Starting phenix.real_space_refine on Wed Jun 3 15:09:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o59_70128/06_2026/9o59_70128.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o59_70128/06_2026/9o59_70128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o59_70128/06_2026/9o59_70128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o59_70128/06_2026/9o59_70128.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o59_70128/06_2026/9o59_70128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o59_70128/06_2026/9o59_70128.map" } resolution = 3.3 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 3 5.16 5 C 4128 2.51 5 N 1098 2.21 5 O 1396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6625 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2188 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain: "D" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2188 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain: "G" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2188 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Time building chain proxies: 1.89, per 1000 atoms: 0.29 Number of scatterers: 6625 At special positions: 0 Unit cell: (110.625, 117.705, 49.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 3 16.00 O 1396 8.00 N 1098 7.00 C 4128 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: 0.59 Conformation dependent library (CDL) restraints added in 382.5 milliseconds 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1650 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 0 sheets defined 91.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 1 through 20 removed outlier: 3.695A pdb=" N THR A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 38 removed outlier: 3.523A pdb=" N GLN A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU A 30 " --> pdb=" O ARG A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 57 removed outlier: 3.691A pdb=" N LEU A 45 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 78 removed outlier: 4.092A pdb=" N ALA A 66 " --> pdb=" O ASN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 94 through 107 Processing helix chain 'A' and resid 109 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 141 through 160 removed outlier: 3.674A pdb=" N LEU A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 179 removed outlier: 3.871A pdb=" N GLU A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 200 removed outlier: 3.963A pdb=" N SER A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 217 removed outlier: 3.584A pdb=" N ILE A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 221 Processing helix chain 'A' and resid 222 through 237 removed outlier: 4.075A pdb=" N TYR A 227 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 228 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 252 removed outlier: 3.619A pdb=" N LEU A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) Proline residue: A 249 - end of helix Processing helix chain 'A' and resid 256 through 270 Processing helix chain 'A' and resid 272 through 280 Processing helix chain 'D' and resid 2 through 20 removed outlier: 3.613A pdb=" N THR D 14 " --> pdb=" O SER D 10 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG D 17 " --> pdb=" O SER D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 38 removed outlier: 3.571A pdb=" N GLU D 30 " --> pdb=" O ARG D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 57 Processing helix chain 'D' and resid 62 through 78 removed outlier: 3.907A pdb=" N ALA D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 92 Processing helix chain 'D' and resid 94 through 107 Processing helix chain 'D' and resid 109 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 141 through 160 removed outlier: 3.679A pdb=" N THR D 150 " --> pdb=" O SER D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 179 removed outlier: 3.813A pdb=" N GLU D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA D 179 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 200 removed outlier: 3.670A pdb=" N LYS D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG D 197 " --> pdb=" O SER D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 217 removed outlier: 3.721A pdb=" N GLU D 210 " --> pdb=" O ARG D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 238 removed outlier: 3.541A pdb=" N ARG D 226 " --> pdb=" O THR D 222 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TYR D 227 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE D 228 " --> pdb=" O PRO D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 252 Proline residue: D 249 - end of helix Processing helix chain 'D' and resid 256 through 270 Processing helix chain 'D' and resid 272 