Starting phenix.real_space_refine on Thu Jul 2 16:43:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vui_32129/07_2026/7vui_32129.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vui_32129/07_2026/7vui_32129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7vui_32129/07_2026/7vui_32129.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vui_32129/07_2026/7vui_32129.cif" model { file = "/net/cci-nas-00/data/ceres_data/7vui_32129/07_2026/7vui_32129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vui_32129/07_2026/7vui_32129.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vui_32129/07_2026/7vui_32129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vui_32129/07_2026/7vui_32129.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1050 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 49 5.16 5 Cl 1 4.86 5 C 5274 2.51 5 N 1433 2.21 5 O 1526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8287 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1940 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2295 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 12, 'TRANS': 266} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'7ZQ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.85, per 1000 atoms: 0.22 Number of scatterers: 8287 At special positions: 0 Unit cell: (76.96, 98.8, 134.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 49 16.00 P 3 15.00 Mg 1 11.99 O 1526 8.00 N 1433 7.00 C 5274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 425.7 milliseconds 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 41.5% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 9 through 38 removed outlier: 3.795A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.669A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.147A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 removed outlier: 3.797A pdb=" N ALA A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 306' Processing helix chain 'A' and resid 321 through 342 removed outlier: 3.875A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.595A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 53 removed outlier: 3.973A pdb=" N SER R 34 " --> pdb=" O VAL R 30 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU R 35 " --> pdb=" O VAL R 31 " (cutoff:3.500A) Proline residue: R 42 - end of helix removed outlier: 3.706A pdb=" N GLN R 53 " --> pdb=" O ILE R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 54 through 58 removed outlier: 3.887A pdb=" N ARG R 58 " --> pdb=" O VAL R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 82 removed outlier: 3.574A pdb=" N TYR R 65 " --> pdb=" O SER R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 91 removed outlier: 5.342A pdb=" N ASP R 89 " --> pdb=" O PHE R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 132 removed outlier: 3.861A pdb=" N VAL R 106 " --> pdb=" O LYS R 102 " (cutoff:3.500A) Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 135 through 140 Processing helix chain 'R' and resid 141 through 160 removed outlier: 3.560A pdb=" N LYS R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL R 152 " --> pdb=" O VAL R 148 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR R 153 " --> pdb=" O ILE R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 166 removed outlier: 3.655A pdb=" N TRP R 165 " --> pdb=" O PRO R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 192 removed outlier: 3.873A pdb=" N HIS R 181 " --> pdb=" O THR R 177 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL R 182 " --> pdb=" O SER R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 213 Processing helix chain 'R' and resid 222 through 253 Proline residue: R 243 - end of helix Processing helix chain 'R' and resid 259 through 286 removed outlier: 4.087A pdb=" N MET R 266 " --> pdb=" O LEU R 262 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER R 267 " --> pdb=" O VAL R 263 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU R 273 " --> pdb=" O ILE R 269 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA R 274 " --> pdb=" O ALA R 270 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU R 275 " --> pdb=" O ASN R 271 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE R 282 " --> pdb=" O THR R 278 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE R 283 " --> pdb=" O ALA R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 301 removed outlier: 3.740A pdb=" N MET R 295 " --> pdb=" O ARG R 291 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS R 301 " --> pdb=" O ALA R 297 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214 