Starting phenix.real_space_refine on Tue Aug 4 19:33:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vu6_63963/08_2026/9vu6_63963.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vu6_63963/08_2026/9vu6_63963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vu6_63963/08_2026/9vu6_63963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vu6_63963/08_2026/9vu6_63963.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vu6_63963/08_2026/9vu6_63963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vu6_63963/08_2026/9vu6_63963.map" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.085 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 44 5.49 5 S 24 5.16 5 C 3840 2.51 5 N 1065 2.21 5 O 1275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6248 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1832 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain breaks: 1 Chain: "B" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2150 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 10, 'TRANS': 249} Chain breaks: 1 Chain: "C" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 278 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "D" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1059 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "E" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 460 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "F" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 442 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Time building chain proxies: 1.41, per 1000 atoms: 0.23 Number of scatterers: 6248 At special positions: 0 Unit cell: (90.4932, 95.8797, 116.348, 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 24 16.00 P 44 15.00 O 1275 8.00 N 1065 7.00 C 3840 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: 0.37 Conformation dependent library (CDL) restraints added in 290.8 milliseconds 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1230 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 2 sheets defined 40.2% alpha, 13.1% beta 21 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 135 through 166 Processing helix chain 'A' and resid 187 through 199 removed outlier: 4.248A pdb=" N LEU A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.598A pdb=" N MET A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 243 removed outlier: 3.613A pdb=" N LEU A 243 " --> pdb=" O PRO A 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 239 through 243' Processing helix chain 'A' and resid 258 through 269 removed outlier: 3.751A pdb=" N GLY A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 removed outlier: 3.521A pdb=" N GLN A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 110 through 116 removed outlier: 4.301A pdb=" N LEU B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 147 Processing helix chain 'B' and resid 163 through 174 Processing helix chain 'B' and resid 201 through 209 Processing helix chain 'B' and resid 216 through 220 removed outlier: 4.013A pdb=" N ASP B 219 " --> pdb=" O TYR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 Processing helix chain 'B' and resid 288 through 291 Processing helix chain 'C' and resid 153 through 157 Processing helix chain 'C' and resid 162 through 184 Processing helix chain 'D' and resid 13 through 25 removed outlier: 4.263A pdb=" N TYR D 17 " --> pdb=" O ASP D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 43 removed outlier: 4.048A pdb=" N PHE D 42 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 43 " --> pdb=" O HIS D 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 38 through 43' Processing helix chain 'D' and resid 51 through 62 Processing helix chain 'D' and resid 69 through 76 removed outlier: 3.981A pdb=" N ILE D 73 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP D 76 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 96 removed outlier: 3.944A pdb=" N CYS D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N MET D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE D 94 " --> pdb=" O ARG D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 removed outlier: 3.896A pdb=" N TYR D 104 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 127 Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 180 removed outlier: 3.682A pdb=" N ILE A 179 " --> pdb=" O SER A 367 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU A 352 " --> pdb=" O PHE A 203 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL A 