through 279 removed outlier: 3.764A pdb=" N LEU D 279 " --> pdb=" O PHE D 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 20 Processing helix chain 'G' and resid 21 through 39 removed outlier: 3.508A pdb=" N GLU G 30 " --> pdb=" O ARG G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 57 removed outlier: 3.537A pdb=" N PHE G 57 " --> pdb=" O THR G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 78 removed outlier: 3.819A pdb=" N ALA G 66 " --> pdb=" O ASN G 62 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 92 Processing helix chain 'G' and resid 94 through 106 Processing helix chain 'G' and resid 109 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 141 through 160 removed outlier: 3.608A pdb=" N THR G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 180 removed outlier: 3.550A pdb=" N LEU G 174 " --> pdb=" O ARG G 170 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE G 177 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU G 178 " --> pdb=" O LEU G 174 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA G 179 " --> pdb=" O LEU G 175 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS G 180 " --> pdb=" O ALA G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 200 removed outlier: 3.850A pdb=" N SER G 190 " --> pdb=" O SER G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 217 removed outlier: 3.568A pdb=" N GLU G 210 " --> pdb=" O ARG G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 238 removed outlier: 3.797A pdb=" N ARG G 226 " --> pdb=" O THR G 222 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TYR G 227 " --> pdb=" O VAL G 223 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE G 228 " --> pdb=" O PRO G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 252 Proline residue: G 249 - end of helix Processing helix chain 'G' and resid 256 through 270 Processing helix chain 'G' and resid 272 through 280 525 hydrogen bonds defined for protein. 1572 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: 1.01 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2260 1.34 - 1.46: 489 1.46 - 1.57: 3857 1.57 - 1.69: 0 1.69 - 1.80: 6 Bond restraints: 6612 Sorted by residual: bond pdb=" N LEU A 280 " pdb=" CA LEU A 280 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 8.04e-01 bond pdb=" CB VAL G 32 " pdb=" CG1 VAL G 32 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.20e-01 bond pdb=" CG1 ILE A 177 " pdb=" CD1 ILE A 177 " ideal model delta sigma weight residual 1.513 1.483 0.030 3.90e-02 6.57e+02 5.87e-01 bond pdb=" CA GLN D 40 " pdb=" CB GLN D 40 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.21e-02 6.83e+03 5.82e-01 bond pdb=" CB VAL A 32 " pdb=" CG1 VAL A 32 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.15e-01 ... (remaining 6607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 8707 1.36 - 2.72: 175 2.72 - 4.08: 39 4.08 - 5.43: 14 5.43 - 6.79: 5 Bond angle restraints: 8940 Sorted by residual: angle pdb=" C THR G 222 " pdb=" N VAL G 223 " pdb=" CA VAL G 223 " ideal model delta sigma weight residual 120.33 123.06 -2.73 8.00e-01 1.56e+00 1.17e+01 angle pdb=" N PRO A 253 " pdb=" CA PRO A 253 " pdb=" C PRO A 253 " ideal model delta sigma weight residual 112.47 119.26 -6.79 2.06e+00 2.36e-01 1.09e+01 angle pdb=" N PRO G 253 " pdb=" CA PRO G 253 " pdb=" C PRO G 253 " ideal model delta sigma weight residual 112.47 118.47 -6.00 2.06e+00 2.36e-01 8.48e+00 angle pdb=" C VAL G 223 " pdb=" CA VAL G 223 " pdb=" CB VAL G 223 " ideal model delta sigma weight residual 114.00 110.47 3.53 1.31e+00 5.83e-01 7.27e+00 angle pdb=" N PRO D 253 " pdb=" CA PRO D 253 " pdb=" C PRO D 253 " ideal model delta sigma weight residual 112.47 117.66 -5.19 2.06e+00 2.36e-01 6.35e+00 ... (remaining 8935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 3893 16.96 - 33.92: 219 33.92 - 50.88: 62 50.88 - 67.84: 17 67.84 - 84.80: 6 Dihedral angle restraints: 4197 sinusoidal: 1686 harmonic: 2511 Sorted by residual: dihedral pdb=" CA TYR A 252 " pdb=" C TYR A 252 " pdb=" N PRO A 253 " pdb=" CA PRO A 253 " ideal model delta harmonic sigma weight residual -180.00 -151.67 -28.33 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA PRO A 253 " pdb=" C PRO A 253 " pdb=" N GLU A 254 " pdb=" CA GLU A 254 " ideal model delta harmonic sigma weight residual -180.00 -153.36 -26.64 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA TYR G 252 " pdb=" C TYR G 252 " pdb=" N PRO G 253 " pdb=" CA PRO G 253 " ideal model delta harmonic sigma weight residual 180.00 -154.13 -25.87 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 4194 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 864 0.042 - 0.085: 223 0.085 - 0.127: 25 0.127 - 0.170: 5 0.170 - 0.212: 2 Chirality restraints: 