removed outlier: 3.517A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 221 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 4.035A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 63 removed outlier: 3.540A pdb=" N HIS B 62 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.537A pdb=" N ALA B 104 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.597A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.702A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.656A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.532A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.803A pdb=" N LEU N 20 " --> pdb=" O LEU N 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 59 through 60 removed outlier: 6.680A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1328 1.31 - 1.44: 2379 1.44 - 1.56: 4686 1.56 - 1.69: 5 1.69 - 1.81: 70 Bond restraints: 8468 Sorted by residual: bond pdb=" C9 7ZQ R 401 " pdb=" N2 7ZQ R 401 " ideal model delta sigma weight residual 1.341 1.450 -0.109 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C7 7ZQ R 401 " pdb=" N1 7ZQ R 401 " ideal model delta sigma weight residual 1.344 1.450 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" C2 GTP A 401 " pdb=" N3 GTP A 401 " ideal model delta sigma weight residual 1.380 1.321 0.059 2.00e-02 2.50e+03 8.61e+00 bond pdb=" C3 7ZQ R 401 " pdb="CL1 7ZQ R 401 " ideal model delta sigma weight residual 1.732 1.784 -0.052 2.00e-02 2.50e+03 6.88e+00 bond pdb=" C8 GTP A 401 " pdb=" N7 GTP A 401 " ideal model delta sigma weight residual 1.350 1.300 0.050 2.00e-02 2.50e+03 6.24e+00 ... (remaining 8463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 11264 1.81 - 3.62: 177 3.62 - 5.43: 32 5.43 - 7.25: 12 7.25 - 9.06: 7 Bond angle restraints: 11492 Sorted by residual: angle pdb=" C4 GTP A 401 " pdb=" N9 GTP A 401 " pdb=" C8 GTP A 401 " ideal model delta sigma weight residual 108.00 117.06 -9.06 3.00e+00 1.11e-01 9.11e+00 angle pdb=" CB ARG A 270 " pdb=" CG ARG A 270 " pdb=" CD ARG A 270 " ideal model delta sigma weight residual 111.30 118.16 -6.86 2.30e+00 1.89e-01 8.88e+00 angle pdb=" C5 GTP A 401 " pdb=" C4 GTP A 401 " pdb=" N9 GTP A 401 " ideal model delta sigma weight residual 108.00 99.48 8.52 3.00e+00 1.11e-01 8.07e+00 angle pdb=" O1B GTP A 401 " pdb=" PB GTP A 401 " pdb=" O2B GTP A 401 " ideal model delta sigma weight residual 109.50 101.13 8.37 3.00e+00 1.11e-01 7.78e+00 angle pdb=" O1A GTP A 401 " pdb=" PA GTP A 401 " pdb=" O2A GTP A 401 " ideal model delta sigma weight residual 109.50 101.18 8.32 3.00e+00 1.11e-01 7.69e+00 ... (remaining 11487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.60: 4925 33.60 - 67.20: 85 67.20 - 100.81: 13 100.81 - 134.41: 2 134.41 - 168.01: 3 Dihedral angle restraints: 5028 sinusoidal: 1999 harmonic: 3029 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -6.48 -79.52 1 1.00e+01 1.00e-02 7.85e+01 dihedral pdb=" O2G GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PG GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sinusoidal sigma weight residual 177.30 -14.69 -168.01 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -49.86 154.45 1 2.00e+01 2.50e-03 4.57e+01 ... (remaining 5025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 893 0.038 - 0.076: 297 0.076 - 0.114: 88 0.114 - 0.152: 13 0.152 - 0.190: 4 Chirality restraints: 1295 Sorted by residual: chirality pdb=" C3' GTP A 401 " pdb=" C2' GTP A 401 " pdb=" C4' GTP A 401 " pdb=" O3' GTP A 401 " both_signs ideal model delta sigma weight residual False -2.47 -2.66 0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" C10 7ZQ R 401 " pdb=" C11 7ZQ R 401 " pdb=" C12 7ZQ R 401 " pdb=" N2 7ZQ R 401 " both_signs ideal model delta sigma weight residual False -2.45 -2.62 0.17 2.00e-01 2.50e+01 6.94e-01 chirality pdb=" C4' GTP A 401 " pdb=" C3' GTP A 401 " pdb=" C5' GTP A 401 " pdb=" O4' GTP A 401 " both_signs ideal model delta sigma weight residual False -2.47 -2.63 0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 1292 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 80 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" C ILE R 80 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE R 80 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL R 81 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 82 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C PHE R 82 " -0.034 2.00e-02 2.50e+03 pdb=" O PHE R 82 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL R 83 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 321 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO A 322 