Starting phenix.real_space_refine on Tue Feb 3 18:58:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vu6_63963/02_2026/9vu6_63963.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vu6_63963/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9vu6_63963/02_2026/9vu6_63963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vu6_63963/02_2026/9vu6_63963.map" model { file = "/net/cci-nas-00/data/ceres_data/9vu6_63963/02_2026/9vu6_63963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vu6_63963/02_2026/9vu6_63963.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 1.59, per 1000 atoms: 0.25 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: 0.69 Conformation dependent library (CDL) restraints added in 202.1 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: 0.72 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: 1.02 Time building geometry restraints manager: 0.86 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=" CG1 ILE A 150 " pdb=" CD1 ILE A 150 " ideal model delta sigma weight residual 1.513 1.433 0.080 3.90e-02 6.57e+02 4.21e+00 bond pdb=" CB ARG B 171 " pdb=" CG ARG B 171 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.12e+00 bond pdb=" CG ARG B 171 " pdb=" CD ARG B 171 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.50e+00 bond pdb=" CB ASP B 69 " pdb=" CG ASP B 69 " ideal model delta sigma weight residual 1.516 1.553 -0.037 2.50e-02 1.60e+03 2.20e+00 bond pdb=" CB GLN A 144 " pdb=" CG GLN A 144 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.18e+00 ... (remaining 6452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 8788 3.65 - 7.30: 74 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=" CB ARG B 171 " pdb=" CG ARG B 171 " pdb=" CD ARG B 171 " ideal model delta sigma weight residual 111.30 122.02 -10.72 2.30e+00 1.89e-01 2.17e+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: 661 0.044 - 0.087: 226 0.087 - 0.131: 53 0.131 - 0.174: 10 0.174 - 0.218: 2 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=" CB ILE A 319 " pdb=" CA ILE A 319 " pdb=" CG1 ILE A 319 " pdb=" CG2 ILE A 319 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.29e-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: 0.010 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.200 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 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= 0.210 Angle : 0.876 18.238 8871 Z= 0.471 Chirality : 0.047 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 covalent geometry : bond 0.00486 ( 6457) covalent geometry : angle 0.87611 ( 8871) hydrogen bonds : bond 0.15331 ( 230) hydrogen bonds : angle 6.56896 ( 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 : 0.244 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: 0.0849 time to fit residues: 13.5843 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 : 0.242 ------------------------------------------------------------------------------- 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: 5.9990 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4514 r_free = 0.4514 target = 0.212656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.165839 restraints weight = 7745.642| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 2.49 r_work: 0.3801 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6457 Z= 0.148 Angle : 0.658 13.500 8871 Z= 0.358 Chirality : 0.042 0.211 952 Planarity : 0.004 0.064 986 Dihedral : 23.726 154.461 1258 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 5.45 % Allowed : 32.54 % Favored : 62.01 % 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: -1.90 (0.33), residues: 635 helix: -0.31 (0.33), residues: 234 sheet: -1.56 (0.53), residues: 98 loop : -1.89 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 197 TYR 0.012 0.001 TYR B 152 PHE 0.012 0.001 PHE B 259 TRP 0.009 0.001 TRP D 70 HIS 0.002 0.000 HIS C 169 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6457) covalent