1119 Sorted by residual: chirality pdb=" CA PRO A 253 " pdb=" N PRO A 253 " pdb=" C PRO A 253 " pdb=" CB PRO A 253 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA PRO G 253 " pdb=" N PRO G 253 " pdb=" C PRO G 253 " pdb=" CB PRO G 253 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.49e-01 chirality pdb=" CA PRO D 253 " pdb=" N PRO D 253 " pdb=" C PRO D 253 " pdb=" CB PRO D 253 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.63e-01 ... (remaining 1116 not shown) Planarity restraints: 1149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 244 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" C LEU D 244 " 0.032 2.00e-02 2.50e+03 pdb=" O LEU D 244 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU D 245 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 150 " 0.007 2.00e-02 2.50e+03 1.32e-02 1.75e+00 pdb=" C THR D 150 " -0.023 2.00e-02 2.50e+03 pdb=" O THR D 150 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA D 151 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 279 " 0.006 2.00e-02 2.50e+03 1.27e-02 1.63e+00 pdb=" C LEU A 279 " -0.022 2.00e-02 2.50e+03 pdb=" O LEU A 279 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU A 280 " 0.007 2.00e-02 2.50e+03 ... (remaining 1146 not shown) Histogram of nonbonded interaction distances: 2.66 - 3.11: 4922 3.11 - 3.56: 7114 3.56 - 4.00: 8994 4.00 - 4.45: 11918 4.45 - 4.90: 17729 Nonbonded interactions: 50677 Sorted by model distance: nonbonded pdb=" N THR A 43 " pdb=" OG1 THR A 43 " model vdw 2.659 2.496 nonbonded pdb=" C SER A 13 " pdb=" OG SER A 13 " model vdw 2.661 2.616 nonbonded pdb=" C THR A 3 " pdb=" OG1 THR A 3 " model vdw 2.668 2.616 nonbonded pdb=" O ARG A 278 " pdb=" CA LEU A 279 " model vdw 2.672 2.776 nonbonded pdb=" C ILE D 263 " pdb=" CG2 ILE D 263 " model vdw 2.681 2.952 ... (remaining 50672 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } 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: 7.390 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.190 Find NCS groups from input model: 0.100 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6612 Z= 0.155 Angle : 0.565 6.792 8940 Z= 0.310 Chirality : 0.037 0.212 1119 Planarity : 0.003 0.024 1149 Dihedral : 12.768 84.804 2547 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.84 % Favored : 97.04 % Rotamer: Outliers : 3.26 % Allowed : 3.83 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.67 (0.28), residues: 846 helix: 0.94 (0.19), residues: 711 sheet: None (None), residues: 0 loop : -1.91 (0.47), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 70 TYR 0.018 0.002 TYR A 252 PHE 0.014 0.002 PHE G 275 HIS 0.002 0.001 HIS D 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 6612) covalent geometry : angle 0.56547 / 0.31 ( 8940) hydrogen bonds : bond 0.13071 / 8.62 ( 525) hydrogen bonds : angle 4.77019 / 3.46 ( 1572) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.7328 (tp30) cc_final: 0.6958 (tp30) REVERT: A 259 ASP cc_start: 0.7624 (m-30) cc_final: 0.6929 (m-30) REVERT: D 30 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7201 (mm-30) REVERT: D 210 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6688 (mt-10) REVERT: G 45 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7994 (tt) REVERT: G 186 SER cc_start: 0.8666 (t) cc_final: 0.8351 (m) REVERT: G 263 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7289 (mp) outliers start: 23 outliers final: 4 residues processed: 197 average time/residue: 0.1101 time to fit residues: 27.1887 Evaluate side-chains 114 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 274 TYR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 274 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.151189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.115717 restraints weight = 8521.806| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.65 r_work: 0.3307 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6612 Z= 0.166 Angle : 0.609 6.206 8940 Z= 0.315 Chirality : 0.037 0.191 1119 Planarity : 0.004 0.046 1149 Dihedral : 6.127 59.722 929 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.55 % Allowed : 12.06 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.92 (0.29), residues: 846 helix: 1.85 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -2.14 (0.47), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 226 TYR 0.016 0.002 TYR D 277 PHE 0.030 0.003 PHE G 275 HIS 0.002 0.000 HIS G 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 6612) covalent geometry : angle 0.60862 / 0.31 ( 8940) hydrogen bonds : bond 0.04592 / 3.12 ( 525) hydrogen bonds : angle 3.77462 / 2.75 ( 1572) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8223 (tp30) cc_final: 0.7793 (tp30) REVERT: A 147 