Starting phenix.real_space_refine on Thu Jul 2 15:09:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jso_36625/07_2026/8jso_36625.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jso_36625/07_2026/8jso_36625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8jso_36625/07_2026/8jso_36625.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jso_36625/07_2026/8jso_36625.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jso_36625/07_2026/8jso_36625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jso_36625/07_2026/8jso_36625.map" model { file = "/net/cci-nas-00/data/ceres_data/8jso_36625/07_2026/8jso_36625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jso_36625/07_2026/8jso_36625.cif" } resolution = 3.4 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= 0.031 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 68 5.16 5 C 5764 2.51 5 N 1546 2.21 5 O 1667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 9045 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1928 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 1 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2292 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 1 Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1777 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'1WE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.77, per 1000 atoms: 0.20 Number of scatterers: 9045 At special positions: 0 Unit cell: (113.9, 130.05, 111.35, 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 68 16.00 O 1667 8.00 N 1546 7.00 C 5764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.03 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=2.03 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: 0.75 Conformation dependent library (CDL) restraints added in 551.2 milliseconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 1WE R 401 " Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 37.6% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.046A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.649A pdb=" N ARG A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 244 Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.113A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.883A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.616A pdb=" N THR A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 358 Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.557A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.664A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 51 removed outlier: 3.706A pdb=" N PHE R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 76 Processing helix chain 'R' and resid 76 through 86 removed outlier: 3.576A pdb=" N GLU R 86 " --> pdb=" O VAL R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 123 removed outlier: 4.403A pdb=" N PHE R 95 " --> pdb=" O PHE R 91 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS R 96 " --> pdb=" O GLY R 92 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS R 97 " --> pdb=" O GLU R 93 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE R 98 " --> pdb=" O VAL R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 131 removed outlier: 3.860A pdb=" N TYR R 131 " --> pdb=" O PRO R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 160 Proline residue: R 151 - end of helix removed outlier: 4.256A pdb=" N MET R 158 " --> pdb=" O PHE R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 178 Processing helix chain 'R' and resid 187 through 199 Processing helix chain 'R' and resid 200 through 228 removed outlier: 4.116A pdb=" N ILE R 205 " --> pdb=" O ILE R 201 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET R 206 " --> pdb=" O PRO R 202 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU R 207 " --> pdb=" O GLY R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 277 removed outlier: 4.058A pdb=" N VAL R 259 " --> pdb=" O ILE R 255 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE R 260 " --> pdb=" O VAL R 256 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS R 263 " --> pdb=" O VAL R 259 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TRP R 264 " --> pdb=" O PHE R 260 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N CYS R 265 " --> pdb=" O LEU R 261 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 282 through 305 removed outlier: 3.963A pdb=" N ASN R 286 " --> pdb=" O PRO R 282 " (cutoff:3.500A) Proline residue: R 301 - end of helix removed outlier: 3.614A pdb=" N ALA R 305 " --> pdb=" O PRO R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 319 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.926A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.871A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 23 Processing helix chain 'Y' and resid 29 through 44 removed outlier: 3.657A pdb=" N ALA Y 33 " --> pdb=" O LYS Y 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 191 removed outlier: 7.332A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.385A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.153A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.518A pdb=" N CYS B 114 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.518A pdb=" N CYS B 114 " --> pdb=" O SER B 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.594A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.621A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.963A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.589A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.797A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU S 79 " --> pdb=" O CYS S 22 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN S 82 " --> pdb=" O THR S 69 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR S 69 " --> pdb=" O GLN S 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.510A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142 removed outlier: 3.580A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.961A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 194 through 195 removed outlier: 4.022A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1164 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: 1.23 Time building geometry restraints manager: 1.05 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: 2899 1.34 - 1.46: 2070 1.46 - 1.58: 4177 1.58 - 1.70: 0 1.70 - 1.82: 102 Bond restraints: 9248 Sorted by residual: bond pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.26e-02 6.30e+03 7.22e+00 bond pdb=" CA SER B 331 " pdb=" CB SER B 331 " ideal model delta sigma weight residual 1.534 1.498 0.036 1.57e-02 4.06e+03 5.25e+00 bond pdb=" CA VAL R 150 " pdb=" CB VAL R 150 " ideal model delta sigma weight residual 1.539 1.528 0.011 5.40e-03 3.43e+04 3.95e+00 bond pdb=" N SER B 331 " pdb=" CA SER B 331 " ideal model delta sigma weight residual 1.455 1.479 -0.023 1.41e-02 5.03e+03 2.74e+00 bond pdb=" CG MET Y 38 " pdb=" SD MET Y 38 " ideal model delta sigma weight residual 1.803 1.773 0.030 2.50e-02 1.60e+03 1.43e+00 ... (remaining 9243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 12028 1.52 - 3.04: 400 3.04 - 4.56: 71 4.56 - 6.09: 15 6.09 - 7.61: 6 Bond angle restraints: 12520 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.47 109.24 4.23 1.01e+00 9.80e-01 1.75e+01 angle pdb=" N ILE A 212 " pdb=" CA ILE A 212 " pdb=" C ILE A 212 " ideal model delta sigma weight residual 112.96 109.01 3.95 1.00e+00 1.00e+00 1.56e+01 angle pdb=" CA MET Y 38 " pdb=" CB MET Y 38 " pdb=" CG MET Y 38 " ideal model delta sigma weight residual 114.10 120.59 -6.49 2.00e+00 2.50e-01 1.05e+01 angle pdb=" C LEU Y 37 " pdb=" N MET Y 38 " pdb=" CA MET Y 38 " ideal model delta sigma weight residual 121.14 115.75 5.39 1.75e+00 3.27e-01 9.48e+00 angle pdb=" N ASP B 333 " pdb=" CA ASP B 333 " pdb=" C ASP B 333 " ideal model delta sigma weight residual 112.92 109.20 3.72 1.23e+00 6.61e-01 9.15e+00 ... (remaining 12515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4938 17.91 - 35.82: 439 35.82 - 53.72: 86 53.72 - 71.63: 12 71.63 - 89.54: 6 Dihedral angle restraints: 5481 