205 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE A 354 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N MET A 207 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASP A 204 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 274 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL A 306 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU A 272 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ILE A 324 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR A 277 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N SER A 326 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N VAL A 279 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 72 through 73 removed outlier: 6.771A pdb=" N LYS B 72 " --> pdb=" O SER B 319 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N MET B 303 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA B 93 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU B 305 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE B 95 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N SER B 92 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N PHE B 130 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU B 94 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N TRP B 132 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ILE B 96 " --> pdb=" O TRP B 132 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE B 235 " --> pdb=" O SER B 133 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU B 236 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN B 155 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N MET B 238 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 9.428A pdb=" N PHE B 259 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N MET B 157 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ASP B 261 " --> pdb=" O MET B 157 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ASN B 159 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE B 263 " --> pdb=" O ASN B 159 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU B 161 " --> pdb=" O PHE B 263 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 528 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1772 1.34 - 1.46: 1415 1.46 - 1.58: 3142 1.58 - 1.70: 86 1.70 - 1.82: 42 Bond restraints: 6457 Sorted by residual: bond pdb=" C1' DC F 12 " pdb=" N1 DC F 12 " ideal model delta sigma weight residual 1.468 1.522 -0.054 1.40e-02 5.10e+03 1.47e+01 bond pdb=" C3' DC F 20 " pdb=" C2' DC F 20 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DA E 12 " pdb=" C2' DA E 12 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.42e+00 bond pdb=" C3' DA F 19 " pdb=" C2' DA F 19 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.38e+00 bond pdb=" C3' DA E 14 " pdb=" C2' DA E 14 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.04e+00 ... (remaining 6452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 8784 3.65 - 7.30: 78 7.30 - 10.94: 8 10.94 - 14.59: 0 14.59 - 18.24: 1 Bond angle restraints: 8871 Sorted by residual: angle pdb=" N ASN B 125 " pdb=" CA ASN B 125 " pdb=" C ASN B 125 " ideal model delta sigma weight residual 113.43 106.81 6.62 1.26e+00 6.30e-01 2.76e+01 angle pdb=" CA LEU C 173 " pdb=" CB LEU C 173 " pdb=" CG LEU C 173 " ideal model delta sigma weight residual 116.30 134.54 -18.24 3.50e+00 8.16e-02 2.72e+01 angle pdb=" N ASN D 133 " pdb=" CA ASN D 133 " pdb=" CB ASN D 133 " ideal model delta sigma weight residual 114.17 108.46 5.71 1.14e+00 7.69e-01 2.51e+01 angle pdb=" CA ILE A 276 " pdb=" CB ILE A 276 " pdb=" CG1 ILE A 276 " ideal model delta sigma weight residual 110.40 118.42 -8.02 1.70e+00 3.46e-01 2.23e+01 angle pdb=" N3 DT E 17 " pdb=" C4 DT E 17 " pdb=" O4 DT E 17 " ideal model delta sigma weight residual 119.90 122.72 -2.82 6.00e-01 2.78e+00 2.20e+01 ... (remaining 8866 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.47: 3355 30.47 - 60.94: 460 60.94 - 91.42: 41 91.42 - 121.89: 0 121.89 - 152.36: 2 Dihedral angle restraints: 3858 sinusoidal: 1963 harmonic: 1895 Sorted by residual: dihedral pdb=" CA VAL A 366 " pdb=" C VAL A 366 " pdb=" N SER A 367 " pdb=" CA SER A 367 " ideal model delta harmonic sigma weight residual 180.00 -155.95 -24.05 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ASP D 13 " pdb=" C ASP D 13 " pdb=" N PHE D 14 " pdb=" CA PHE D 14 " ideal model delta harmonic sigma weight residual -180.00 -157.24 -22.76 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA HIS B 252 " pdb=" C HIS B 