geometry : angle 0.65776 ( 8871) hydrogen bonds : bond 0.05057 ( 230) hydrogen bonds : angle 4.88201 ( 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 158 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.232 Fit side-chains REVERT: A 202 MET cc_start: 0.5851 (tpt) cc_final: 0.5598 (tpt) REVERT: A 257 LYS cc_start: 0.7406 (mmtm) cc_final: 0.7151 (mmmm) REVERT: A 274 ASP cc_start: 0.8447 (t0) cc_final: 0.8155 (t0) REVERT: A 275 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6420 (mt-10) REVERT: B 71 TYR cc_start: 0.8004 (p90) cc_final: 0.7476 (p90) REVERT: D 32 LEU cc_start: 0.7220 (mp) cc_final: 0.6835 (mt) REVERT: D 41 TYR cc_start: 0.7969 (t80) cc_final: 0.7700 (t80) REVERT: D 73 ILE cc_start: 0.5375 (OUTLIER) cc_final: 0.4883 (tp) REVERT: D 88 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7173 (mt-10) REVERT: D 102 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.5782 (pm20) REVERT: D 111 GLU cc_start: 0.8647 (pm20) cc_final: 0.8289 (pm20) REVERT: D 112 GLU cc_start: 0.8726 (mp0) cc_final: 0.7817 (mp0) REVERT: D 115 GLU cc_start: 0.8456 (tp30) cc_final: 0.8196 (tm-30) REVERT: D 116 ILE cc_start: 0.7790 (pt) cc_final: 0.7200 (tp) outliers start: 32 outliers final: 12 residues processed: 143 average time/residue: 0.0855 time to fit residues: 16.1375 Evaluate side-chains 133 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 275 GLU 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 250 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: 0.8980 chunk 0 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 0.0010 chunk 27 optimal weight: 0.0670 chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 overall best weight: 0.4924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN B 126 ASN ** B 214 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 = 0.4519 r_free = 0.4519 target = 0.213208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.166097 restraints weight = 7745.486| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.46 r_work: 0.3799 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6457 Z= 0.149 Angle : 0.648 14.025 8871 Z= 0.353 Chirality : 0.042 0.220 952 Planarity : 0.004 0.064 986 Dihedral : 23.588 153.252 1236 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 6.64 % Allowed : 31.35 % Favored : 62.01 % 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: -1.71 (0.33), residues: 635 helix: -0.11 (0.33), residues: 234 sheet: -1.73 (0.49), residues: 108 loop : -1.69 (0.38), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 180 TYR 0.012 0.001 TYR D 103 PHE 0.012 0.001 PHE A 250 TRP 0.018 0.001 TRP D 70 HIS 0.001 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6457) covalent geometry : angle 0.64849 ( 8871) hydrogen bonds : bond 0.04893 ( 230) hydrogen bonds : angle 4.73007 ( 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 163 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 0.221 Fit side-chains REVERT: A 202 MET cc_start: 0.5967 (tpt) cc_final: 0.5708 (tpt) REVERT: A 274 ASP cc_start: 0.8412 (t0) cc_final: 0.8190 (t0) REVERT: B 66 THR cc_start: 0.8218 (m) cc_final: 0.8009 (p) REVERT: B 71 TYR cc_start: 0.7967 (p90) cc_final: 0.7423 (p90) REVERT: B 116 LYS cc_start: 0.7543 (mmmt) cc_final: 0.7180 (tptp) REVERT: B 153 ILE cc_start: 0.6335 (OUTLIER) cc_final: 0.6022 (pp) REVERT: D 41 TYR cc_start: 0.7983 (t80) cc_final: 0.7642 (t80) REVERT: D 56 LYS cc_start: 0.9115 (mmmm) cc_final: 0.8373 (mmtm) REVERT: D 60 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8021 (ptp-170) REVERT: D 73 ILE cc_start: 0.5358 (OUTLIER) cc_final: 0.4812 (tp) REVERT: D 88 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7068 (mt-10) REVERT: D 102 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.5738 (pm20) REVERT: D 111 GLU cc_start: 0.8659 (pm20) cc_final: 0.8186 (pm20) REVERT: D 112 GLU cc_start: 0.8793 (mp0) cc_final: 