sinusoidal: 2150 harmonic: 3331 Sorted by residual: dihedral pdb=" CB CYS S 159 " pdb=" SG CYS S 159 " pdb=" SG CYS S 229 " pdb=" CB CYS S 229 " ideal model delta sinusoidal sigma weight residual -86.00 -113.68 27.68 1 1.00e+01 1.00e-02 1.10e+01 dihedral pdb=" CA ILE R 201 " pdb=" C ILE R 201 " pdb=" N PRO R 202 " pdb=" CA PRO R 202 " ideal model delta harmonic sigma weight residual 180.00 163.60 16.40 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CG ARG B 150 " pdb=" CD ARG B 150 " pdb=" NE ARG B 150 " pdb=" CZ ARG B 150 " ideal model delta sinusoidal sigma weight residual -180.00 -135.81 -44.19 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 5478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1084 0.047 - 0.094: 250 0.094 - 0.140: 60 0.140 - 0.187: 1 0.187 - 0.234: 2 Chirality restraints: 1397 Sorted by residual: chirality pdb=" CB ILE R 201 " pdb=" CA ILE R 201 " pdb=" CG1 ILE R 201 " pdb=" CG2 ILE R 201 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB THR A 292 " pdb=" CA THR A 292 " pdb=" OG1 THR A 292 " pdb=" CG2 THR A 292 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" CA PRO A 299 " pdb=" N PRO A 299 " pdb=" C PRO A 299 " pdb=" CB PRO A 299 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 1394 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 201 " 0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO R 202 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO R 202 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO R 202 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 281 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO R 282 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO R 282 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 282 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR S 150 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO S 151 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO S 151 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO S 151 " -0.023 5.00e-02 4.00e+02 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1323 2.76 - 3.29: 8742 3.29 - 3.83: 14254 3.83 - 4.36: 16207 4.36 - 4.90: 28857 Nonbonded interactions: 69383 Sorted by model distance: nonbonded pdb=" NE2 GLN A 52 " pdb=" OD1 ASP A 335 " model vdw 2.220 3.120 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.227 3.040 nonbonded pdb=" O ARG A 250 " pdb=" OG1 THR A 251 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR R 56 " pdb=" OD1 ASN R 59 " model vdw 2.271 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.278 3.040 ... (remaining 69378 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: 1.280 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.380 Find NCS groups from input model: 0.040 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 0.050 9251 Z= 0.161 Angle : 0.668 7.608 12526 Z= 0.374 Chirality : 0.042 0.234 1397 Planarity : 0.004 0.079 1584 Dihedral : 13.922 89.539 3324 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.10 % Allowed : 0.41 % Favored : 99.49 % 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: -0.64 (0.25), residues: 1129 helix: 1.54 (0.27), residues: 393 sheet: -0.72 (0.33), residues: 243 loop : -1.94 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 68 TYR 0.009 0.001 TYR S 173 PHE 0.024 0.001 PHE A 307 TRP 0.015 0.001 TRP R 148 HIS 0.005 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 ( 9248) covalent geometry : angle 0.66753 / 0.37 (12520) SS BOND : bond 0.00380 / 0.18 ( 3) SS BOND : angle 0.83426 / 0.46 ( 6) hydrogen bonds : bond 0.19090 / 13.07 ( 403) hydrogen bonds : angle 6.77514 / 4.70 ( 1164) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.365 Fit side-chains REVERT: B 17 GLN cc_start: 0.9261 (tm-30) cc_final: 0.9056 (tm-30) REVERT: B 295 ASN cc_start: 0.8143 (m-40) cc_final: 0.7904 (m-40) REVERT: B 308 LEU cc_start: 0.8041 (mp) cc_final: 0.7781 (mp) REVERT: R 31 VAL cc_start: 0.8535 (p) cc_final: 0.8286 (p) REVERT: R 222 ARG cc_start: 0.7210 (ttp80) cc_final: 0.6744 (tmm160) REVERT: S 11 LEU cc_start: 0.6560 (pt) cc_final: 0.5728 (tt) REVERT: S 95 TYR cc_start: 0.6714 (m-10) cc_final: 0.6118 (m-10) REVERT: S 227 TYR cc_start: 0.6983 (m-80) cc_final: 0.6499 (m-80) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.0893 time to fit residues: 22.2548 Evaluate side-chains 147 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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: 20.0000 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 40.