252 " pdb=" N GLN B 253 " pdb=" CA GLN B 253 " ideal model delta harmonic sigma weight residual -180.00 -157.54 -22.46 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 3855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 627 0.044 - 0.087: 251 0.087 - 0.131: 60 0.131 - 0.174: 11 0.174 - 0.218: 3 Chirality restraints: 952 Sorted by residual: chirality pdb=" CG LEU C 173 " pdb=" CB LEU C 173 " pdb=" CD1 LEU C 173 " pdb=" CD2 LEU C 173 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ASN D 128 " pdb=" N ASN D 128 " pdb=" C ASN D 128 " pdb=" CB ASN D 128 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" C3' DA F 13 " pdb=" C4' DA F 13 " pdb=" O3' DA F 13 " pdb=" C2' DA F 13 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.91e-01 ... (remaining 949 not shown) Planarity restraints: 986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 70 " -0.017 2.00e-02 2.50e+03 1.72e-02 7.40e+00 pdb=" CG TRP D 70 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP D 70 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP D 70 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 70 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 70 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 70 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 70 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 70 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 70 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 193 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" CG ASP A 193 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP A 193 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP A 193 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 13 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" CG ASP D 13 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASP D 13 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP D 13 " -0.013 2.00e-02 2.50e+03 ... (remaining 983 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 572 2.74 - 3.28: 6031 3.28 - 3.82: 10659 3.82 - 4.36: 12682 4.36 - 4.90: 20392 Nonbonded interactions: 50336 Sorted by model distance: nonbonded pdb=" OG SER B 110 " pdb=" OE1 GLU B 112 " model vdw 2.203 3.040 nonbonded pdb=" NE2 HIS A 198 " pdb=" OD2 ASP D 24 " model vdw 2.266 3.120 nonbonded pdb=" O CYS A 346 " pdb=" OH TYR A 351 " model vdw 2.271 3.040 nonbonded pdb=" O ASP A 174 " pdb=" NH2 ARG D 22 " model vdw 2.285 3.120 nonbonded pdb=" N THR C 152 " pdb=" OD1 ASP C 155 " model vdw 2.300 3.120 ... (remaining 50331 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.900 Find NCS groups from input model: 0.030 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 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 : 0.005 0.080 6457 Z= 0.346 Angle : 0.925 18.238 8871 Z= 0.600 Chirality : 0.050 0.218 952 Planarity : 0.005 0.076 986 Dihedral : 24.310 152.358 2628 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.29 % Favored : 90.55 % Rotamer: Outliers : 3.24 % Allowed : 37.65 % Favored : 59.11 % 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: -2.41 (0.31), residues: 635 helix: -0.99 (0.31), residues: 226 sheet: -1.61 (0.52), residues: 98 loop : -2.02 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 197 TYR 0.020 0.002 TYR D 103 PHE 0.030 0.002 PHE B 130 TRP 0.046 0.002 TRP D 70 HIS 0.002 0.001 HIS D 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.35 ( 6457) covalent geometry : angle 0.92509 / 0.60 ( 8871) hydrogen bonds : bond 0.15331 / 9.64 ( 230) hydrogen bonds : angle 6.56896 / 4.86 ( 620) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: B 71 TYR cc_start: 0.7837 (p90) cc_final: 0.7440 (p90) REVERT: B 276 MET cc_start: 0.5133 (OUTLIER) cc_final: 0.3937 (mmt) REVERT: D 56 LYS cc_start: 0.8950 (mmmm) cc_final: 0.8561 (mmtm) REVERT: D 70 TRP cc_start: 0.6355 (m100) cc_final: 0.5801 (m100) REVERT: D 73 ILE cc_start: 0.5499 (OUTLIER) cc_final: 0.4912 (tp) REVERT: D 88 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: D 111 GLU cc_start: 0.8720 (pm20) cc_final: 0.8406 (pm20) REVERT: D 115 GLU cc_start: 0.8658 (tp30) cc_final: 0.8323 (tm-30) outliers start: 19 outliers final: 14 residues processed: 122 average time/residue: 0.0872 time to fit residues: 13.8792 Evaluate side-chains 120 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 40.0000 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.1980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 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 = 0.4511 r_free = 0.4511 target = 0.212359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.166986 restraints weight = 7794.878| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 2.56 r_work: 0.3794 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6457 Z= 0.153 Angle : 0.712 14.581 8871 Z= 0.386 Chirality : 0.047 0.255 952 Planarity : 0.004 0.068 986 Dihedral : 23.800 157.310 1258 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 5.62 % Allowed : 32.71 % Favored : 61.67 % 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: -1.93 (0.33), residues: 635 helix: -0.40 (0.32), residues: 234 sheet: -1.46 (0.53), residues: 98 loop : -1.90 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 197 TYR 0.012 0.001 TYR B 152 PHE 0.013 0.001 PHE B 259 TRP 0.013 0.001 TRP D 70 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 6457) covalent geometry : angle 0.71208 / 0.39 ( 8871) hydrogen bonds : bond 0.06307 / 3.93 ( 230) hydrogen bonds : angle 5.03103 / 3.67 ( 620) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.243 Fit side-chains REVERT: A 257 LYS cc_start: 0.7425 (mmtm) cc_final: 0.7154 (mmmm) REVERT: B 71 TYR cc_start: 0.7930 (p90) cc_final: 0.7421 (p90) REVERT: C 172 ASN cc_start: 0.8505 (m110) cc_final: 0.8303 (m110) REVERT: C 180 ARG cc_start: 0.7959 (tmm-80) cc_final: 0.7655 (tmm-80) REVERT: D 32 LEU cc_start: 0.7306 (mp) cc_final: 0.6948 (mt) REVERT: D 41 TYR cc_start: 0.7944 (t80) cc_final: 0.7623 (t80) REVERT: D 56 LYS cc_start: 0.9117 (mmmm) cc_final: 0.8657 (mmtm) REVERT: D 73 ILE cc_start: 0.5360 (OUTLIER) cc_final: 0.4884 (tp) REVERT: D 102 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.5792 (pm20) REVERT: D 111 GLU cc_start: 0.8681 (pm20) cc_final: 0.8372 (pm20) REVERT: D 112 GLU cc_start: 0.8831 (mp0) cc_final: 0.8038 (mp0) REVERT: D 115 GLU cc_start: 0.8539 (tp30) cc_final: 0.8263 (tm-30) REVERT: D 116 ILE cc_start: 0.7897 (pt) cc_final: 0.7350 (tp) outliers start: 33 outliers final: 14 residues processed: 140 average time/residue: 0.0834 time to fit residues: 15.3269 Evaluate side-chains 126 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.208182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.161246 restraints weight = 7768.884| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.49 r_work: 0.3742 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6457 Z= 0.201 Angle : 0.710 7.282 8871 Z= 0.391 Chirality : 0.047 0.219 952 Planarity : 0.004 0.051 986 Dihedral : 23.916 156.395 1238 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 6.98 % Allowed : 31.86 % Favored : 61.16 % 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: -1.99 (0.33), residues: 635 helix: -0.36 (0.33), residues: 234 sheet: -1.76 (0.50), residues: 98 loop : -1.91 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 180 TYR 0.017 0.002 TYR D 103 PHE 0.018 0.002 PHE A 250 TRP 0.017 0.002 TRP D 70 HIS 0.005 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 ( 6457) covalent geometry : angle 0.70995 / 0.39 ( 8871) hydrogen bonds : bond 0.06146 / 3.82 ( 230) hydrogen bonds : angle 4.94617 / 3.59 ( 620) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 109 time to evaluate : 0.223 Fit side-chains REVERT: A 257 LYS cc_start: 0.7478 (mmtm) cc_final: 0.7204 (mmmm) REVERT: A 275 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6284 (mt-10) REVERT: B 71 TYR cc_start: 0.7971 (p90) cc_final: 0.7421 (p90) REVERT: B 77 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6985 (pmmt) REVERT: B 116 LYS cc_start: 0.7572 (mmmt) cc_final: 0.7057 (tptp) REVERT: B 153 ILE cc_start: 0.6358 (OUTLIER) cc_final: 0.5990 (pp) REVERT: B 236 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7571 (mp) REVERT: D 56 LYS cc_start: 0.9131 (mmmm) cc_final: 0.8396 (mmtm) REVERT: D 60 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8067 (ptp-170) REVERT: D 73 ILE cc_start: 0.5312 (OUTLIER) cc_final: 0.4760 (tp) REVERT: D 88 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6900 (mt-10) REVERT: D 102 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.5775 (pm20) REVERT: D 116 ILE cc_start: 0.7809 (pt) cc_final: 0.7429 (tp) outliers start: 41 outliers final: 20 residues processed: 131 average time/residue: 0.0934 time to fit residues: 15.8913 Evaluate side-chains 132 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 13 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 65 optimal weight: 40.0000 chunk 11 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 HIS B 126 