0.7883 (mp0) REVERT: D 115 GLU cc_start: 0.8491 (tp30) cc_final: 0.8229 (tm-30) REVERT: D 116 ILE cc_start: 0.7815 (pt) cc_final: 0.7266 (tp) outliers start: 39 outliers final: 16 residues processed: 144 average time/residue: 0.0933 time to fit residues: 17.3408 Evaluate side-chains 135 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 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 137 ILE Chi-restraints excluded: chain B residue 153 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 13 optimal weight: 0.0970 chunk 2 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 52 optimal weight: 0.0870 chunk 34 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.213414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.165775 restraints weight = 7817.159| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 2.51 r_work: 0.3801 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6457 Z= 0.142 Angle : 0.632 12.268 8871 Z= 0.346 Chirality : 0.042 0.216 952 Planarity : 0.004 0.064 986 Dihedral : 23.446 153.127 1230 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 6.13 % Allowed : 31.18 % Favored : 62.69 % 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 (0.33), residues: 235 sheet: -1.69 (0.50), residues: 108 loop : -1.70 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.012 0.001 TYR D 103 PHE 0.012 0.001 PHE A 250 TRP 0.010 0.001 TRP D 70 HIS 0.003 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 6457) covalent geometry : angle 0.63223 ( 8871) hydrogen bonds : bond 0.04403 ( 230) hydrogen bonds : angle 4.63415 ( 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 154 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 275 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6319 (mt-10) REVERT: B 71 TYR cc_start: 0.7910 (p90) cc_final: 0.7326 (p90) REVERT: B 116 LYS cc_start: 0.7574 (mmmt) cc_final: 0.7202 (tptp) REVERT: B 153 ILE cc_start: 0.6293 (OUTLIER) cc_final: 0.6015 (pp) REVERT: C 174 LYS cc_start: 0.8301 (ptpp) cc_final: 0.8030 (ptpp) REVERT: D 41 TYR cc_start: 0.8043 (t80) cc_final: 0.7771 (t80) REVERT: D 60 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7963 (ptp-170) REVERT: D 73 ILE cc_start: 0.5385 (OUTLIER) cc_final: 0.4865 (tp) REVERT: D 88 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6953 (mt-10) REVERT: D 102 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.5756 (pm20) REVERT: D 110 GLU cc_start: 0.8411 (pp20) cc_final: 0.8181 (pp20) REVERT: D 111 GLU cc_start: 0.8642 (pm20) cc_final: 0.8041 (pm20) REVERT: D 112 GLU cc_start: 0.8754 (mp0) cc_final: 0.7863 (mp0) REVERT: D 115 GLU cc_start: 0.8492 (tp30) cc_final: 0.8239 (tm-30) REVERT: D 116 ILE cc_start: 0.7804 (pt) cc_final: 0.7236 (tp) outliers start: 36 outliers final: 20 residues processed: 138 average time/residue: 0.0908 time to fit residues: 16.2840 Evaluate side-chains 132 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 150 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 47 optimal weight: 4.9990 chunk 21 optimal weight: 0.0020 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4476 r_free = 0.4476 target = 0.208500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.160995 restraints weight = 7865.487| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.47 r_work: 0.3747 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 6457 Z= 0.211 Angle : 0.698 9.856 8871 Z= 0.378 Chirality : 0.044 0.230 952 Planarity : 0.004 0.060 986 Dihedral : 23.515 152.063 1230 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 6.98 % Allowed : 30.32 % Favored : 62.69 % 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: -1.85 (0.49), residues: 98 loop : -1.84 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.015 0.002 TYR A 258 PHE 0.017 0.002 PHE A 250 TRP 0.009 0.002 TRP A 212 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 6457) covalent geometry : angle 0.69820 ( 8871) hydrogen bonds : bond 0.04896 ( 230) hydrogen bonds : angle 4.76913 ( 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 157 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.6069 (mt-10) REVERT: A 280 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8126 (mttp) REVERT: B 71 TYR cc_start: 0.8001 (p90) cc_final: 0.7374 (p90) REVERT: B 116 LYS cc_start: 0.7673 (mmmt) cc_final: 0.7284 (tptp) REVERT: B 153 ILE cc_start: 0.6362 (OUTLIER) cc_final: 0.5998 (pp) REVERT: B 257 ASP cc_start: 0.7623 (p0) cc_final: 0.7409 (p0) REVERT: C 174 LYS cc_start: 0.8351 (ptpp) cc_final: 0.8058 (ptpp) REVERT: D 60 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7917 (ptp-170) REVERT: D 88 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6824 (mt-10) REVERT: D 102 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.5825 (pm20) REVERT: D 111 GLU cc_start: 0.8653 (pm20) cc_final: 0.8022 (pm20) REVERT: D 112 GLU cc_start: 0.8740 (mp0) cc_final: 0.7870 (mp0) REVERT: D 115 GLU cc_start: 0.8450 (tp30) cc_final: 0.8222 (tm-30) REVERT: D 116 ILE cc_start: 0.7839 (pt) cc_final: 0.7252 (tp) outliers start: 41 outliers final: 24 residues processed: 141 average time/residue: 0.0894 time to fit residues: 16.2579 Evaluate side-chains 141 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 300 GLU 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 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 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 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: 0.4980 chunk 41 optimal weight: 0.0060 chunk 58 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4500 r_free = 0.4500 target = 0.211216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.162548 restraints weight = 7808.215| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.53 r_work: 0.3765 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6457 Z= 0.152 Angle : 0.658 9.412 8871 Z= 0.357 Chirality : 0.043 0.245 952 Planarity : 0.004 0.060 986 Dihedral : 23.421 152.863 1230 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 6.13 % Allowed : 31.01 % 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: -1.63 (0.33), residues: 635 helix: 0.09 (0.33), residues: 235 sheet: -1.81 (0.49), residues: 98 loop : -1.76 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 180 TYR 0.010 0.001 TYR D 103 PHE 0.012 0.001 PHE B 259 TRP 0.008 0.001 TRP D 70 HIS 0.001 0.000 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6457) covalent geometry : angle 0.65828 ( 8871) hydrogen bonds : bond 0.04354 ( 230) hydrogen bonds : angle 4.65162 ( 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: 36 poor density : 111 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.5955 (mt-10) REVERT: B 71 TYR cc_start: 0.7952 (p90) cc_final: 0.7356 (p90) REVERT: B 116 LYS cc_start: 0.7647 (mmmt) cc_final: 0.7295 (tptp) REVERT: B 153 ILE cc_start: 0.6308 (OUTLIER) cc_final: 0.6018 (pp) REVERT: B 251 ARG cc_start: 0.7421 (ptp-170) cc_final: 0.7026 (mtm110) REVERT: C 174 LYS cc_start: 0.8375 (ptpp) cc_final: 0.8157 (ptpp) REVERT: D 60 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7951 (ptp-170) REVERT: D 102 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.5923 (pm20) REVERT: D 110 GLU cc_start: 0.8391 (pp20) cc_final: 0.8088 (pp20) REVERT: D 111 GLU cc_start: 0.8682 (pm20) cc_final: 0.8277 (pm20) REVERT: D 112 GLU cc_start: 0.8784 (mp0) cc_final: 0.8474 (mp0) REVERT: D 115 GLU cc_start: 0.8518 (tp30) cc_final: 0.8278 (tm-30) REVERT: D 116 ILE cc_start: 0.7816 (pt) cc_final: 0.7246 (tp) outliers start: 36 outliers final: 23 residues processed: 131 average time/residue: 0.0950 time to fit residues: 15.8220 Evaluate side-chains 135 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 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 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 C residue 170 