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8072 (tp) REVERT: A 210 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7221 (tt0) REVERT: A 259 ASP cc_start: 0.8307 (m-30) cc_final: 0.7752 (m-30) REVERT: G 45 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8387 (tt) REVERT: G 221 ASP cc_start: 0.6121 (m-30) cc_final: 0.5672 (p0) REVERT: G 259 ASP cc_start: 0.8191 (m-30) cc_final: 0.7590 (m-30) REVERT: G 263 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7422 (mp) outliers start: 18 outliers final: 5 residues processed: 126 average time/residue: 0.0944 time to fit residues: 15.4829 Evaluate side-chains 100 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 ASP Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 274 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 76 optimal weight: 0.9990 chunk 24 optimal weight: 0.0040 chunk 71 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 64 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.155140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.119854 restraints weight = 8364.823| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.56 r_work: 0.3358 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6612 Z= 0.127 Angle : 0.524 5.480 8940 Z= 0.275 Chirality : 0.036 0.181 1119 Planarity : 0.003 0.032 1149 Dihedral : 5.336 52.170 925 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.70 % Allowed : 12.48 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.29), residues: 846 helix: 2.23 (0.19), residues: 726 sheet: None (None), residues: 0 loop : -2.34 (0.45), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 226 TYR 0.015 0.002 TYR G 277 PHE 0.020 0.002 PHE G 275 HIS 0.001 0.000 HIS A 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 6612) covalent geometry : angle 0.52442 / 0.28 ( 8940) hydrogen bonds : bond 0.03615 / 2.43 ( 525) hydrogen bonds : angle 3.49919 / 2.56 ( 1572) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8269 (tp30) cc_final: 0.7866 (tp30) REVERT: A 76 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8295 (tt) REVERT: A 210 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7156 (tt0) REVERT: D 30 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7705 (mm-30) REVERT: D 119 GLU cc_start: 0.7935 (tp30) cc_final: 0.7530 (mm-30) REVERT: G 45 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8446 (tt) REVERT: G 261 MET cc_start: 0.8233 (mtt) cc_final: 0.7818 (mtt) REVERT: G 263 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7562 (mp) outliers start: 19 outliers final: 11 residues processed: 121 average time/residue: 0.0720 time to fit residues: 11.5495 Evaluate side-chains 100 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 ASP Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 274 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 25 optimal weight: 0.0570 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN D 281 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.153480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116399 restraints weight = 8514.554| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.72 r_work: 0.3300 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6612 Z= 0.137 Angle : 0.539 6.000 8940 Z= 0.277 Chirality : 0.036 0.170 1119 Planarity : 0.003 0.030 1149 Dihedral : 5.287 58.373 925 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.84 % Allowed : 13.19 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.65 (0.29), residues: 846 helix: 2.36 (0.19), residues: 726 sheet: None (None), residues: 0 loop : -2.33 (0.46), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 226 TYR 0.013 0.001 TYR A 277 PHE 0.024 0.002 PHE A 275 HIS 0.001 0.000 HIS G 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 6612) covalent geometry : angle 0.53931 / 0.28 ( 8940) hydrogen bonds : bond 0.03584 / 2.39 ( 525) hydrogen bonds : angle 3.47895 / 2.55 ( 1572) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8204 (tp30) cc_final: 0.7770 (tp30) REVERT: A 76 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8094 (tt) REVERT: A 128 GLU cc_start: 0.8158 (mp0) cc_final: 0.7943 (pm20) REVERT: A 147 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8178 (tp) REVERT: A 210 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7126 (tt0) REVERT: D 30 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7681 (mm-30) REVERT: D 181 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.7023 (m-30) REVERT: G 45 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8360 (tt) REVERT: G 261 MET cc_start: 0.8325 (mtt) cc_final: 0.7882 (mtt) REVERT: G 263 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7475 (mp) outliers start: 20 outliers final: 9 residues processed: 111 average