Starting phenix.real_space_refine on Wed Aug 5 08:53:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8j6r_36012/08_2026/8j6r_36012.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6r_36012/08_2026/8j6r_36012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j6r_36012/08_2026/8j6r_36012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6r_36012/08_2026/8j6r_36012.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8j6r_36012/08_2026/8j6r_36012.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8j6r_36012/08_2026/8j6r_36012.cif" model { file = "/net/cci-nas-00/data/ceres_data/8j6r_36012/08_2026/8j6r_36012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6r_36012/08_2026/8j6r_36012.cif" } resolution = 2.76 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= 0.002 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 5811 2.51 5 N 1554 2.21 5 O 1686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9120 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1795 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2420 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 284} Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'FI7': 1, 'NAG': 1} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.45, per 1000 atoms: 0.27 Number of scatterers: 9120 At special positions: 0 Unit cell: (108.498, 122.694, 112.554, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 1686 8.00 N 1554 7.00 C 5811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.04 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " 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 Links applied NAG-ASN " NAG R 402 " - " ASN R 17 " Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 416.5 milliseconds 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 37.9% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.387A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.691A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 removed outlier: 4.512A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.242A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.648A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.581A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 23 through 55 removed outlier: 4.010A pdb=" N VAL R 27 " --> pdb=" O ASP R 23 " (cutoff:3.500A) Proline residue: R 31 - end of helix Processing helix chain 'R' and resid 60 through 78 Processing helix chain 'R' and resid 79 through 89 removed outlier: 3.923A pdb=" N LEU R 83 " --> pdb=" O CYS R 79 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG R 89 " --> pdb=" O ASP R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 130 removed outlier: 3.756A pdb=" N CYS R 100 " --> pdb=" O GLY R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 139 removed outlier: 3.615A pdb=" N ILE R 139 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 160 Processing helix chain 'R' and resid 161 through 163 No H-bonds generated for 'chain 'R' and resid 161 through 163' Processing helix chain 'R' and resid 187 through 218 removed outlier: 3.798A pdb=" N LEU R 194 " --> pdb=" O GLU R 190 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 200 - end of helix Processing helix chain 'R' and resid 219 through 222 removed outlier: 4.105A pdb=" N ARG R 222 " --> pdb=" O GLN R 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 219 through 222' Processing helix chain 'R' and resid 223 through 261 Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 265 through 268 removed outlier: 3.863A pdb=" N VAL R 268 " --> pdb=" O ASN R 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 265 through 268' Processing helix chain 'R' and resid 269 through 295 removed outlier: 3.812A pdb=" N PHE R 277 " --> pdb=" O ASP R 273 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER R 287 " --> pdb=" O THR R 283 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.699A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.569A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.970A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.104A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.558A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.084A 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: 6.850A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.400A 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: 3.599A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.581A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.961A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.961A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.786A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.540A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 10 through 11 removed outlier: 4.034A pdb=" N CYS R 18 " --> pdb=" O LEU R 11 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 169 through 170 442 hydrogen bonds defined for protein. 