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN B 293 ASN R 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.197012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.125287 restraints weight = 11563.123| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.27 r_work: 0.3329 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 9251 Z= 0.293 Angle : 0.730 11.247 12526 Z= 0.382 Chirality : 0.048 0.199 1397 Planarity : 0.005 0.070 1584 Dihedral : 4.722 49.808 1250 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.93 % Allowed : 10.24 % Favored : 87.83 % 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: -0.90 (0.25), residues: 1129 helix: 1.33 (0.26), residues: 395 sheet: -0.86 (0.32), residues: 255 loop : -2.14 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 68 TYR 0.019 0.002 TYR R 172 PHE 0.020 0.002 PHE R 311 TRP 0.021 0.002 TRP R 148 HIS 0.009 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00718 / 0.29 ( 9248) covalent geometry : angle 0.72921 / 0.38 (12520) SS BOND : bond 0.00706 / 0.34 ( 3) SS BOND : angle 1.28680 / 0.72 ( 6) hydrogen bonds : bond 0.06801 / 4.54 ( 403) hydrogen bonds : angle 5.43671 / 3.78 ( 1164) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.332 Fit side-chains REVERT: B 17 GLN cc_start: 0.9301 (tm-30) cc_final: 0.9095 (tm-30) REVERT: B 217 MET cc_start: 0.8402 (ptm) cc_final: 0.8128 (ppp) REVERT: B 295 ASN cc_start: 0.8546 (m-40) cc_final: 0.8028 (m-40) REVERT: R 143 MET cc_start: 0.7984 (mtt) cc_final: 0.7604 (mtt) REVERT: S 95 TYR cc_start: 0.6915 (m-10) cc_final: 0.6341 (m-10) REVERT: S 174 LEU cc_start: 0.6682 (tp) cc_final: 0.6164 (mp) REVERT: S 228 TYR cc_start: 0.6581 (m-80) cc_final: 0.6371 (m-80) REVERT: Y 44 HIS cc_start: 0.8364 (m90) cc_final: 0.7702 (m-70) outliers start: 19 outliers final: 13 residues processed: 166 average time/residue: 0.0871 time to fit residues: 20.4709 Evaluate side-chains 156 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN B 266 HIS R 296 ASN R 300 ASN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.203873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.131750 restraints weight = 11761.938| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.06 r_work: 0.3453 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9251 Z= 0.122 Angle : 0.581 10.943 12526 Z= 0.297 Chirality : 0.042 0.160 1397 Planarity : 0.004 0.048 1584 Dihedral : 4.296 48.776 1250 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.52 % Allowed : 12.47 % Favored : 86.00 % 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: -0.47 (0.26), residues: 1129 helix: 1.83 (0.27), residues: 395 sheet: -0.74 (0.31), residues: 268 loop : -1.99 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 68 TYR 0.019 0.001 TYR R 27 PHE 0.015 0.001 PHE R 91 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 9248) covalent geometry : angle 0.58059 / 0.30 (12520) SS BOND : bond 0.00464 / 0.20 ( 3) SS BOND : angle 0.64424 / 0.35 ( 6) hydrogen bonds : bond 0.04692 / 3.09 ( 403) hydrogen bonds : angle 4.76018 / 3.31 ( 1164) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.363 Fit side-chains REVERT: A 38 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8713 (tt) REVERT: A 186 GLU cc_start: 0.7564 (tt0) cc_final: 0.7362 (tm-30) REVERT: B 10 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7554 (pm20) REVERT: B 253 PHE cc_start: 0.8276 (m-10) cc_final: 0.7957 (m-10) REVERT: B 256 ARG cc_start: 0.9026 (tpp80) cc_final: 0.8491 (tpt170) REVERT: B 295 ASN cc_start: 0.8464 (m-40) cc_final: 0.7910 (m-40) REVERT: R 81 MET cc_start: 