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " 0.026 5.00e-02 4.00e+02 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 257 2.71 - 3.26: 8379 3.26 - 3.81: 13443 3.81 - 4.35: 16385 4.35 - 4.90: 27938 Nonbonded interactions: 66402 Sorted by model distance: nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.165 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.174 3.040 nonbonded pdb=" OH TYR A 308 " pdb=" OD2 ASP A 333 " model vdw 2.176 3.040 nonbonded pdb=" O2G GTP A 401 " pdb="MG MG A 402 " model vdw 2.179 2.170 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.181 3.040 ... (remaining 66397 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.310 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 8470 Z= 0.162 Angle : 0.628 9.057 11496 Z= 0.306 Chirality : 0.042 0.190 1295 Planarity : 0.004 0.047 1452 Dihedral : 14.775 168.009 3062 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.11 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.27), residues: 1022 helix: 1.06 (0.27), residues: 400 sheet: -0.97 (0.36), residues: 215 loop : -1.00 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 270 TYR 0.010 0.001 TYR B 59 PHE 0.017 0.001 PHE R 287 TRP 0.026 0.001 TRP R 170 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 ( 8468) covalent geometry : angle 0.62813 / 0.31 (11492) SS BOND : bond 0.00116 / 0.06 ( 2) SS BOND : angle 0.50142 / 0.30 ( 4) hydrogen bonds : bond 0.17414 / 11.71 ( 384) hydrogen bonds : angle 6.36338 / 4.49 ( 1104) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.6845 (tmm160) cc_final: 0.5875 (tmm160) REVERT: A 270 ARG cc_start: 0.6386 (ppt170) cc_final: 0.6171 (ppt170) REVERT: A 289 GLU cc_start: 0.7270 (tp30) cc_final: 0.6706 (tp30) REVERT: A 309 THR cc_start: 0.7900 (p) cc_final: 0.7698 (t) REVERT: A 317 GLU cc_start: 0.6478 (mp0) cc_final: 0.6091 (mp0) REVERT: A 371 ASP cc_start: 0.7313 (t70) cc_final: 0.6717 (t0) REVERT: B 66 ASP cc_start: 0.7062 (p0) cc_final: 0.6724 (p0) REVERT: B 67 SER cc_start: 0.8411 (m) cc_final: 0.7871 (t) REVERT: B 103 CYS cc_start: 0.7243 (m) cc_final: 0.6816 (m) REVERT: B 121 CYS cc_start: 0.7334 (t) cc_final: 0.6837 (t) REVERT: B 155 ASN cc_start: 0.7740 (t0) cc_final: 0.7236 (t0) REVERT: B 169 TRP cc_start: 0.8099 (m100) cc_final: 0.7657 (m100) REVERT: B 212 ASP cc_start: 0.7515 (t0) cc_final: 0.7293 (t70) REVERT: B 256 ARG cc_start: 0.7847 (ptp-110) cc_final: 0.7634 (ptp-110) REVERT: B 258 ASP cc_start: 0.7495 (t70) cc_final: 0.6828 (t0) REVERT: B 273 ILE cc_start: 0.8184 (mp) cc_final: 0.7878 (mp) REVERT: G 28 ILE cc_start: 0.8119 (mp) cc_final: 0.7866 (mp) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.0936 time to fit residues: 26.9615 Evaluate side-chains 194 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 ASN A 377 ASN B 119 ASN B 239 ASN N 53 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.149709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.131299 restraints weight = 11873.946| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.20 r_work: 0.3539 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8470 Z= 0.173 Angle : 0.625 8.736 11496 Z= 0.320 Chirality : 0.044 0.168 1295 Planarity : 0.004 0.054 1452 Dihedral : 10.019 149.535 1155 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.11 % Favored : 95.69 % Rotamer: Outliers : 1.79 % Allowed : 11.38 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.27), residues: 1022 helix: 1.08 (0.27), residues: 399 sheet: -0.62 (0.36), residues: 217 loop : -1.00 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 270 TYR 0.016 0.001 TYR B 59 PHE 0.022 0.002 PHE R 82 TRP 0.027 0.002 TRP R 170 HIS 0.008 0.002 HIS R 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 8468) covalent geometry : angle 0.62485 / 0.32 (11492) SS BOND : bond 0.00081 / 0.04 ( 2) SS BOND : angle 1.28026 / 0.69 ( 4) hydrogen bonds : bond 0.04551 / 2.98 ( 384) hydrogen bonds : angle 5.04811 / 3.54 ( 1104) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8216 (ttpp) cc_final: 0.7938 (ttmm) REVERT: A 289 GLU cc_start: 0.8010 (tp30) cc_final: 0.7387 (tp30) REVERT: A 317 GLU cc_start: 0.6675 (mp0) cc_final: 0.6086 (mp0) REVERT: A 366 PHE cc_start: 0.8004 (t80) cc_final: 0.7664 (t80) REVERT: A 371 ASP cc_start: 0.8170 (t70) cc_final: 0.7746 (t0) REVERT: B 67 SER cc_start: 0.8786 (m) cc_final: 0.8383 (t) REVERT: B 103 CYS cc_start: 0.7833 (m) cc_final: 0.7385 (m) REVERT: B 121 CYS cc_start: 0.8034 (t) cc_final: 0.7744 (t) REVERT: B 169 TRP cc_start: 0.8471 (m100) cc_final: 0.8070 (m100) REVERT: B 212 ASP cc_start: 0.8180 (t0) cc_final: 0.7979 (t0) REVERT: B 220 GLN cc_start: 