1227 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.56 Time building geometry restraints manager: 1.56 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: 2928 1.34 - 1.46: 2278 1.46 - 1.58: 4012 1.58 - 1.71: 1 1.71 - 1.83: 100 Bond restraints: 9319 Sorted by residual: bond pdb=" C20 FI7 R 401 " pdb=" N19 FI7 R 401 " ideal model delta sigma weight residual 1.396 1.486 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C07 FI7 R 401 " pdb=" C08 FI7 R 401 " ideal model delta sigma weight residual 1.466 1.546 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C04 FI7 R 401 " pdb=" C05 FI7 R 401 " ideal model delta sigma weight residual 1.483 1.563 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C05 FI7 R 401 " pdb=" O16 FI7 R 401 " ideal model delta sigma weight residual 1.330 1.406 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C17 FI7 R 401 " pdb=" N19 FI7 R 401 " ideal model delta sigma weight residual 1.348 1.420 -0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 9314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 12395 2.03 - 4.06: 168 4.06 - 6.08: 38 6.08 - 8.11: 7 8.11 - 10.14: 2 Bond angle restraints: 12610 Sorted by residual: angle pdb=" C MET R 167 " pdb=" N PRO R 168 " pdb=" CA PRO R 168 " ideal model delta sigma weight residual 127.00 136.86 -9.86 2.40e+00 1.74e-01 1.69e+01 angle pdb=" C ASP R 14 " pdb=" N LYS R 15 " pdb=" CA LYS R 15 " ideal model delta sigma weight residual 121.54 129.12 -7.58 1.91e+00 2.74e-01 1.57e+01 angle pdb=" C MET R 167 " pdb=" N PRO R 168 " pdb=" CD PRO R 168 " ideal model delta sigma weight residual 120.60 112.67 7.93 2.20e+00 2.07e-01 1.30e+01 angle pdb=" C02 FI7 R 401 " pdb=" C17 FI7 R 401 " pdb=" N19 FI7 R 401 " ideal model delta sigma weight residual 113.44 123.58 -10.14 3.00e+00 1.11e-01 1.14e+01 angle pdb=" N HIS R 184 " pdb=" CA HIS R 184 " pdb=" C HIS R 184 " ideal model delta sigma weight residual 111.30 115.76 -4.46 1.36e+00 5.41e-01 1.08e+01 ... (remaining 12605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 4976 16.57 - 33.13: 451 33.13 - 49.70: 102 49.70 - 66.26: 17 66.26 - 82.83: 7 Dihedral angle restraints: 5553 sinusoidal: 2218 harmonic: 3335 Sorted by residual: dihedral pdb=" CB CYS R 100 " pdb=" SG CYS R 100 " pdb=" SG CYS R 177 " pdb=" CB CYS R 177 " ideal model delta sinusoidal sigma weight residual 93.00 138.69 -45.69 1 1.00e+01 1.00e-02 2.89e+01 dihedral pdb=" CB CYS R 18 " pdb=" SG CYS R 18 " pdb=" SG CYS R 183 " pdb=" CB CYS R 183 " ideal model delta sinusoidal sigma weight residual 93.00 53.83 39.17 1 1.00e+01 1.00e-02 2.16e+01 dihedral pdb=" CA PHE A 323 " pdb=" C PHE A 323 " pdb=" N THR A 324 " pdb=" CA THR A 324 " ideal model delta harmonic sigma weight residual -180.00 -160.03 -19.97 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 5550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.244: 1411 0.244 - 0.489: 0 0.489 - 0.733: 0 0.733 - 0.977: 0 0.977 - 1.222: 1 Chirality restraints: 1412 Sorted by residual: chirality pdb=" C1 NAG R 402 " pdb=" ND2 ASN R 17 " pdb=" C2 NAG R 402 " pdb=" O5 NAG R 402 " both_signs ideal model delta sigma weight residual False -2.40 -1.18 -1.22 2.00e-01 2.50e+01 3.73e+01 chirality pdb=" CA TRP R 59 " pdb=" N TRP R 59 " pdb=" C TRP R 59 " pdb=" CB TRP R 59 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA TYR S 190 " pdb=" N TYR S 190 " pdb=" C TYR S 190 " pdb=" CB TYR S 190 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1409 not shown) Planarity restraints: 1595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 402 " 0.350 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG R 402 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG R 402 " 0.154 2.00e-02 2.50e+03 pdb=" N2 NAG R 402 " -0.533 2.00e-02 2.50e+03 pdb=" O7 NAG R 402 " 0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.059 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO S 75 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 17 " 0.026 2.00e-02 2.50e+03 2.89e-02 1.05e+01 pdb=" CG ASN R 17 " -0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN R 17 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN R 17 " -0.047 2.00e-02 2.50e+03 pdb=" C1 NAG R 402 " 0.035 2.00e-02 2.50e+03 ... (remaining 1592 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 137 2.67 - 3.23: 8076 3.23 - 3.79: 13912 3.79 - 4.34: 18688 4.34 - 4.90: 32033 Nonbonded interactions: 72846 Sorted by model distance: nonbonded pdb=" O GLU R 196 " pdb=" CG PRO R 200 " model vdw 2.116 3.440 nonbonded pdb=" O GLU R 196 " pdb=" CD PRO R 200 " model vdw 2.125 3.