0.8571 (ttp) cc_final: 0.8257 (ttt) REVERT: R 143 MET cc_start: 0.8015 (mtt) cc_final: 0.7742 (mtt) REVERT: R 222 ARG cc_start: 0.7442 (ttp80) cc_final: 0.6989 (tmm160) REVERT: R 317 MET cc_start: 0.7888 (tmm) cc_final: 0.7649 (tmm) REVERT: S 95 TYR cc_start: 0.6901 (m-10) cc_final: 0.6466 (m-10) REVERT: S 174 LEU cc_start: 0.6713 (tp) cc_final: 0.6267 (mp) REVERT: S 228 TYR cc_start: 0.6503 (m-80) cc_final: 0.6301 (m-80) REVERT: Y 28 ILE cc_start: 0.8710 (pt) cc_final: 0.8368 (pt) REVERT: Y 44 HIS cc_start: 0.8269 (m90) cc_final: 0.7650 (m-70) outliers start: 15 outliers final: 8 residues processed: 174 average time/residue: 0.0881 time to fit residues: 21.6919 Evaluate side-chains 160 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 0.0030 chunk 15 optimal weight: 9.9990 chunk 104 optimal weight: 30.0000 chunk 76 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 63 HIS ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.203527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.134974 restraints weight = 11935.829| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.37 r_work: 0.3416 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9251 Z= 0.126 Angle : 0.576 10.834 12526 Z= 0.294 Chirality : 0.042 0.155 1397 Planarity : 0.004 0.044 1584 Dihedral : 4.178 46.727 1250 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.93 % Allowed : 14.60 % Favored : 83.47 % 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: -0.40 (0.26), residues: 1129 helix: 1.90 (0.27), residues: 395 sheet: -0.80 (0.31), residues: 272 loop : -1.90 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.016 0.001 TYR R 172 PHE 0.018 0.001 PHE R 165 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 9248) covalent geometry : angle 0.57551 / 0.29 (12520) SS BOND : bond 0.00406 / 0.17 ( 3) SS BOND : angle 0.83074 / 0.50 ( 6) hydrogen bonds : bond 0.04565 / 3.03 ( 403) hydrogen bonds : angle 4.59177 / 3.21 ( 1164) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.342 Fit side-chains REVERT: A 24 GLN cc_start: 0.8389 (tm-30) cc_final: 0.8156 (tm-30) REVERT: A 38 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8757 (tt) REVERT: A 186 GLU cc_start: 0.7606 (tt0) cc_final: 0.7393 (tm-30) REVERT: B 10 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7615 (pm20) REVERT: B 246 ASP cc_start: 0.8380 (m-30) cc_final: 0.8173 (m-30) REVERT: B 256 ARG cc_start: 0.8984 (tpp80) cc_final: 0.8387 (tpt90) REVERT: B 295 ASN cc_start: 0.8452 (m-40) cc_final: 0.7990 (m-40) REVERT: R 81 MET cc_start: 0.8573 (ttp) cc_final: 0.8223 (ttm) REVERT: R 143 MET cc_start: 0.8040 (mtt) cc_final: 0.7764 (mtt) REVERT: R 222 ARG cc_start: 0.7457 (ttp80) cc_final: 0.6993 (tmm160) REVERT: R 317 MET cc_start: 0.7859 (tmm) cc_final: 0.7634 (tmm) REVERT: S 95 TYR cc_start: 0.6743 (m-10) cc_final: 0.6398 (m-10) REVERT: S 174 LEU cc_start: 0.6702 (tp) cc_final: 0.6316 (mp) REVERT: S 230 MET cc_start: 0.3184 (mmm) cc_final: 0.2911 (mmm) REVERT: Y 28 ILE cc_start: 0.8714 (pt) cc_final: 0.8401 (pt) REVERT: Y 38 MET cc_start: 0.8428 (pmm) cc_final: 0.8061 (pmm) REVERT: Y 44 HIS cc_start: 0.8234 (m90) cc_final: 0.7367 (m170) outliers start: 19 outliers final: 12 residues processed: 170 average time/residue: 0.0895 time to fit residues: 21.6145 Evaluate side-chains 163 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 302 MET Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 85 optimal weight: 30.0000 chunk 23 optimal weight: 20.0000 chunk 92 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.198541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.127438 restraints weight = 11898.471| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 3.49 r_work: 0.3321 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9251 Z= 0.217 Angle : 0.657 10.664 12526 Z= 0.337 Chirality : 0.045 0.161 1397 Planarity : 0.005 0.049 1584 Dihedral : 4.439 47.051 1250 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.45 % Allowed : 14.71 % Favored : 81.85 % 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: -0.63 (0.25), residues: 1129 helix: 1.58 (0.26), residues: 397 sheet: -0.77 (0.32), residues: 263 loop : -2.01 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.020 0.002 TYR R 27 PHE 0.021 0.002 PHE R 91 TRP 0.030 0.002 TRP B 339 HIS 0.007 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.22 ( 9248) covalent geometry : angle 0.65725 / 0.34 (12520) SS BOND : bond 0.00645 / 0.30 ( 3) SS BOND : angle 0.90267 / 0.50 ( 6) hydrogen bonds : bond 0.05816 / 3.88 ( 403) hydrogen bonds : angle 4.81234 / 3.38 ( 1164) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.337 Fit side-chains REVERT: A 24 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8149 (tm-30) REVERT: A 186 GLU cc_start: 0.7657 (tt0) cc_final: 0.7393 (tm-30) REVERT: B 10 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7591 (pm20) REVERT: B 254 ASP cc_start: 0.8800 (t0) cc_final: 0.7701 (p0) REVERT: B 256 ARG cc_start: 0.9004 (tpp80) cc_final: 0.8449 (tpt170) REVERT: B 295 ASN cc_start: 0.8538 (m-40) cc_final: 0.8024 (m-40) REVERT: R 81 MET cc_start: 0.8674 (ttp) cc_final: 0.8352 (ttm) REVERT: S 51 ILE cc_start: 0.6386 (OUTLIER) cc_final: 0.5772 (mp) REVERT: S 95 TYR cc_start: 0.6795 (m-10) cc_final: 0.6346 (m-10) REVERT: S 174 LEU cc_start: 0.6700 (tp) cc_final: 0.6409 (mp) REVERT: Y 38 MET cc_start: 0.8293 (pmm) cc_final: 0.7966 (pmm) REVERT: Y 44 HIS cc_start: 0.8357 (m90) cc_final: 0.7491 (m170) outliers start: 34 outliers final: 20 residues processed: 175 average time/residue: 0.0912 time to fit residues: 22.4980 Evaluate side-chains 168 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 98 optimal weight: 6.9990 chunk 5 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN B 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.202943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.131452 restraints weight = 11938.303| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.08 r_work: 0.3451 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9251 Z= 0.122 Angle : 0.609 10.965 12526 Z= 0.303 Chirality : 0.042 0.158 1397 Planarity : 0.004 0.048 1584 Dihedral : 4.180 45.449 1250 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.84 % Allowed : 16.02 % Favored : 81.14 % 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: -0.35 (0.26), residues: 1129 helix: 1.85 (0.27), residues: 396 sheet: -0.68 (0.31), residues: 270 loop : -1.83 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 222 TYR 0.021 0.001 TYR R 172 PHE 0.017 0.001 PHE R 91 TRP 0.017 0.001 TRP B 339 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 9248) covalent geometry : angle 0.60934 / 0.30 (12520) SS BOND : bond 0.00473 / 0.20 ( 3) SS BOND : angle 0.49838 / 0.27 ( 6) hydrogen bonds : bond 0.04440 / 2.93 ( 403) hydrogen bonds : angle 4.42899 / 3.11 ( 1164) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.503 Fit side-chains REVERT: A 24 GLN cc_start: 0.8284 (tm-30) cc_final: 0.8018 (tm-30) REVERT: A 38 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8694 (tt) REVERT: A 186 GLU cc_start: 0.7530 (tt0) cc_final: 0.7322 (tm-30) REVERT: B 10 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7629 (pm20) REVERT: B 121 CYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6772 (m) REVERT: B 254 ASP cc_start: 0.8706 (t0) cc_final: 0.7651 (p0) REVERT: B 256 ARG cc_start: 0.8987 (tpp80) cc_final: 0.8472 (tpt170) REVERT: B 295 ASN cc_start: 0.8510 (m-40) cc_final: 0.8070 (m-40) REVERT: R 81 MET cc_start: 0.8558 (ttp) cc_final: 0.8193 (ttm) REVERT: R 143 MET cc_start: 0.7989 (mtt) cc_final: 0.7705 (mtt) REVERT: R 222 ARG cc_start: 0.7452 (ttp80) cc_final: 0.7068 (tmm160) REVERT: S 51 ILE cc_start: 0.6240 (OUTLIER) cc_final: 0.5786 (mp) REVERT: S 95 TYR cc_start: 0.6763 (m-10) cc_final: 0.6354 (m-10) REVERT: S 174 LEU cc_start: 0.6812 (tp) cc_final: 0.6530 (mp) REVERT: Y 44 HIS cc_start: 0.8286 (m90) cc_final: 0.7435 (m170) outliers start: 28 outliers final: 18 residues processed: 173 average time/residue: 0.0835 time to fit residues: 20.9164 Evaluate side-chains 177 