time/residue: 0.0804 time to fit residues: 12.0028 Evaluate side-chains 103 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 274 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 80 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 25 optimal weight: 0.0870 chunk 83 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.153261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116010 restraints weight = 8593.997| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.73 r_work: 0.3296 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6612 Z= 0.139 Angle : 0.544 6.219 8940 Z= 0.280 Chirality : 0.036 0.168 1119 Planarity : 0.003 0.028 1149 Dihedral : 5.219 59.743 925 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.83 % Allowed : 13.19 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.66 (0.30), residues: 846 helix: 2.35 (0.19), residues: 732 sheet: None (None), residues: 0 loop : -2.42 (0.45), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 226 TYR 0.019 0.002 TYR A 277 PHE 0.032 0.002 PHE G 275 HIS 0.001 0.000 HIS G 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 6612) covalent geometry : angle 0.54406 / 0.28 ( 8940) hydrogen bonds : bond 0.03574 / 2.37 ( 525) hydrogen bonds : angle 3.47902 / 2.55 ( 1572) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8264 (tp30) cc_final: 0.7843 (tp30) REVERT: A 100 GLU cc_start: 0.7887 (pt0) cc_final: 0.7210 (mm-30) REVERT: A 147 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8177 (tp) REVERT: A 210 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7216 (tt0) REVERT: D 119 GLU cc_start: 0.7947 (tp30) cc_final: 0.7739 (mm-30) REVERT: D 181 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.7073 (m-30) REVERT: G 45 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8334 (tt) REVERT: G 261 MET cc_start: 0.8315 (mtt) cc_final: 0.7890 (mtt) REVERT: G 263 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7476 (mp) outliers start: 27 outliers final: 13 residues processed: 115 average time/residue: 0.0810 time to fit residues: 12.7699 Evaluate side-chains 101 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 ASP Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 274 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 28 optimal weight: 0.1980 chunk 53 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN D 281 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.152731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115677 restraints weight = 8510.154| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.72 r_work: 0.3294 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6612 Z= 0.142 Angle : 0.562 6.936 8940 Z= 0.288 Chirality : 0.037 0.216 1119 Planarity : 0.003 0.027 1149 Dihedral : 5.108 56.059 925 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.98 % Allowed : 14.75 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.68 (0.30), residues: 846 helix: 2.34 (0.19), residues: 735 sheet: None (None), residues: 0 loop : -2.37 (0.47), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 226 TYR 0.018 0.002 TYR G 277 PHE 0.034 0.003 PHE G 275 HIS 0.001 0.000 HIS G 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 ( 6612) covalent geometry : angle 0.56227 / 0.29 ( 8940) hydrogen bonds : bond 0.03616 / 2.40 ( 525) hydrogen bonds : angle 3.55759 / 2.60 ( 1572) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8267 (tp30) cc_final: 0.7872 (tp30) REVERT: A 100 GLU cc_start: 0.7886 (pt0) cc_final: 0.7539 (mm-30) REVERT: A 147 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8186 (tp) REVERT: A 210 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7241 (tt0) REVERT: D 90 ARG cc_start: 0.6502 (ptp-170) cc_final: 0.6165 (ptp-170) REVERT: D 119 GLU cc_start: 0.7978 (tp30) cc_final: 0.7555 (tp30) REVERT: D 181 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7113 (m-30) REVERT: D 257 ILE cc_start: 0.6573 (OUTLIER) cc_final: 0.6032 (mm) REVERT: G 45 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8337 (tt) REVERT: G 261 MET cc_start: 0.8302 (mtt) cc_final: 0.7862 (mtt) REVERT: G 263 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7488 (mp) outliers start: 21 outliers final: 13 residues processed: 108 average time/residue: 0.0778 time to fit residues: 11.7169 Evaluate side-chains 103 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 ASP Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 281 GLN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 274 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 77 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 56 optimal weight: 0.0270 chunk 24 optimal weight: 0.2980 chunk 37 optimal weight: 0.2980 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.154682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117486 