ASN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.210615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.162992 restraints weight = 7811.285| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 2.48 r_work: 0.3760 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6457 Z= 0.158 Angle : 0.674 11.911 8871 Z= 0.372 Chirality : 0.045 0.225 952 Planarity : 0.004 0.045 986 Dihedral : 23.877 157.641 1232 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 6.30 % Allowed : 31.18 % Favored : 62.52 % 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: -1.84 (0.33), residues: 635 helix: -0.18 (0.33), residues: 234 sheet: -1.71 (0.51), residues: 98 loop : -1.87 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 180 TYR 0.016 0.001 TYR D 103 PHE 0.013 0.001 PHE A 250 TRP 0.010 0.001 TRP D 70 HIS 0.004 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 6457) covalent geometry : angle 0.67366 / 0.37 ( 8871) hydrogen bonds : bond 0.05555 / 3.43 ( 230) hydrogen bonds : angle 4.82642 / 3.51 ( 620) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 0.130 Fit side-chains REVERT: A 257 LYS cc_start: 0.7472 (mmtm) cc_final: 0.7201 (mmmm) REVERT: A 275 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.6031 (mt-10) REVERT: B 71 TYR cc_start: 0.7937 (p90) cc_final: 0.7372 (p90) REVERT: B 77 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6928 (pmmt) REVERT: B 116 LYS cc_start: 0.7606 (mmmt) cc_final: 0.7084 (tptp) REVERT: B 153 ILE cc_start: 0.6306 (OUTLIER) cc_final: 0.5972 (pp) REVERT: C 174 LYS cc_start: 0.8173 (ptpp) cc_final: 0.7874 (ptpp) REVERT: D 25 LEU cc_start: 0.5629 (OUTLIER) cc_final: 0.5241 (pp) REVERT: D 56 LYS cc_start: 0.9123 (mmmm) cc_final: 0.8388 (mmtm) REVERT: D 60 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8060 (ptp-170) REVERT: D 73 ILE cc_start: 0.5326 (OUTLIER) cc_final: 0.4785 (tp) REVERT: D 88 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6830 (mt-10) REVERT: D 102 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.5719 (pm20) REVERT: D 116 ILE cc_start: 0.7826 (pt) cc_final: 0.7461 (tp) outliers start: 37 outliers final: 19 residues processed: 132 average time/residue: 0.0807 time to fit residues: 13.8241 Evaluate side-chains 129 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 47 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 3 optimal weight: 0.0060 chunk 60 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 0.0070 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 63 optimal weight: 30.0000 chunk 57 optimal weight: 8.9990 overall best weight: 0.6216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 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 = 0.4502 r_free = 0.4502 target = 0.210978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.163225 restraints weight = 7828.840| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.47 r_work: 0.3772 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6457 Z= 0.150 Angle : 0.667 11.334 8871 Z= 0.368 Chirality : 0.046 0.226 952 Planarity : 0.004 0.054 986 Dihedral : 23.821 157.759 1230 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 5.79 % Allowed : 31.35 % Favored : 62.86 % 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: -1.72 (0.33), residues: 635 helix: -0.06 (0.33), residues: 234 sheet: -1.63 (0.52), residues: 98 loop : -1.83 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.019 0.001 TYR D 103 PHE 0.013 0.001 PHE A 250 TRP 0.008 0.001 TRP D 70 HIS 0.004 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 6457) covalent geometry : angle 0.66703 / 0.37 ( 8871) hydrogen bonds : bond 0.05276 / 3.26 ( 230) hydrogen bonds : angle 4.74964 / 3.46 ( 620) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 257 LYS cc_start: 0.7457 (mmtm) cc_final: 0.7204 (mmmm) REVERT: A 275 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6025 (mt-10) REVERT: B 66 THR cc_start: 0.8281 (m) cc_final: 0.8039 (p) REVERT: B 71 TYR cc_start: 0.7919 (p90) cc_final: 0.7360 (p90) REVERT: B 77 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6896 (pmmt) REVERT: B 116 LYS cc_start: 0.7581 (mmmt) cc_final: 0.7161 (tptp) REVERT: B 153 ILE cc_start: 0.6346 (OUTLIER) cc_final: 0.6018 (pp) REVERT: D 56 LYS cc_start: 0.9111 (mmmm) cc_final: 0.8357 (mmtm) REVERT: D 60 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8028 (ptp-170) REVERT: D 73 ILE cc_start: 0.5303 (OUTLIER) cc_final: 0.4758 (tp) REVERT: D 88 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6768 (mt-10) REVERT: D 102 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.5633 (pm20) REVERT: D 106 LYS cc_start: 0.6474 (pttm) cc_final: 0.5972 (pptt) REVERT: D 116 ILE cc_start: 0.7805 (pt) cc_final: 0.7465 (tp) outliers start: 34 outliers final: 20 residues processed: 126 average time/residue: 0.0856 time to fit residues: 14.0487 Evaluate side-chains 130 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 60 optimal weight: 0.0020 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 30.0000 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS ** D 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.209477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.161871 restraints weight = 7826.577| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 2.43 r_work: 0.3750 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6457 Z= 0.168 Angle : 0.677 10.409 8871 Z= 0.372 Chirality : 0.046 0.210 952 Planarity : 0.004 0.057 986 Dihedral : 23.791 157.444 1230 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 7.16 % Allowed : 30.49 % Favored : 62.35 % 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: -1.76 (0.33), residues: 635 helix: -0.01 (0.33), residues: 235 sheet: -1.82 (0.50), residues: 98 loop : -1.85 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.013 0.001 TYR D 103 PHE 0.016 0.001 PHE A 250 TRP 0.007 0.001 TRP D 70 HIS 0.003 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 6457) covalent geometry : angle 0.67651 / 0.37 ( 8871) hydrogen bonds : bond 0.05220 / 3.24 ( 230) hydrogen bonds : angle 4.73665 / 3.45 ( 620) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 105 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.5960 (mt-10) REVERT: B 66 THR cc_start: 0.8309 (m) cc_final: 0.8099 (p) REVERT: B 71 TYR cc_start: 0.7957 (p90) cc_final: 0.7440 (p90) REVERT: B 77 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6952 (pmmt) REVERT: B 116 LYS cc_start: 0.7656 (mmmt) cc_final: 0.7243 (tptp) REVERT: B 153 ILE cc_start: 0.6327 (OUTLIER) cc_final: 0.5988 (pp) REVERT: C 184 GLN cc_start: 0.4138 (OUTLIER) cc_final: 0.3812 (pm20) REVERT: D 56 LYS cc_start: 0.9116 (mmmm) cc_final: 0.8344 (mmtm) REVERT: D 60 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8014 (ptp-170) REVERT: D 73 ILE cc_start: 0.5409 (OUTLIER) cc_final: 0.4837 (tp) REVERT: D 88 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6666 (mt-10) REVERT: D 102 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.5644 (pm20) REVERT: D 106 LYS cc_start: 0.6516 (pttm) cc_final: 0.6068 (pptt) REVERT: D 116 ILE cc_start: 0.7810 (pt) cc_final: 0.7465 (tp) outliers start: 42 outliers final: 22 residues processed: 130 average time/residue: 0.0893 time to fit residues: 14.9597 Evaluate side-chains 131 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 GLN B 265 GLN ** D 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.209940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.163174 restraints weight = 7698.437| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.53 r_work: 0.3767 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6457 Z= 0.155 Angle : 0.677 10.923 8871 Z= 0.372 Chirality : 0.045 0.209 952 Planarity : 0.004 0.046 986 Dihedral : 23.765 157.966 1230 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 6.98 % Allowed : 30.49 % Favored : 62.52 % 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: -1.68 (0.33), residues: 635 helix: 0.04 (0.33), residues: 235 sheet: -1.75 (0.50), residues: 98 loop : -1.81 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.009 0.001 TYR B 152 PHE 0.013 0.001 PHE B 259 TRP 0.014 0.001 TRP B 197 HIS 0.001 0.001 HIS A 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 6457) covalent geometry : angle 0.67657 / 0.37 ( 8871) hydrogen bonds : bond 0.04995 / 3.13 ( 230) hydrogen bonds : angle 4.69079 / 3.43 ( 620) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.5902 (mt-10) REVERT: B 66 THR cc_start: 0.8336 (m) cc_final: 0.8112 (p) REVERT: B 71 TYR cc_start: 0.8057 (p90) cc_final: 0.7451 (p90) REVERT: B 77 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6903 (pmmt) REVERT: B 116 LYS cc_start: 0.7650 (mmmt) cc_final: 0.7285 (tptp) REVERT: B 153 ILE cc_start: 0.6346 (OUTLIER) cc_final: 0.6018 (pp) REVERT: B 204 GLN cc_start: 0.7552 (tp-100) cc_final: 0.6826 (tp-100) REVERT: C 184 GLN cc_start: 0.4319 (OUTLIER) cc_final: 0.3968 (pm20) REVERT: D 25 LEU cc_start: 0.5580 (OUTLIER) cc_final: 0.5192 (pp) REVERT: D 56 LYS cc_start: 