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.211425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.162910 restraints weight = 7742.564| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.50 r_work: 0.3772 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6457 Z= 0.152 Angle : 0.666 13.801 8871 Z= 0.359 Chirality : 0.043 0.242 952 Planarity : 0.004 0.060 986 Dihedral : 23.338 152.271 1230 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % 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: -1.62 (0.33), residues: 635 helix: 0.12 (0.33), residues: 235 sheet: -1.98 (0.47), residues: 110 loop : -1.66 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 180 TYR 0.011 0.001 TYR D 103 PHE 0.013 0.001 PHE A 250 TRP 0.017 0.001 TRP B 197 HIS 0.001 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 6457) covalent geometry : angle 0.66620 ( 8871) hydrogen bonds : bond 0.04240 ( 230) hydrogen bonds : angle 4.60604 ( 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 147 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 71 TYR cc_start: 0.7981 (p90) cc_final: 0.7315 (p90) REVERT: B 116 LYS cc_start: 0.7709 (mmmt) cc_final: 0.7334 (tptp) REVERT: B 153 ILE cc_start: 0.6285 (OUTLIER) cc_final: 0.6013 (pp) REVERT: B 251 ARG cc_start: 0.7405 (ptp-170) cc_final: 0.7018 (mtm110) REVERT: C 152 THR cc_start: 0.7155 (t) cc_final: 0.6851 (p) REVERT: C 174 LYS cc_start: 0.8158 (ptpp) cc_final: 0.7928 (ptpp) REVERT: D 41 TYR cc_start: 0.8075 (t80) cc_final: 0.7724 (t80) REVERT: D 60 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7920 (ptp-170) REVERT: D 102 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6004 (pm20) REVERT: D 110 GLU cc_start: 0.8345 (pp20) cc_final: 0.8017 (pp20) REVERT: D 111 GLU cc_start: 0.8656 (pm20) cc_final: 0.8224 (pm20) REVERT: D 112 GLU cc_start: 0.8749 (mp0) cc_final: 0.8441 (mp0) REVERT: D 115 GLU cc_start: 0.8467 (tp30) cc_final: 0.8250 (tm-30) REVERT: D 116 ILE cc_start: 0.7812 (pt) cc_final: 0.7236 (tp) outliers start: 34 outliers final: 26 residues processed: 131 average time/residue: 0.0967 time to fit residues: 16.2803 Evaluate side-chains 135 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 299 LYS Chi-restraints excluded: chain A residue 300 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 361 LEU Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain B residue 84 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4464 r_free = 0.4464 target = 0.207459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.158240 restraints weight = 7825.903| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.53 r_work: 0.3716 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6457 Z= 0.212 Angle : 0.729 11.870 8871 Z= 0.394 Chirality : 0.045 0.326 952 Planarity : 0.004 0.057 986 Dihedral : 23.444 151.489 1230 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 5.62 % Allowed : 31.69 % Favored : 62.69 % 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: -1.78 (0.33), residues: 635 helix: 0.06 (0.33), residues: 235 sheet: -2.12 (0.47), residues: 100 loop : -1.82 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 180 TYR 0.015 0.002 TYR A 258 PHE 0.015 0.002 PHE A 250 TRP 0.032 0.002 TRP D 70 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00503 ( 6457) covalent geometry : angle 0.72909 ( 8871) hydrogen bonds : bond 0.04728 ( 230) hydrogen bonds : angle 4.81254 ( 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 143 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.6185 (OUTLIER) cc_final: 0.5909 (tpt) REVERT: A 357 ARG cc_start: 0.6695 (ttp-170) cc_final: 0.6450 (ttm110) REVERT: B 71 TYR cc_start: 0.7964 (p90) cc_final: 0.7345 (p90) REVERT: B 116 LYS cc_start: 0.7701 (mmmt) cc_final: 0.7394 (tptp) REVERT: B 153 ILE cc_start: 0.6372 (OUTLIER) cc_final: 0.6048 (pp) REVERT: B 251 ARG cc_start: 0.7451 (ptp-170) cc_final: 0.7016 (mtm110) REVERT: B 293 SER cc_start: 0.7330 (p) cc_final: 0.7060 (t) REVERT: C 152 THR cc_start: 0.7180 (t) cc_final: 0.6881 (p) REVERT: C 174 LYS cc_start: 0.8207 (ptpp) cc_final: 0.7936 (ptpp) REVERT: D 60 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7877 (ptp-170) REVERT: D 88 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6876 (mt-10) REVERT: D 102 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6076 (pm20) REVERT: D 104 TYR cc_start: 0.6816 (OUTLIER) cc_final: 0.5863 (t80) REVERT: D 110 GLU cc_start: 0.8417 (pp20) cc_final: 0.8088 (pp20) REVERT: D 111 GLU cc_start: 0.8713 (pm20) cc_final: 0.8285 (pm20) REVERT: D 112 GLU cc_start: 0.8805 (mp0) cc_final: 0.8488 (mp0) REVERT: D 115 GLU cc_start: 0.8526 (tp30) cc_final: 0.8303 (tm-30) REVERT: D 116 ILE cc_start: 0.7824 (pt) cc_final: 0.7276 (tp) outliers start: 33 outliers final: 23 residues processed: 129 average time/residue: 0.0942 time to fit residues: 15.4368 Evaluate side-chains 135 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 260 VAL Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 300 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 84 LEU 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 Chi-restraints excluded: chain D residue 104 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 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 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 = 0.4496 r_free = 0.4496 target = 0.210788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.162193 restraints weight = 7780.654| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 2.50 r_work: 0.3767 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6457 Z= 0.154 Angle : 0.685 13.187 8871 Z= 0.369 Chirality : 0.043 0.345 952 Planarity : 0.004 0.054 986 Dihedral : 23.289 152.425 1230 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 5.11 % Allowed : 32.54 % 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: -1.62 (0.33), residues: 635 helix: 0.24 (0.33), residues: 234 sheet: -2.15 (0.46), residues: 110 loop : -1.68 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.010 0.001 TYR D 103 PHE 0.012 0.001 PHE B 259 TRP 0.022 0.002 TRP D 70 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 6457) covalent geometry : angle 0.68498 ( 8871) hydrogen bonds : bond 0.04078 ( 230) hydrogen bonds : angle 4.66037 ( 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 141 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 71 TYR cc_start: 0.7967 (p90) cc_final: 0.7328 (p90) REVERT: B 116 LYS cc_start: 0.7703 (mmmt) cc_final: 0.7421 (tptp) REVERT: B 153 ILE cc_start: 0.6300 (OUTLIER) cc_final: 0.6030 (pp) REVERT: B 251 ARG cc_start: 0.7466 (ptp-170) cc_final: 0.7095 (mtm110) REVERT: B 293 SER cc_start: 0.7315 (p) cc_final: 0.7001 (t) REVERT: C 152 THR cc_start: 0.7147 (t) cc_final: 0.6863 (p) REVERT: D 41 TYR cc_start: 0.8079 (t80) cc_final: 0.7727 (t80) REVERT: D 60 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7946 (ptp-170) REVERT: D 73 ILE cc_start: 0.5562 (OUTLIER) cc_final: 0.4962 (tp) REVERT: D 102 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6077 (pm20) REVERT: D 104 TYR cc_start: 0.6766 (OUTLIER) cc_final: 0.5758 (t80) REVERT: D 110 GLU cc_start: 0.8420 (pp20) cc_final: 0.8090 (pp20) REVERT: D 111 GLU cc_start: 0.8680 (pm20) cc_final: 0.8245 (pm20) REVERT: D 112 GLU cc_start: 0.8767 (mp0) cc_final: 0.8453 (mp0) REVERT: D 115 GLU cc_start: 0.8502 (tp30) cc_final: 0.8281 (tm-30) REVERT: D 116 ILE cc_start: 0.7860 (pt) cc_final: 0.7291 (tp) outliers start: 30 outliers final: 24 residues processed: 125 average time/residue: 0.0777 time to fit residues: 12.6204 Evaluate side-chains 138 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 150 ILE 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 300 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 84 LEU 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 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 Chi-restraints