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.208 3.040 nonbonded pdb=" O LYS R 60 " pdb=" N ARG R 63 " model vdw 2.228 3.120 nonbonded pdb=" O LEU B 30 " pdb=" OG1 THR B 34 " model vdw 2.280 3.040 ... (remaining 72841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.390 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 9325 Z= 0.203 Angle : 0.638 11.606 12623 Z= 0.328 Chirality : 0.055 1.222 1412 Planarity : 0.009 0.300 1594 Dihedral : 13.554 82.831 3382 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.52 (0.25), residues: 1137 helix: 1.31 (0.27), residues: 387 sheet: 0.50 (0.31), residues: 295 loop : -0.53 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 253 TYR 0.016 0.001 TYR S 190 PHE 0.015 0.001 PHE R 52 TRP 0.012 0.001 TRP R 59 HIS 0.004 0.001 HIS R 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 ( 9319) covalent geometry : angle 0.62494 / 0.32 (12610) SS BOND : bond 0.00438 / 0.24 ( 5) SS BOND : angle 0.97055 / 0.58 ( 10) hydrogen bonds : bond 0.16613 / 10.90 ( 438) hydrogen bonds : angle 6.09129 / 4.11 ( 1227) link_NAG-ASN : bond 0.06041 / 3.18 ( 1) link_NAG-ASN : angle 8.20026 / 4.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.308 Fit side-chains REVERT: A 25 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6707 (mm-30) REVERT: A 28 GLU cc_start: 0.6756 (mp0) cc_final: 0.6365 (mp0) REVERT: A 270 LYS cc_start: 0.8072 (mtmm) cc_final: 0.7775 (mttm) REVERT: A 337 ASP cc_start: 0.7542 (m-30) cc_final: 0.7334 (m-30) REVERT: B 89 LYS cc_start: 0.8421 (mttp) cc_final: 0.8198 (mttt) REVERT: B 254 ASP cc_start: 0.7008 (t70) cc_final: 0.6596 (t0) REVERT: B 268 ASN cc_start: 0.7227 (m110) cc_final: 0.7021 (m110) REVERT: S 219 LEU cc_start: 0.8014 (tt) cc_final: 0.7812 (tt) REVERT: R 22 ARG cc_start: 0.6712 (mtm-85) cc_final: 0.6482 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.5177 time to fit residues: 113.3951 Evaluate side-chains 190 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.1164 > 50:) chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN S 186 GLN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.145670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.123887 restraints weight = 12231.878| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.96 r_work: 0.3491 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9325 Z= 0.161 Angle : 0.562 8.223 12623 Z= 0.299 Chirality : 0.043 0.211 1412 Planarity : 0.005 0.071 1594 Dihedral : 5.569 39.744 1290 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.21 % Allowed : 8.84 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.79 (0.26), residues: 1137 helix: 1.57 (0.27), residues: 392 sheet: 0.59 (0.31), residues: 287 loop : -0.37 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 270 TYR 0.027 0.002 TYR S 190 PHE 0.013 0.001 PHE R 117 TRP 0.019 0.002 TRP R 59 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 9319) covalent geometry : angle 0.55550 / 0.30 (12610) SS BOND : bond 0.00596 / 0.30 ( 5) SS BOND : angle 1.09060 / 0.64 ( 10) hydrogen bonds : bond 0.04653 / 3.02 ( 438) hydrogen bonds : angle 4.70215 / 3.24 ( 1227) link_NAG-ASN : bond 0.00750 / 0.39 ( 1) link_NAG-ASN : angle 5.26148 / 2.97 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 0.218 Fit side-chains REVERT: A 190 THR cc_start: 0.8608 (t) cc_final: 0.8370 (m) REVERT: A 210 LYS cc_start: 0.8223 (mmtt) cc_final: 0.8020 (mptp) REVERT: A 337 ASP cc_start: 0.8083 (m-30) cc_final: 0.7847 (m-30) REVERT: B 158 VAL cc_start: 0.8713 (p) cc_final: 0.8480 (t) REVERT: B 254 ASP cc_start: 0.7779 (t70) cc_final: 0.7420 (t0) REVERT: B 268 ASN cc_start: 0.7643 (m110) cc_final: 0.7409 (m-40) REVERT: R 146 ILE cc_start: 0.7207 (OUTLIER) cc_final: 0.6824 (mp) outliers start: 22 outliers final: 12 residues processed: 207 average time/residue: 0.4423 time to fit residues: 97.8355 Evaluate side-chains 208 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 195 