restraints weight = 8442.506| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.73 r_work: 0.3322 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6612 Z= 0.123 Angle : 0.560 6.562 8940 Z= 0.295 Chirality : 0.037 0.204 1119 Planarity : 0.003 0.029 1149 Dihedral : 5.012 55.483 925 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.55 % Allowed : 15.46 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.82 (0.29), residues: 846 helix: 2.43 (0.19), residues: 735 sheet: None (None), residues: 0 loop : -2.29 (0.47), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 90 TYR 0.011 0.001 TYR A 277 PHE 0.035 0.002 PHE G 275 HIS 0.001 0.000 HIS G 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 6612) covalent geometry : angle 0.56005 / 0.30 ( 8940) hydrogen bonds : bond 0.03411 / 2.24 ( 525) hydrogen bonds : angle 3.44399 / 2.52 ( 1572) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8285 (tp30) cc_final: 0.7895 (tp30) REVERT: A 147 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8189 (tp) REVERT: A 210 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7179 (tt0) REVERT: D 30 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7772 (mm-30) REVERT: D 181 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.7210 (m-30) REVERT: D 240 ASP cc_start: 0.8170 (t0) cc_final: 0.7834 (p0) REVERT: G 45 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8308 (tt) REVERT: G 261 MET cc_start: 0.8265 (mtt) cc_final: 0.7855 (mtt) REVERT: G 263 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7510 (mp) outliers start: 18 outliers final: 9 residues processed: 104 average time/residue: 0.0700 time to fit residues: 10.3462 Evaluate side-chains 102 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 ASP Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 274 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 72 optimal weight: 0.1980 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN D 281 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.153118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.116120 restraints weight = 8476.965| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.75 r_work: 0.3295 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6612 Z= 0.142 Angle : 0.577 7.156 8940 Z= 0.299 Chirality : 0.037 0.159 1119 Planarity : 0.003 0.028 1149 Dihedral : 4.969 54.620 925 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.70 % Allowed : 15.32 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.80 (0.29), residues: 846 helix: 2.41 (0.19), residues: 735 sheet: None (None), residues: 0 loop : -2.25 (0.49), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 90 TYR 0.024 0.002 TYR D 277 PHE 0.034 0.002 PHE G 275 HIS 0.001 0.000 HIS G 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 ( 6612) covalent geometry : angle 0.57660 / 0.30 ( 8940) hydrogen bonds : bond 0.03633 / 2.40 ( 525) hydrogen bonds : angle 3.52278 / 2.57 ( 1572) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8273 (tp30) cc_final: 0.7879 (tp30) REVERT: A 147 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8132 (tp) REVERT: A 210 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7213 (tt0) REVERT: D 68 GLN cc_start: 0.7355 (tt0) cc_final: 0.7133 (tt0) REVERT: D 181 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7241 (m-30) REVERT: D 240 ASP cc_start: 0.8198 (t0) cc_final: 0.7797 (p0) REVERT: G 45 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8281 (tt) REVERT: G 261 MET cc_start: 0.8324 (mtt) cc_final: 0.7877 (mtt) REVERT: G 263 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7411 (mp) outliers start: 19 outliers final: 10 residues processed: 103 average time/residue: 0.0698 time to fit residues: 10.2213 Evaluate side-chains 102 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 ASP Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 274 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.152631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.115418 restraints weight = 8534.456| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.75 r_work: 0.3292 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6612 Z= 0.154 Angle : 0.592 7.781 8940 Z= 0.308 Chirality : 0.037 0.160 1119 Planarity : 0.003 0.026 1149 Dihedral : 4.967 54.106 925 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.55 % Allowed : 15.46 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.77 (0.30), residues: 846 helix: 2.40 (0.19), residues: 732 sheet: None (None), residues: 0 loop : -2.20 (0.49), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 90 TYR 0.021 0.002 TYR D 277 PHE 0.031 0.002 PHE G 275 HIS 0.001 0.000 HIS G 