excluded: chain D residue 104 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4423 r_free = 0.4423 target = 0.203179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.156553 restraints weight = 7820.617| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.44 r_work: 0.3688 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.103 6457 Z= 0.336 Angle : 0.865 14.420 8871 Z= 0.459 Chirality : 0.050 0.318 952 Planarity : 0.004 0.049 986 Dihedral : 23.621 150.676 1230 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 5.11 % Allowed : 32.88 % Favored : 62.01 % 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: -2.17 (0.32), residues: 635 helix: -0.31 (0.32), residues: 237 sheet: -2.37 (0.46), residues: 100 loop : -2.00 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 90 TYR 0.021 0.002 TYR A 258 PHE 0.019 0.003 PHE B 229 TRP 0.016 0.003 TRP A 212 HIS 0.006 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00811 ( 6457) covalent geometry : angle 0.86476 ( 8871) hydrogen bonds : bond 0.05735 ( 230) hydrogen bonds : angle 5.17427 ( 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 139 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.6317 (OUTLIER) cc_final: 0.6018 (tpt) REVERT: A 322 ASP cc_start: 0.7921 (p0) cc_final: 0.7601 (p0) REVERT: A 357 ARG cc_start: 0.6986 (ttp-170) cc_final: 0.6683 (ttm170) REVERT: B 71 TYR cc_start: 0.8090 (p90) cc_final: 0.7434 (p90) REVERT: B 116 LYS cc_start: 0.7901 (mmmt) cc_final: 0.7351 (tptp) REVERT: B 153 ILE cc_start: 0.6485 (OUTLIER) cc_final: 0.6128 (pp) REVERT: B 251 ARG cc_start: 0.7500 (ptp-170) cc_final: 0.6987 (mtm110) REVERT: B 293 SER cc_start: 0.7799 (p) cc_final: 0.7523 (t) REVERT: D 14 PHE cc_start: 0.6949 (m-80) cc_final: 0.6317 (m-10) REVERT: D 88 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6835 (mt-10) REVERT: D 102 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.5983 (pm20) REVERT: D 104 TYR cc_start: 0.6977 (OUTLIER) cc_final: 0.5977 (t80) REVERT: D 111 GLU cc_start: 0.8681 (pm20) cc_final: 0.8249 (pm20) REVERT: D 112 GLU cc_start: 0.8804 (mp0) cc_final: 0.8528 (mp0) REVERT: D 116 ILE cc_start: 0.7858 (pt) cc_final: 0.7343 (tp) outliers start: 30 outliers final: 21 residues processed: 124 average time/residue: 0.0937 time to fit residues: 14.9248 Evaluate side-chains 129 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 150 ILE 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 260 VAL Chi-restraints excluded: chain A residue 300 GLU 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 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 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 73 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 104 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 52 optimal weight: 0.0570 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4478 r_free = 0.4478 target = 0.208909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.160159 restraints weight = 7756.417| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.52 r_work: 0.3740 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 6457 Z= 0.172 Angle : 0.739 15.248 8871 Z= 0.396 Chirality : 0.045 0.318 952 Planarity : 0.004 0.049 986 Dihedral : 23.407 152.866 1230 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.92 % Allowed : 33.56 % 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: -1.92 (0.33), residues: 635 helix: -0.02 (0.33), residues: 235 sheet: -2.35 (0.47), residues: 100 loop : -1.88 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.010 0.001 TYR D 103 PHE 0.014 0.001 PHE B 259 TRP 0.021 0.002 TRP D 70 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 6457) covalent geometry : angle 0.73874 ( 8871) hydrogen bonds : bond 0.04401 ( 230) hydrogen bonds : angle 4.84986 ( 620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1790.28 seconds wall clock time: 31 minutes 24.23 seconds (1884.23 seconds total)