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 192 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 103 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 30 optimal weight: 0.4980 chunk 90 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN B 340 ASN S 186 GLN R 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.144762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.122851 restraints weight = 12267.321| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.97 r_work: 0.3480 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9325 Z= 0.171 Angle : 0.559 6.563 12623 Z= 0.298 Chirality : 0.043 0.219 1412 Planarity : 0.004 0.066 1594 Dihedral : 5.594 41.380 1290 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.51 % Allowed : 11.36 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.77 (0.25), residues: 1137 helix: 1.60 (0.27), residues: 393 sheet: 0.61 (0.30), residues: 298 loop : -0.48 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 270 TYR 0.026 0.002 TYR S 190 PHE 0.014 0.002 PHE R 117 TRP 0.011 0.002 TRP B 82 HIS 0.006 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 9319) covalent geometry : angle 0.55429 / 0.30 (12610) SS BOND : bond 0.00577 / 0.29 ( 5) SS BOND : angle 1.11825 / 0.65 ( 10) hydrogen bonds : bond 0.04489 / 2.91 ( 438) hydrogen bonds : angle 4.57934 / 3.20 ( 1227) link_NAG-ASN : bond 0.00554 / 0.29 ( 1) link_NAG-ASN : angle 4.40868 / 2.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.311 Fit side-chains REVERT: A 190 THR cc_start: 0.8611 (t) cc_final: 0.8408 (m) REVERT: A 337 ASP cc_start: 0.8135 (m-30) cc_final: 0.7914 (m-30) REVERT: B 254 ASP cc_start: 0.7790 (t70) cc_final: 0.7430 (t70) REVERT: B 268 ASN cc_start: 0.7672 (m110) cc_final: 0.7427 (m-40) REVERT: R 83 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6705 (mp) REVERT: R 128 ARG cc_start: 0.8801 (mtt90) cc_final: 0.8583 (mtt90) REVERT: R 146 ILE cc_start: 0.7192 (OUTLIER) cc_final: 0.6812 (mp) outliers start: 25 outliers final: 16 residues processed: 207 average time/residue: 0.4348 time to fit residues: 96.4095 Evaluate side-chains 209 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 192 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 86 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 102 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.145561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.123717 restraints weight = 12402.103| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.00 r_work: 0.3492 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9325 Z= 0.124 Angle : 0.516 6.097 12623 Z= 0.278 Chirality : 0.042 0.191 1412 Planarity : 0.004 0.064 1594 Dihedral : 5.430 39.332 1290 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.41 % Allowed : 13.07 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.83 (0.25), residues: 1137 helix: 1.73 (0.27), residues: 393 sheet: 0.59 (0.30), residues: 293 loop : -0.47 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 270 TYR 0.024 0.001 TYR S 190 PHE 0.009 0.001 PHE B 151 TRP 0.010 0.001 TRP R 256 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 9319) covalent geometry : angle 0.51212 / 0.28 (12610) SS BOND : bond 0.00422 / 0.21 ( 5) SS BOND : angle 0.91671 / 0.52 ( 10) hydrogen bonds : bond 0.03941 / 2.55 ( 438) hydrogen bonds : angle 4.47669 / 3.14 ( 1227) link_NAG-ASN : bond 0.00495 / 0.26 ( 1) link_NAG-ASN : angle 3.94211 / 2.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.193 Fit side-chains REVERT: A 28 GLU cc_start: 0.7531 (mp0) cc_final: 0.7331 (mp0) REVERT: A 337 ASP cc_start: 0.8166 (m-30) cc_final: 0.7929 (m-30) REVERT: B 254 ASP cc_start: 0.7781 (t70) cc_final: 0.7418 (t70) REVERT: B 268 ASN cc_start: 0.7709 (m110) cc_final: 0.7479 (m-40) REVERT: S 140 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7847 (mtm) REVERT: R 83 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6579 (mp) REVERT: R 146 ILE cc_start: 0.7174 (OUTLIER) cc_final: 0.6795 (mp) outliers start: 24 outliers final: 15 residues processed: 205 average time/residue: 0.4613 time to fit residues: 100.8868 Evaluate side-chains 207 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 146 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.143993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.122227 restraints weight = 12350.009| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.98 r_work: 0.3471 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9325 Z= 0.180 Angle : 0.561 6.626 12623 Z= 0.299 Chirality : 0.043 0.220 1412 Planarity : 0.004 0.062 1594 Dihedral : 5.644 41.008 1290 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.91 % Allowed : 14.37 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.71 (0.25), residues: 1137 helix: 1.57 (0.27), residues: 393 sheet: 0.55 (0.30), residues: 293 loop : -0.50 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 270 TYR 0.025 0.002 TYR S 190 PHE 0.015 0.002 PHE R 117 TRP 0.013 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 ( 9319) covalent geometry : angle 0.55634 / 0.30 (12610) SS BOND : bond 0.00585 / 0.29 ( 5) SS BOND : angle 1.18718 / 0.67 ( 10) hydrogen bonds : bond 0.04404 / 2.86 ( 438) hydrogen bonds : angle 4.53427 / 3.19 ( 1227) link_NAG-ASN : bond 0.00338 / 0.18 ( 1) link_NAG-ASN : angle 4.15158 / 2.34 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 0.347 Fit side-chains REVERT: A 28 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7258 (mp0) REVERT: A 260 THR cc_start: 0.8289 (m) cc_final: 0.7939 (p) REVERT: A 337 ASP cc_start: 0.8168 (m-30) cc_final: 0.7932 (m-30) REVERT: B 254 ASP cc_start: 0.7804 (t70) cc_final: 0.7443 (t70) REVERT: B 268 ASN cc_start: 0.7672 (m110) cc_final: 0.7441 (m-40) REVERT: R 83 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6582 (mp) REVERT: R 84 MET cc_start: 0.5046 (mtm) cc_final: 0.4193 (mmm) REVERT: R 146 ILE cc_start: 0.7194 (OUTLIER) cc_final: 0.6820 (mp) outliers start: 29 outliers final: 19 residues processed: 213 average time/residue: 0.4322 time to fit residues: 98.5479 Evaluate side-chains 217 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 146 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 82 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 72.0269 > 50:) chunk 55 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.144411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.122526 restraints weight = 12351.851| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.99 r_work: 0.3477 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9325 Z= 0.154 Angle : 0.538 6.063 12623 Z= 0.288 Chirality : 0.043 0.205 1412 Planarity : 0.004 0.060 1594 Dihedral : 5.578 40.148 1290 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.12 % Allowed : 14.97 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.77 (0.25), residues: 1137 helix: 1.65 (0.27), residues: 392 sheet: 0.54 (0.30), residues: 293 loop : -0.47 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 270 TYR 0.024 0.002 TYR S 190 PHE 0.012 0.001 PHE R 276 TRP 0.011 0.002 TRP B 82 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 9319) covalent geometry : angle 0.53438 / 0.29 (12610) SS BOND : bond 0.00520 / 0.26 ( 5) SS BOND : angle 1.10310 / 0.64 ( 10) hydrogen bonds : bond 0.04193 / 2.72 ( 438) hydrogen bonds : angle 4.50446 / 3.18 ( 1227) link_NAG-ASN : bond 0.00411 / 0.22 ( 1) link_NAG-ASN : angle 3.90581 / 2.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.252 Fit side-chains REVERT: A 28 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: A 337 ASP cc_start: 0.8198 (m-30) cc_final: 0.7962 (m-30) REVERT: B 254 ASP cc_start: 0.7797 (t70) cc_final: 0.7430 (t70) REVERT: B 268 ASN cc_start: 0.7669 (m110) cc_final: 0.7446 (m-40) REVERT: S 140 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7879 (mtm) REVERT: R 83 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6606 (mp) REVERT: R 146 ILE cc_start: 0.7177 (OUTLIER) cc_final: 0.6800 (mp) outliers start: 31 outliers final: 18 residues processed: 207 average time/residue: 0.4665 time to fit residues: 103.0822 Evaluate side-chains 214 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 91 optimal weight: 0.0670 chunk 100 optimal weight: 0.2980 chunk 56 optimal weight: 8.9990 chunk 50 optimal weight: 0.1980 chunk 3 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.144492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.122712 restraints weight = 12306.842| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.97 r_work: 0.3480 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9325 Z= 0.143 Angle : 0.542 7.108 12623 Z= 0.290 Chirality : 0.042 0.199 1412 Planarity : 0.004 0.059 1594 Dihedral : 5.553 40.359 1290 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.12 % Allowed : 15.68 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.76 (0.25), residues: 1137 helix: 1.65 (0.27), residues: 392 sheet: 0.52 (0.30), residues: 293 loop : -0.47 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG R 270 TYR 0.024 0.001 TYR S 190 PHE 0.010 0.001 PHE R 117 TRP 0.010 0.001 TRP R 256 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 9319) covalent geometry : angle 0.53823 / 0.29 (12610) SS BOND : bond 0.00492 / 0.24 ( 5) SS BOND : angle 1.03127 / 0.59 ( 10) hydrogen bonds : bond 0.04092 / 2.66 ( 438) hydrogen bonds : angle 4.50559 / 3.17 ( 1227) link_NAG-ASN : bond 0.00408 / 0.21 ( 1) link_NAG-ASN : angle 3.68142 / 2.