0.7973 (pt0) cc_final: 0.7724 (pt0) REVERT: B 223 THR cc_start: 0.7814 (m) cc_final: 0.7573 (p) REVERT: B 258 ASP cc_start: 0.8102 (t70) cc_final: 0.7599 (t0) REVERT: B 259 GLN cc_start: 0.8441 (tt0) cc_final: 0.8150 (tt0) REVERT: B 304 ARG cc_start: 0.8204 (ttm-80) cc_final: 0.7910 (ttm-80) REVERT: R 239 THR cc_start: 0.7975 (p) cc_final: 0.7735 (t) outliers start: 16 outliers final: 11 residues processed: 214 average time/residue: 0.0936 time to fit residues: 25.9108 Evaluate side-chains 218 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 207 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 252 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 77 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN A 282 ASN A 377 ASN N 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.146541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.128090 restraints weight = 11799.598| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.18 r_work: 0.3533 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8470 Z= 0.162 Angle : 0.577 7.719 11496 Z= 0.300 Chirality : 0.043 0.155 1295 Planarity : 0.004 0.050 1452 Dihedral : 9.840 147.082 1155 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.52 % Favored : 96.28 % Rotamer: Outliers : 2.12 % Allowed : 16.18 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.27), residues: 1022 helix: 1.14 (0.27), residues: 399 sheet: -0.47 (0.35), residues: 225 loop : -1.15 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.014 0.001 TYR B 59 PHE 0.019 0.001 PHE R 82 TRP 0.016 0.001 TRP R 170 HIS 0.005 0.001 HIS R 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 8468) covalent geometry : angle 0.57680 / 0.30 (11492) SS BOND : bond 0.00151 / 0.07 ( 2) SS BOND : angle 0.91677 / 0.51 ( 4) hydrogen bonds : bond 0.04323 / 2.86 ( 384) hydrogen bonds : angle 4.88438 / 3.42 ( 1104) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8188 (ttpp) cc_final: 0.7918 (ttmm) REVERT: A 289 GLU cc_start: 0.7979 (tp30) cc_final: 0.7370 (tp30) REVERT: A 317 GLU cc_start: 0.6730 (mp0) cc_final: 0.6156 (mp0) REVERT: A 366 PHE cc_start: 0.8043 (t80) cc_final: 0.7006 (t80) REVERT: A 371 ASP cc_start: 0.8173 (t70) cc_final: 0.7692 (t70) REVERT: B 49 ARG cc_start: 0.7813 (mtt90) cc_final: 0.7596 (mtt90) REVERT: B 67 SER cc_start: 0.8791 (m) cc_final: 0.8396 (t) REVERT: B 103 CYS cc_start: 0.7802 (m) cc_final: 0.7371 (m) REVERT: B 121 CYS cc_start: 0.7998 (t) cc_final: 0.7620 (t) REVERT: B 169 TRP cc_start: 0.8508 (m100) cc_final: 0.8092 (m100) REVERT: B 220 GLN cc_start: 0.8007 (pt0) cc_final: 0.7710 (pt0) REVERT: B 258 ASP cc_start: 0.8091 (t70) cc_final: 0.7461 (t0) REVERT: R 239 THR cc_start: 0.7978 (p) cc_final: 0.7766 (t) outliers start: 19 outliers final: 14 residues processed: 212 average time/residue: 0.1062 time to fit residues: 28.7769 Evaluate side-chains 215 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 252 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 ASN A 377 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.143387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.124059 restraints weight = 12179.301| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.24 r_work: 0.3499 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8470 Z= 0.176 Angle : 0.584 7.555 11496 Z= 0.303 Chirality : 0.044 0.153 1295 Planarity : 0.004 0.048 1452 Dihedral : 9.653 144.992 1155 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.91 % Favored : 95.89 % Rotamer: Outliers : 2.46 % Allowed : 19.75 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.27), residues: 1022 helix: 1.23 (0.27), residues: 394 sheet: -0.36 (0.36), residues: 226 loop : -1.15 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.017 0.001 TYR R 32 PHE 0.022 0.001 PHE R 82 TRP 0.017 0.002 TRP R 170 HIS 0.005 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 ( 8468) covalent geometry : angle 0.58350 / 0.30 (11492) SS BOND : bond 0.00174 / 0.09 ( 2) SS BOND : angle 0.94266 / 0.53 ( 4) hydrogen bonds : bond 0.04315 / 2.87 ( 384) hydrogen bonds : angle 4.85359 / 3.39 ( 1104) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8102 (ttpp) cc_final: 0.7803 (ttmm) REVERT: A 289 GLU cc_start: 0.8012 (tp30) cc_final: 0.7360 (tp30) REVERT: A 309 THR cc_start: 0.8206 (t) cc_final: 0.7928 (p) REVERT: A 317 GLU cc_start: 0.6780 (mp0) cc_final: 0.6201 (mp0) REVERT: A 346 ARG cc_start: 0.8042 (mtt-85) cc_final: 0.7606 (mtt-85) REVERT: A 371 ASP cc_start: 0.8174 (t70) cc_final: 0.7584 (t70) REVERT: B 49 ARG cc_start: 0.7923 (mtt90) cc_final: 0.7631 (mtt90) REVERT: B 67 SER cc_start: 0.8806 (m) cc_final: 