 200 HIS 0.005 0.001 HIS X 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 ( 7458) covalent geometry : angle 0.64045 / 0.33 (10454) hydrogen bonds : bond 0.05041 / 3.68 ( 366) hydrogen bonds : angle 4.16873 / 2.99 ( 966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1518.21 seconds wall clock time: 26 minutes 54.96 seconds (1614.96 seconds total)