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.15 ( 6612) covalent geometry : angle 0.59212 / 0.31 ( 8940) hydrogen bonds : bond 0.03749 / 2.48 ( 525) hydrogen bonds : angle 3.58262 / 2.62 ( 1572) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8276 (tp30) cc_final: 0.7893 (tp30) REVERT: A 87 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7931 (mm-30) REVERT: A 147 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8108 (tp) REVERT: A 210 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7219 (tt0) REVERT: D 68 GLN cc_start: 0.7279 (tt0) cc_final: 0.7035 (tt0) REVERT: D 119 GLU cc_start: 0.7988 (tp30) cc_final: 0.7567 (tp30) REVERT: D 181 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7268 (m-30) REVERT: D 240 ASP cc_start: 0.8182 (t0) cc_final: 0.7766 (p0) REVERT: G 45 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8283 (tt) REVERT: G 261 MET cc_start: 0.8260 (mtt) cc_final: 0.7855 (mtt) REVERT: G 263 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7433 (mp) outliers start: 18 outliers final: 10 residues processed: 97 average time/residue: 0.0735 time to fit residues: 9.9802 Evaluate side-chains 97 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 ASP Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 274 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 68 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 75 optimal weight: 0.6980 chunk 83 optimal weight: 0.0020 chunk 36 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.153386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116362 restraints weight = 8482.548| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.75 r_work: 0.3304 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6612 Z= 0.133 Angle : 0.584 7.839 8940 Z= 0.303 Chirality : 0.037 0.162 1119 Planarity : 0.003 0.028 1149 Dihedral : 4.918 54.244 925 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.99 % Allowed : 16.31 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.83 (0.29), residues: 846 helix: 2.44 (0.19), residues: 732 sheet: None (None), residues: 0 loop : -2.22 (0.49), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 90 TYR 0.021 0.002 TYR D 277 PHE 0.042 0.002 PHE G 275 HIS 0.001 0.000 HIS G 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 6612) covalent geometry : angle 0.58368 / 0.30 ( 8940) hydrogen bonds : bond 0.03554 / 2.35 ( 525) hydrogen bonds : angle 3.60783 / 2.65 ( 1572) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.8280 (tp30) cc_final: 0.7895 (tp30) REVERT: A 87 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7867 (mm-30) REVERT: A 147 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8112 (tp) REVERT: A 210 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7189 (tt0) REVERT: D 206 ARG cc_start: 0.7873 (ttm170) cc_final: 0.7650 (mtm180) REVERT: D 240 ASP cc_start: 0.8161 (t0) cc_final: 0.7642 (p0) REVERT: G 45 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8256 (tt) REVERT: G 261 MET cc_start: 0.8280 (mtt) cc_final: 0.7829 (mtt) REVERT: G 263 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7336 (mp) outliers start: 14 outliers final: 9 residues processed: 94 average time/residue: 0.0728 time to fit residues: 9.7061 Evaluate side-chains 96 residues out of total 705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 ASP Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 274 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 83 optimal weight: 0.0070 chunk 65 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 0.0670 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 68 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 = 0.3941 r_free = 0.3941 target = 0.154240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.117237 restraints weight = 8474.728| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.76 r_work: 0.3313 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6612 Z= 0.128 Angle : 0.568 7.589 8940 Z= 0.296 Chirality : 0.037 0.155 1119 Planarity : 0.003 0.029 1149 Dihedral : 4.843 53.915 925 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.13 % Allowed : 16.60 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.83 (0.29), residues: 846 helix: 2.46 (0.19), residues: 732 sheet: None (None), residues: 0 loop : -2.29 (0.48), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 90 TYR 0.021 0.002 TYR D 277 PHE 0.044 0.002 PHE G 275 HIS 0.001 0.000 HIS G 270 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 6612) covalent geometry : angle 0.56794 / 0.30 ( 8940) hydrogen bonds : bond 0.03456 / 2.28 ( 525) hydrogen bonds : angle 3.60449 / 2.65 ( 1572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1737.31 seconds wall clock time: 30 minutes 58.27 seconds (1858.27 seconds total)