0.8376 (t) REVERT: B 103 CYS cc_start: 0.7746 (m) cc_final: 0.7277 (m) REVERT: B 121 CYS cc_start: 0.8028 (t) cc_final: 0.7619 (t) REVERT: B 169 TRP cc_start: 0.8600 (m100) cc_final: 0.8136 (m100) REVERT: B 220 GLN cc_start: 0.7983 (pt0) cc_final: 0.7616 (pt0) REVERT: B 258 ASP cc_start: 0.8116 (t70) cc_final: 0.7389 (t0) REVERT: G 28 ILE cc_start: 0.8107 (mp) cc_final: 0.7872 (mp) REVERT: R 199 PHE cc_start: 0.6911 (m-10) cc_final: 0.6513 (m-80) REVERT: R 239 THR cc_start: 0.7981 (p) cc_final: 0.7770 (t) outliers start: 22 outliers final: 14 residues processed: 214 average time/residue: 0.1007 time to fit residues: 27.9398 Evaluate side-chains 217 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 203 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 252 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 85 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 ASN A 282 ASN A 377 ASN N 53 GLN R 277 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.146619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.127310 restraints weight = 12086.684| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.27 r_work: 0.3502 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8470 Z= 0.171 Angle : 0.585 7.217 11496 Z= 0.303 Chirality : 0.043 0.148 1295 Planarity : 0.004 0.048 1452 Dihedral : 9.553 143.039 1155 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.42 % Favored : 96.38 % Rotamer: Outliers : 3.01 % Allowed : 20.42 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.27), residues: 1022 helix: 1.22 (0.27), residues: 394 sheet: -0.32 (0.36), residues: 225 loop : -1.21 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.019 0.001 TYR R 32 PHE 0.023 0.001 PHE R 82 TRP 0.020 0.002 TRP R 170 HIS 0.009 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 8468) covalent geometry : angle 0.58460 / 0.30 (11492) SS BOND : bond 0.00199 / 0.10 ( 2) SS BOND : angle 0.87253 / 0.49 ( 4) hydrogen bonds : bond 0.04302 / 2.87 ( 384) hydrogen bonds : angle 4.86114 / 3.39 ( 1104) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8117 (ttpp) cc_final: 0.7807 (ttmm) REVERT: A 289 GLU cc_start: 0.8010 (tp30) cc_final: 0.7370 (tp30) REVERT: A 309 THR cc_start: 0.8205 (t) cc_final: 0.7934 (p) REVERT: A 317 GLU cc_start: 0.6851 (mp0) cc_final: 0.6275 (mp0) REVERT: A 346 ARG cc_start: 0.8036 (mtt-85) cc_final: 0.7599 (mtt-85) REVERT: A 366 PHE cc_start: 0.7937 (t80) cc_final: 0.6915 (t80) REVERT: A 371 ASP cc_start: 0.8178 (t70) cc_final: 0.7660 (t70) REVERT: B 49 ARG cc_start: 0.7930 (mtt90) cc_final: 0.7664 (mtt90) REVERT: B 61 MET cc_start: 0.7992 (ppp) cc_final: 0.7637 (ppp) REVERT: B 67 SER cc_start: 0.8823 (m) cc_final: 0.8375 (t) REVERT: B 103 CYS cc_start: 0.7757 (m) cc_final: 0.7291 (m) REVERT: B 121 CYS cc_start: 0.8024 (t) cc_final: 0.7637 (t) REVERT: B 169 TRP cc_start: 0.8616 (m100) cc_final: 0.8123 (m100) REVERT: B 220 GLN cc_start: 0.8020 (pt0) cc_final: 0.7645 (pt0) REVERT: B 258 ASP cc_start: 0.8095 (t70) cc_final: 0.7368 (t0) REVERT: G 28 ILE cc_start: 0.8115 (mp) cc_final: 0.7887 (mp) outliers start: 27 outliers final: 22 residues processed: 222 average time/residue: 0.0974 time to fit residues: 27.9919 Evaluate side-chains 228 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 252 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 97 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 ASN A 282 ASN A 377 ASN N 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.146338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.127164 restraints weight = 12005.383| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.25 r_work: 0.3516 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8470 Z= 0.172 Angle : 0.598 7.105 11496 Z= 0.308 Chirality : 0.044 0.147 1295 Planarity : 0.004 0.047 1452 Dihedral : 9.495 142.583 1155 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.62 % Favored : 96.18 % Rotamer: Outliers : 4.13 % Allowed : 20.65 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.27), residues: 1022 helix: 1.22 (0.27), residues: 394 sheet: -0.11 (0.37), residues: 217 loop : -1.22 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.020 0.001 TYR R 32 PHE 0.028 0.002 PHE R 199 TRP 0.022 0.002 TRP R 170 HIS 0.008 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 8468) covalent geometry : angle 0.59802 / 0.31 (11492) SS BOND : bond 0.00219 / 0.11 ( 2) SS BOND : angle 0.89400 / 0.50 ( 4) hydrogen bonds : bond 0.04331 / 2.89 ( 384) hydrogen bonds : angle 4.85092 / 3.38 ( 1104) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 210 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8085 (ttpp) cc_final: 0.7748 (ttmm) REVERT: A 289 GLU cc_start: 0.7989 (tp30) cc_final: 0.7348 (tp30) REVERT: A 309 THR cc_start: 0.8182 (t) cc_final: 0.7915 (p) REVERT: A 317 GLU cc_start: 0.6855 (mp0) cc_final: 0.6290 (mp0) REVERT: A 346 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7531 (mtt-85) REVERT: A 366 PHE cc_start: 0.7925 (t80) cc_final: 0.6898 (t80) REVERT: A 371 ASP cc_start: 0.8186 (t70) cc_final: 0.7647 (t70) REVERT: B 49 ARG cc_start: 0.7954 (mtt90) cc_final: 0.7686 (mtt90) REVERT: B 67 SER cc_start: 0.8829 (m) cc_final: 0.8370 (t) REVERT: B 121 CYS cc_start: 0.8043 (t) cc_final: 0.7645 (t) REVERT: B 169 TRP cc_start: 0.8648 (m100) cc_final: 0.8157 (m100) REVERT: B 220 GLN cc_start: 0.7999 (pt0) cc_final: 0.7608 (pt0) REVERT: B 258 ASP cc_start: 0.8032 (t70) cc_final: 0.7286 (t0) REVERT: B 259 GLN cc_start: 0.8550 (tt0) cc_final: 0.8327 (tt0) REVERT: G 28 ILE cc_start: 0.8097 (mp) cc_final: 0.7857 (mp) REVERT: R 65 TYR cc_start: 0.8065 (m-80) cc_final: 0.7476 (m-80) outliers start: 37 outliers final: 26 residues processed: 231 average time/residue: 0.0939 time to fit residues: 28.3524 Evaluate side-chains 233 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain R residue 210 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 0.0010 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 0.1980 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 ASN A 377 ASN B 239 ASN N 53 GLN R 277 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.147507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.128416 restraints weight = 12133.698| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.30 r_work: 0.3526 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8470 Z= 0.121 Angle : 0.572 6.633 11496 Z= 0.293 Chirality : 0.043 0.150 1295 Planarity : 0.004 0.047 1452 Dihedral : 9.272 142.340 1155 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.52 % Favored : 96.28 % Rotamer: Outliers : 3.46 % Allowed : 21.88 % Favored : 74.67 % 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: 0.05 (0.27), residues: 1022 helix: 1.37 (0.27), residues: 394 sheet: -0.13 (0.36), residues: 217 loop : -1.18 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.024 0.001 TYR R 32 PHE 0.021 0.001 PHE R 199 TRP 0.024 0.001 TRP R 170 HIS 0.006 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 8468) covalent geometry : angle 0.57209 / 0.29 (11492) SS BOND : bond 0.00153 / 0.08 ( 2) SS BOND : angle 0.81703 / 0.45 ( 4) hydrogen bonds : bond 0.03815 / 2.56 ( 384) hydrogen bonds : angle 4.73880 / 3.29 ( 1104) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8111 (ttpp) cc_final: 0.7790 (ttmm) REVERT: A 289 GLU cc_start: 0.8019 (tp30) cc_final: 0.7362 (tp30) REVERT: A 309 THR cc_start: 0.8190 (t) cc_final: 0.7911 (p) REVERT: A 317 GLU cc_start: 0.6884 (mp0) cc_final: 0.6302 (mp0) REVERT: A 346 ARG cc_start: 0.8183 (mtt-85) cc_final: 0.7719 (mtt-85) REVERT: A 371 ASP cc_start: 0.8242 (t70) cc_final: 0.7991 (t0) REVERT: B 49 ARG cc_start: 0.7925 (mtt90) cc_final: 0.7645 (mtt90) REVERT: B 67 SER cc_start: 0.8763 (m) cc_final: 0.8344 (t) REVERT: B 103 CYS cc_start: 0.7715 (m) cc_final: 0.7287 (m) REVERT: B 169 TRP cc_start: 0.8630 (m100) cc_final: 0.8390 (m100) REVERT: B 220 GLN cc_start: 0.7970 (pt0) cc_final: 0.7618 (pt0) REVERT: B 258 ASP cc_start: 0.8069 (t70) cc_final: 0.7336 (t0) REVERT: B 259 GLN cc_start: 0.8582 (tt0) cc_final: 0.8375 (tt0) REVERT: G 28 ILE cc_start: 0.7967 (mp) cc_final: 0.7718 (mp) REVERT: R 65 TYR cc_start: 0.8043 (m-80) cc_final: 0.7528 (m-80) REVERT: R 199 PHE cc_start: 0.7087 (m-80) cc_final: 0.6796 (m-80) REVERT: R 272 MET cc_start: 0.7668 (mtt) cc_final: 0.7457 (mtt) outliers start: 31 outliers final: 22 residues processed: 228 average time/residue: 0.0933 time to fit residues: 27.5163 Evaluate side-chains 232 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 210 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 54 optimal weight: 0.9990 chunk 99 optimal weight: 0.0570 chunk 12 optimal weight: 0.3980 chunk 92 optimal weight: 7.9990 chunk 69 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 ASN A 377 ASN N 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.147954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.128858 restraints weight = 11999.826| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.25 r_work: 0.3524 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8470 Z= 0.137 Angle : 0.602 13.075 11496 Z= 0.304 Chirality : 0.043 0.174 1295 Planarity : 0.004 0.048 1452 Dihedral : 9.179 141.825 1155 