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.320 Fit side-chains REVERT: A 28 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: A 337 ASP cc_start: 0.8203 (m-30) cc_final: 0.7981 (m-30) REVERT: B 254 ASP cc_start: 0.7786 (t70) cc_final: 0.7434 (t70) REVERT: B 268 ASN cc_start: 0.7692 (m110) cc_final: 0.7464 (m-40) REVERT: S 38 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8209 (ptt180) REVERT: S 140 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7861 (mtm) REVERT: R 83 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6582 (mp) REVERT: R 146 ILE cc_start: 0.7182 (OUTLIER) cc_final: 0.6803 (mp) REVERT: R 212 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7316 (mm) outliers start: 31 outliers final: 17 residues processed: 209 average time/residue: 0.5303 time to fit residues: 118.3958 Evaluate side-chains 216 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 95 optimal weight: 0.0570 chunk 17 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.144413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.122612 restraints weight = 12284.511| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.98 r_work: 0.3474 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9325 Z= 0.150 Angle : 0.550 8.009 12623 Z= 0.297 Chirality : 0.043 0.203 1412 Planarity : 0.004 0.058 1594 Dihedral : 5.579 41.466 1290 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.22 % Allowed : 16.28 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.75 (0.25), residues: 1137 helix: 1.59 (0.27), residues: 392 sheet: 0.53 (0.29), residues: 298 loop : -0.44 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 270 TYR 0.024 0.001 TYR S 190 PHE 0.011 0.001 PHE R 117 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 9319) covalent geometry : angle 0.54716 / 0.30 (12610) SS BOND : bond 0.00508 / 0.25 ( 5) SS BOND : angle 1.05765 / 0.60 ( 10) hydrogen bonds : bond 0.04125 / 2.67 ( 438) hydrogen bonds : angle 4.53376 / 3.18 ( 1227) link_NAG-ASN : bond 0.00434 / 0.23 ( 1) link_NAG-ASN : angle 3.55820 / 1.98 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.269 Fit side-chains REVERT: A 28 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: A 337 ASP cc_start: 0.8189 (m-30) cc_final: 0.7959 (m-30) REVERT: B 254 ASP cc_start: 0.7811 (t70) cc_final: 0.7450 (t70) REVERT: B 268 ASN cc_start: 0.7686 (m110) cc_final: 0.7456 (m-40) REVERT: S 38 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8253 (ptt180) REVERT: S 140 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7868 (mtm) REVERT: R 83 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6486 (mp) REVERT: R 146 ILE cc_start: 0.7176 (OUTLIER) cc_final: 0.6799 (mp) REVERT: R 212 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7334 (mm) outliers start: 32 outliers final: 22 residues processed: 210 average time/residue: 0.5171 time to fit residues: 115.7622 Evaluate side-chains 221 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 17 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN S 82 GLN S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.144843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.123027 restraints weight = 12325.829| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.99 r_work: 0.3475 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9325 Z= 0.143 Angle : 0.551 8.565 12623 Z= 0.296 Chirality : 0.043 0.199 1412 Planarity : 0.004 0.058 1594 Dihedral : 5.547 41.315 1290 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.62 % Allowed : 16.28 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.75 (0.25), residues: 1137 helix: 1.58 (0.27), residues: 393 sheet: 0.55 (0.29), residues: 298 loop : -0.46 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG R 270 TYR 0.023 0.001 TYR S 190 PHE 0.010 0.001 PHE R 117 TRP 0.011 0.001 TRP R 256 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 9319) covalent geometry : angle 0.54838 / 0.30 (12610) SS BOND : bond 0.00485 / 0.24 ( 5) SS BOND : angle 1.03038 / 0.59 ( 10) hydrogen bonds : bond 0.04039 / 2.62 ( 438) hydrogen bonds : angle 4.54046 / 3.19 ( 1227) link_NAG-ASN : bond 0.00537 / 0.28 ( 1) link_NAG-ASN : angle 3.46939 / 1.89 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.336 Fit side-chains REVERT: A 28 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: A 337 ASP cc_start: 0.8197 (m-30) cc_final: 0.7970 (m-30) REVERT: B 254 ASP cc_start: 0.7795 (t70) cc_final: 0.7437 (t70) REVERT: B 268 ASN cc_start: 0.7701 (m110) cc_final: 0.7471 (m-40) REVERT: S 38 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7974 (ptt-90) REVERT: S 140 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7864 (mtm) REVERT: R 83 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6473 (mp) REVERT: R 146 ILE cc_start: 0.7176 (OUTLIER) cc_final: 0.6800 (mp) REVERT: R 212 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7336 (mm) outliers start: 36 outliers final: 25 residues processed: 211 average time/residue: 0.4944 time to fit residues: 111.5991 Evaluate side-chains 222 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 91 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.144187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.122855 restraints weight = 12321.633| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.94 r_work: 0.3485 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9325 Z= 0.136 Angle : 0.554 10.518 12623 Z= 0.298 Chirality : 0.043 0.195 1412 Planarity : 0.004 0.061 1594 Dihedral : 5.524 41.405 1290 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.12 % Allowed : 16.78 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.75 (0.25), residues: 1137 helix: 1.58 (0.27), residues: 393 sheet: 0.55 (0.30), residues: 298 loop : -0.46 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG R 270 TYR 0.022 0.001 TYR S 190 PHE 0.009 0.001 PHE A 189 TRP 0.010 0.001 TRP R 256 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 9319) covalent geometry : angle 0.55158 / 0.30 (12610) SS BOND : bond 0.00463 / 0.23 ( 5) SS BOND : angle 0.98627 / 0.57 ( 10) hydrogen bonds : bond 0.03971 / 2.57 ( 438) hydrogen bonds : angle 4.54878 / 3.19 ( 1227) link_NAG-ASN : bond 0.00482 / 0.25 ( 1) link_NAG-ASN : angle 3.38006 / 1.85 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.254 Fit side-chains REVERT: A 28 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: A 337 ASP cc_start: 0.8186 (m-30) cc_final: 0.7963 (m-30) REVERT: B 254 ASP cc_start: 0.7766 (t70) cc_final: 0.7410 (t70) REVERT: B 268 ASN cc_start: 0.7720 (m110) cc_final: 0.7486 (m-40) REVERT: S 38 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7971 (ptt-90) REVERT: S 140 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7839 (mtm) REVERT: R 83 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6430 (mp) REVERT: R 146 ILE cc_start: 0.7178 (OUTLIER) cc_final: 0.6804 (mp) REVERT: R 212 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7322 (mm) outliers start: 31 outliers final: 23 residues processed: 205 average time/residue: 0.5082 time to fit residues: 111.2894 Evaluate side-chains 218 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 17 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN S 82 GLN R 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.144277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.122555 restraints weight = 12206.225| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.97 r_work: 0.3479 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9325 Z= 0.144 Angle : 0.558 11.040 12623 Z= 0.300 Chirality : 0.043 0.200 1412 Planarity : 0.004 0.059 1594 Dihedral : 5.509 41.877 1290 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.12 % Allowed : 16.98 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.74 (0.25), residues: 1137 helix: 1.57 (0.27), residues: 394 sheet: 0.56 (0.30), residues: 298 loop : -0.47 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 270 TYR 0.023 0.001 TYR S 190 PHE 0.010 0.001 PHE R 82 TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 9319) covalent geometry : angle 0.55530 / 0.30 (12610) SS BOND : bond 0.00494 / 0.24 ( 5) SS BOND : angle 1.01487 / 0.58 ( 10) hydrogen bonds : bond 0.04021 / 2.59 ( 438) hydrogen bonds : angle 4.56679 / 3.20 ( 1227) link_NAG-ASN : bond 0.00501 / 0.26 ( 1) link_NAG-ASN : angle 3.40642 / 1.85 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3558.08 seconds wall clock time: 61 minutes 12.92 seconds (3672.92 seconds total)