0.9123 (mmmm) cc_final: 0.8353 (mmtm) REVERT: D 60 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8034 (ptp-170) REVERT: D 73 ILE cc_start: 0.5460 (OUTLIER) cc_final: 0.4865 (tp) REVERT: D 102 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.5693 (pm20) REVERT: D 106 LYS cc_start: 0.6550 (pttm) cc_final: 0.6091 (pptt) REVERT: D 116 ILE cc_start: 0.7795 (pt) cc_final: 0.7451 (tp) outliers start: 41 outliers final: 21 residues processed: 133 average time/residue: 0.0975 time to fit residues: 16.7295 Evaluate side-chains 134 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 265 GLN ** D 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.209318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.162616 restraints weight = 7787.250| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 2.59 r_work: 0.3754 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 6457 Z= 0.175 Angle : 0.699 11.172 8871 Z= 0.382 Chirality : 0.047 0.406 952 Planarity : 0.004 0.043 986 Dihedral : 23.767 157.642 1230 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 5.28 % Allowed : 31.86 % Favored : 62.86 % 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: -1.70 (0.33), residues: 635 helix: 0.07 (0.34), residues: 235 sheet: -1.85 (0.49), residues: 98 loop : -1.83 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.010 0.001 TYR B 152 PHE 0.014 0.001 PHE A 250 TRP 0.014 0.002 TRP B 197 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 ( 6457) covalent geometry : angle 0.69943 / 0.38 ( 8871) hydrogen bonds : bond 0.05011 / 3.15 ( 230) hydrogen bonds : angle 4.71597 / 3.44 ( 620) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.5927 (mt-10) REVERT: B 66 THR cc_start: 0.8340 (m) cc_final: 0.8109 (p) REVERT: B 71 TYR cc_start: 0.8018 (p90) cc_final: 0.7374 (p90) REVERT: B 77 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6935 (pmmt) REVERT: B 116 LYS cc_start: 0.7725 (mmmt) cc_final: 0.7344 (tptp) REVERT: B 153 ILE cc_start: 0.6383 (OUTLIER) cc_final: 0.6048 (pp) REVERT: B 204 GLN cc_start: 0.7600 (tp-100) cc_final: 0.6921 (tp-100) REVERT: B 251 ARG cc_start: 0.7435 (ptp-170) cc_final: 0.7072 (mtm110) REVERT: C 184 GLN cc_start: 0.4337 (OUTLIER) cc_final: 0.3986 (pm20) REVERT: D 25 LEU cc_start: 0.5601 (OUTLIER) cc_final: 0.5198 (pp) REVERT: D 56 LYS cc_start: 0.9118 (mmmm) cc_final: 0.8346 (mmtm) REVERT: D 60 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8026 (ptp-170) REVERT: D 73 ILE cc_start: 0.5453 (OUTLIER) cc_final: 0.4890 (tp) REVERT: D 102 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.5683 (pm20) REVERT: D 106 LYS cc_start: 0.6532 (pttm) cc_final: 0.6096 (pptt) REVERT: D 116 ILE cc_start: 0.7775 (pt) cc_final: 0.7431 (tp) outliers start: 31 outliers final: 20 residues processed: 125 average time/residue: 0.0736 time to fit residues: 11.8838 Evaluate side-chains 132 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 0.0070 chunk 63 optimal weight: 30.0000 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.210676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.163792 restraints weight = 7763.830| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.46 r_work: 0.3783 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 6457 Z= 0.155 Angle : 0.723 18.551 8871 Z= 0.389 Chirality : 0.046 0.338 952 Planarity : 0.004 0.045 986 Dihedral : 23.745 157.966 1230 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 4.60 % Allowed : 32.54 % Favored : 62.86 % 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: -1.66 (0.33), residues: 635 helix: 0.05 (0.34), residues: 235 sheet: -1.73 (0.50), residues: 98 loop : -1.79 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.008 0.001 TYR D 103 PHE 0.013 0.001 PHE B 259 TRP 0.016 0.001 TRP B 197 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 6457) covalent geometry : angle 0.72270 / 0.39 ( 8871) hydrogen bonds : bond 0.04868 / 3.08 ( 230) hydrogen bonds : angle 4.70867 / 3.44 ( 620) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 THR cc_start: 0.8332 (m) cc_final: 0.8113 (p) REVERT: B 71 TYR cc_start: 0.8007 (p90) cc_final: 0.7356 (p90) REVERT: B 77 LYS cc_start: 0.7205 (OUTLIER) cc_final: 0.6912 (pmmt) REVERT: B 116 LYS cc_start: 0.7692 (mmmt) cc_final: 0.7317 (tptp) REVERT: B 153 ILE cc_start: 0.6334 (OUTLIER) cc_final: 0.6007 (pp) REVERT: B 204 GLN cc_start: 0.7576 (tp-100) cc_final: 0.6905 (tp-100) REVERT: B 251 ARG cc_start: 0.7473 (ptp-170) cc_final: 0.7055 (mtm110) REVERT: C 184 GLN cc_start: 0.4295 (OUTLIER) cc_final: 0.3949 (pm20) REVERT: D 56 LYS cc_start: 0.9114 (mmmm) cc_final: 0.8340 (mmtm) REVERT: D 60 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7960 (ptp-170) REVERT: D 73 ILE cc_start: 0.5435 (OUTLIER) cc_final: 0.4911 (tp) REVERT: D 102 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.5751 (pm20) REVERT: D 106 LYS cc_start: 0.6572 (pttm) cc_final: 0.6186 (pptt) REVERT: D 116 ILE cc_start: 0.7772 (pt) cc_final: 0.7432 (tp) outliers start: 27 outliers final: 18 residues processed: 122 average time/residue: 0.0704 time to fit residues: 10.9954 Evaluate side-chains 130 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 21 optimal weight: 0.0980 chunk 62 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 65 optimal weight: 40.0000 chunk 24 optimal weight: 5.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 ASN B 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.207763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.159670 restraints weight = 7748.735| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.48 r_work: 0.3731 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 6457 Z= 0.203 Angle : 0.763 12.271 8871 Z= 0.410 Chirality : 0.049 0.407 952 Planarity : 0.004 0.031 986 Dihedral : 23.803 156.829 1230 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 4.77 % Allowed : 32.71 % Favored : 62.52 % 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: -1.83 (0.33), residues: 635 helix: -0.03 (0.33), residues: 235 sheet: -2.00 (0.49), residues: 98 loop : -1.88 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 180 TYR 0.014 0.002 TYR A 258 PHE 0.015 0.002 PHE A 250 TRP 0.053 0.003 TRP D 70 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 ( 6457) covalent geometry : angle 0.76300 / 0.41 ( 8871) hydrogen bonds : bond 0.05130 / 3.26 ( 230) hydrogen bonds : angle 4.78599 / 3.48 ( 620) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.5857 (mt-10) REVERT: B 66 THR cc_start: 0.8370 (m) cc_final: 0.8144 (p) REVERT: B 71 TYR cc_start: 0.8067 (p90) cc_final: 0.7426 (p90) REVERT: B 77 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6998 (pmmt) REVERT: B 116 LYS cc_start: 0.7732 (mmmt) cc_final: 0.7412 (tptp) REVERT: B 153 ILE cc_start: 0.6382 (OUTLIER) cc_final: 0.6028 (pp) REVERT: B 204 GLN cc_start: 0.7554 (tp-100) cc_final: 0.6913 (tp-100) REVERT: B 251 ARG cc_start: 0.7474 (ptp-170) cc_final: 0.7078 (mtm110) REVERT: B 293 SER cc_start: 0.7135 (p) cc_final: 0.6780 (t) REVERT: C 174 LYS cc_start: 0.7587 (mttt) cc_final: 0.6851 (mttp) REVERT: C 184 GLN cc_start: 0.4303 (OUTLIER) cc_final: 0.3985 (pm20) REVERT: D 56 LYS cc_start: 0.9103 (mmmm) cc_final: 0.8609 (mmtm) REVERT: D 73 ILE cc_start: 0.5636 (OUTLIER) cc_final: 0.5043 (tp) REVERT: D 88 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6645 (mt-10) REVERT: D 102 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.5686 (pm20) REVERT: D 106 LYS cc_start: 0.6707 (pttm) cc_final: 0.6167 (pptt) REVERT: D 116 ILE cc_start: 0.7789 (pt) cc_final: 0.7469 (tp) outliers start: 28 outliers final: 19 residues processed: 126 average time/residue: 0.0673 time to fit residues: 11.0917 Evaluate side-chains 133 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 19 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 63 optimal weight: 30.0000 chunk 31 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.207837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.161178 restraints weight = 7756.247| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.53 r_work: 0.3739 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.376 6457 Z= 0.365 Angle : 1.117 65.900 8871 Z= 0.660 Chirality : 0.048 0.350 952 Planarity : 0.009 0.254 986 Dihedral : 23.805 156.854 1230 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 4.60 % Allowed : 32.54 % Favored : 62.86 % 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: -1.84 (0.33), residues: 635 helix: -0.03 (0.33), residues: 235 sheet: -2.01 (0.49), residues: 98 loop : -1.89 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 180 TYR 0.013 0.001 TYR A 258 PHE 0.015 0.002 PHE A 250 TRP 0.040 0.002 TRP D 70 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00818 / 0.37 ( 6457) covalent geometry : angle 1.11685 / 0.66 ( 8871) hydrogen bonds : bond 0.05118 / 3.26 ( 230) hydrogen bonds : angle 4.78718 / 3.48 ( 620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1618.60 seconds wall clock time: 28 minutes 24.44 seconds (1704.44 seconds total)