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.72 % Favored : 96.09 % Rotamer: Outliers : 3.01 % Allowed : 22.66 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.27), residues: 1022 helix: 1.37 (0.27), residues: 393 sheet: -0.13 (0.36), residues: 217 loop : -1.18 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.025 0.001 TYR R 32 PHE 0.020 0.001 PHE R 199 TRP 0.026 0.001 TRP R 170 HIS 0.006 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 8468) covalent geometry : angle 0.60232 / 0.30 (11492) SS BOND : bond 0.00179 / 0.09 ( 2) SS BOND : angle 0.81542 / 0.45 ( 4) hydrogen bonds : bond 0.03897 / 2.59 ( 384) hydrogen bonds : angle 4.75301 / 3.33 ( 1104) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8092 (ttpp) cc_final: 0.7772 (ttmm) REVERT: A 289 GLU cc_start: 0.8004 (tp30) cc_final: 0.7358 (tp30) REVERT: A 309 THR cc_start: 0.8175 (t) cc_final: 0.7916 (p) REVERT: A 317 GLU cc_start: 0.6906 (mp0) cc_final: 0.6348 (mp0) REVERT: A 346 ARG cc_start: 0.8170 (mtt-85) cc_final: 0.7735 (mtt-85) REVERT: A 364 ARG cc_start: 0.8391 (mtm-85) cc_final: 0.8134 (mtt-85) REVERT: A 371 ASP cc_start: 0.8202 (t70) cc_final: 0.7921 (t0) REVERT: B 49 ARG cc_start: 0.7940 (mtt90) cc_final: 0.7672 (mtt90) REVERT: B 67 SER cc_start: 0.8805 (m) cc_final: 0.8374 (t) REVERT: B 103 CYS cc_start: 0.7715 (m) cc_final: 0.7296 (m) REVERT: B 169 TRP cc_start: 0.8612 (m100) cc_final: 0.8376 (m100) REVERT: B 220 GLN cc_start: 0.7946 (pt0) cc_final: 0.7608 (pt0) REVERT: B 256 ARG cc_start: 0.8205 (ptp-110) cc_final: 0.7941 (ptp-110) REVERT: B 258 ASP cc_start: 0.8077 (t70) cc_final: 0.7331 (t0) REVERT: G 28 ILE cc_start: 0.7973 (mp) cc_final: 0.7727 (mp) REVERT: R 65 TYR cc_start: 0.8055 (m-80) cc_final: 0.7538 (m-80) outliers start: 27 outliers final: 23 residues processed: 226 average time/residue: 0.1185 time to fit residues: 34.5260 Evaluate side-chains 230 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 210 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 0.0050 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 73 optimal weight: 0.0050 chunk 82 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 overall best weight: 0.3608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 ASN A 377 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.148749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.129836 restraints weight = 12016.107| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.26 r_work: 0.3542 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8470 Z= 0.125 Angle : 0.604 12.166 11496 Z= 0.304 Chirality : 0.043 0.159 1295 Planarity : 0.004 0.049 1452 Dihedral : 9.065 141.701 1155 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.72 % Favored : 96.09 % Rotamer: Outliers : 3.12 % Allowed : 22.88 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.27), residues: 1022 helix: 1.38 (0.27), residues: 393 sheet: -0.05 (0.37), residues: 215 loop : -1.16 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.028 0.001 TYR R 32 PHE 0.026 0.001 PHE R 82 TRP 0.028 0.001 TRP R 170 HIS 0.008 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 8468) covalent geometry : angle 0.60441 / 0.30 (11492) SS BOND : bond 0.00163 / 0.08 ( 2) SS BOND : angle 0.78820 / 0.43 ( 4) hydrogen bonds : bond 0.03753 / 2.50 ( 384) hydrogen bonds : angle 4.71240 / 3.29 ( 1104) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8079 (ttpp) cc_final: 0.7767 (ttmm) REVERT: A 289 GLU cc_start: 0.8002 (tp30) cc_final: 0.7355 (tp30) REVERT: A 309 THR cc_start: 0.8175 (t) cc_final: 0.7916 (p) REVERT: A 317 GLU cc_start: 0.6899 (mp0) cc_final: 0.6347 (mp0) REVERT: A 346 ARG cc_start: 0.8200 (mtt-85) cc_final: 0.7744 (mtt-85) REVERT: A 363 ARG cc_start: 0.7889 (tpp-160) cc_final: 0.7668 (tpp-160) REVERT: A 364 ARG cc_start: 0.8387 (mtm-85) cc_final: 0.8169 (mtt-85) REVERT: A 366 PHE cc_start: 0.7914 (t80) cc_final: 0.7433 (t80) REVERT: A 371 ASP cc_start: 0.8228 (t70) cc_final: 0.7937 (t0) REVERT: B 49 ARG cc_start: 0.7928 (mtt90) cc_final: 0.7667 (mtt90) REVERT: B 61 MET cc_start: 0.7901 (ppp) cc_final: 0.7315 (ppp) REVERT: B 67 SER cc_start: 0.8795 (m) cc_final: 0.8354 (t) REVERT: B 103 CYS cc_start: 0.7718 (m) cc_final: 0.7318 (m) REVERT: B 169 TRP cc_start: 0.8612 (m100) cc_final: 0.8375 (m100) REVERT: B 220 GLN cc_start: 0.7942 (pt0) cc_final: 0.7576 (pt0) REVERT: B 234 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.7903 (m-80) REVERT: B 256 ARG cc_start: 0.8193 (ptp-110) cc_final: 0.7969 (ptp-110) REVERT: B 258 ASP cc_start: 0.8104 (t70) cc_final: 0.7352 (t0) REVERT: R 65 TYR cc_start: 0.8060 (m-80) cc_final: 0.7543 (m-80) outliers start: 28 outliers final: 26 residues processed: 227 average time/residue: 0.1215 time to fit residues: 35.6468 Evaluate side-chains 232 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 210 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 86 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 85 optimal weight: 0.0970 chunk 14 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN A 268 ASN A 377 ASN N 53 GLN R 277 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.147619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.128576 restraints weight = 12024.799| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.25 r_work: 0.3517 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8470 Z= 0.152 Angle : 0.630 12.398 11496 Z= 0.316 Chirality : 0.044 0.161 1295 Planarity : 0.004 0.049 1452 Dihedral : 9.026 140.963 1155 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.52 % Favored : 96.28 % Rotamer: Outliers : 3.12 % Allowed : 23.10 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.27), residues: 1022 helix: 1.33 (0.27), residues: 393 sheet: -0.13 (0.37), residues: 217 loop : -1.16 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.028 0.001 TYR R 32 PHE 0.026 0.001 PHE R 82 TRP 0.030 0.002 TRP R 170 HIS 0.009 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 8468) covalent geometry : angle 0.62993 / 0.32 (11492) SS BOND : bond 0.00194 / 0.10 ( 2) SS BOND : angle 0.82496 / 0.45 ( 4) hydrogen bonds : bond 0.03986 / 2.65 ( 384) hydrogen bonds : angle 4.75994 / 3.33 ( 1104) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8088 (ttpp) cc_final: 0.7776 (ttmm) REVERT: A 289 GLU cc_start: 0.7995 (tp30) cc_final: 0.7362 (tp30) REVERT: A 309 THR cc_start: 0.8177 (t) cc_final: 0.7926 (p) REVERT: A 317 GLU cc_start: 0.6899 (mp0) cc_final: 0.6348 (mp0) REVERT: A 366 PHE cc_start: 0.7918 (t80) cc_final: 0.7439 (t80) REVERT: A 371 ASP cc_start: 0.8249 (t70) cc_final: 0.7977 (t0) REVERT: B 49 ARG cc_start: 0.7985 (mtt90) cc_final: 0.7738 (mtt90) REVERT: B 61 MET cc_start: 0.7958 (ppp) cc_final: 0.7288 (ptt) REVERT: B 67 SER cc_start: 0.8859 (m) cc_final: 0.8426 (t) REVERT: B 103 CYS cc_start: 0.7731 (m) cc_final: 0.7299 (m) REVERT: B 169 TRP cc_start: 0.8619 (m100) cc_final: 0.8382 (m100) REVERT: B 220 GLN cc_start: 0.7965 (pt0) cc_final: 0.7584 (pt0) REVERT: B 256 ARG cc_start: 0.8247 (ptp-110) cc_final: 0.7914 (ptp-110) REVERT: B 258 ASP cc_start: 0.8117 (t70) cc_final: 0.7248 (t0) REVERT: B 259 GLN cc_start: 0.8696 (tt0) cc_final: 0.8381 (mt0) REVERT: B 273 ILE cc_start: 0.8485 (mp) cc_final: 0.8092 (mp) REVERT: G 28 ILE cc_start: 0.8012 (mp) cc_final: 0.7779 (mp) REVERT: R 65 TYR cc_start: 0.8130 (m-80) cc_final: 0.7533 (m-80) REVERT: R 272 MET cc_start: 0.7784 (mtt) cc_final: 0.7285 (mmm) outliers start: 28 outliers final: 28 residues processed: 227 average time/residue: 0.1119 time to fit residues: 32.8394 Evaluate side-chains 239 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 200 PHE Chi-restraints excluded: chain R residue 210 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 0.4980 chunk 63 optimal weight: 0.5980 chunk 76 optimal weight: 0.0970 chunk 51 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 56 optimal weight: 0.0020 chunk 55 optimal weight: 0.8980 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 ASN A 377 ASN N 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.148601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.129562 restraints weight = 12133.236| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.26 r_work: 0.3544 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8470 Z= 0.125 Angle : 0.609 11.346 11496 Z= 0.306 Chirality : 0.043 0.159 1295 Planarity : 0.004 0.049 1452 Dihedral : 8.886 141.359 1155 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.82 % Favored : 95.99 % Rotamer: Outliers : 3.35 % Allowed : 23.10 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.27), residues: 1022 helix: 1.39 (0.27), residues: 392 sheet: -0.14 (0.36), residues: 217 loop : -1.18 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 232 TYR 0.029 0.001 TYR R 32 PHE 0.026 0.001 PHE R 82 TRP 0.028 0.001 TRP R 170 HIS 0.004 0.001 HIS R 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 8468) covalent geometry : angle 0.60860 / 0.31 (11492) SS BOND : bond 0.00173 / 0.09 ( 2) SS BOND : angle 0.78752 / 0.43 ( 4) hydrogen bonds : bond 0.03706 / 2.47 ( 384) hydrogen bonds : angle 4.70785 / 3.29 ( 1104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2053.68 seconds wall clock time: 35 minutes 54.77 seconds (2154.77 seconds total)