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.201268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.132728 restraints weight = 11916.140| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.32 r_work: 0.3377 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9251 Z= 0.149 Angle : 0.628 10.911 12526 Z= 0.314 Chirality : 0.043 0.177 1397 Planarity : 0.004 0.051 1584 Dihedral : 4.189 44.536 1250 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.25 % Allowed : 16.33 % Favored : 80.43 % 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: -0.32 (0.26), residues: 1129 helix: 1.78 (0.27), residues: 400 sheet: -0.66 (0.32), residues: 270 loop : -1.77 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 222 TYR 0.015 0.001 TYR S 103 PHE 0.019 0.001 PHE R 91 TRP 0.022 0.001 TRP B 339 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 9248) covalent geometry : angle 0.62790 / 0.31 (12520) SS BOND : bond 0.00599 / 0.25 ( 3) SS BOND : angle 0.61005 / 0.33 ( 6) hydrogen bonds : bond 0.04798 / 3.18 ( 403) hydrogen bonds : angle 4.46466 / 3.14 ( 1164) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.335 Fit side-chains REVERT: A 38 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8763 (tt) REVERT: A 186 GLU cc_start: 0.7572 (tt0) cc_final: 0.7361 (tm-30) REVERT: B 10 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7628 (pm20) REVERT: B 121 CYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6809 (m) REVERT: B 175 GLN cc_start: 0.8124 (pm20) cc_final: 0.7516 (pm20) REVERT: B 256 ARG cc_start: 0.8977 (tpp80) cc_final: 0.8602 (tpt170) REVERT: B 295 ASN cc_start: 0.8567 (m-40) cc_final: 0.8169 (m-40) REVERT: R 61 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7837 (tp) REVERT: R 81 MET cc_start: 0.8627 (ttp) cc_final: 0.8264 (ttm) REVERT: R 222 ARG cc_start: 0.7454 (ttp80) cc_final: 0.7077 (tmm160) REVERT: R 317 MET cc_start: 0.7551 (tmm) cc_final: 0.7331 (tmm) REVERT: S 51 ILE cc_start: 0.6275 (OUTLIER) cc_final: 0.5797 (mp) REVERT: S 95 TYR cc_start: 0.6787 (m-10) cc_final: 0.6378 (m-10) REVERT: S 174 LEU cc_start: 0.6752 (tp) cc_final: 0.6487 (mp) REVERT: Y 44 HIS cc_start: 0.8308 (m90) cc_final: 0.7454 (m170) outliers start: 32 outliers final: 21 residues processed: 180 average time/residue: 0.0824 time to fit residues: 21.4000 Evaluate side-chains 181 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 302 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 15 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 111 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.203418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.132538 restraints weight = 11892.062| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 3.57 r_work: 0.3419 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9251 Z= 0.125 Angle : 0.626 11.129 12526 Z= 0.313 Chirality : 0.042 0.181 1397 Planarity : 0.004 0.052 1584 Dihedral : 4.103 43.133 1250 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.14 % Allowed : 16.33 % Favored : 80.53 % 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: -0.27 (0.26), residues: 1129 helix: 1.91 (0.27), residues: 396 sheet: -0.72 (0.31), residues: 278 loop : -1.74 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 222 TYR 0.020 0.001 TYR R 27 PHE 0.018 0.001 PHE R 91 TRP 0.019 0.001 TRP B 339 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 9248) covalent geometry : angle 0.62556 / 0.31 (12520) SS BOND : bond 0.00458 / 0.20 ( 3) SS BOND : angle 0.50746 / 0.27 ( 6) hydrogen bonds : bond 0.04318 / 2.86 ( 403) hydrogen bonds : angle 4.36832 / 3.07 ( 1164) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.339 Fit side-chains REVERT: A 38 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8756 (tt) REVERT: A 186 GLU cc_start: 0.7558 (tt0) cc_final: 0.7318 (tm-30) REVERT: B 10 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7577 (pm20) REVERT: B 17 GLN cc_start: 0.9019 (pp30) cc_final: 0.8583 (pp30) REVERT: B 121 CYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6871 (m) REVERT: B 175 GLN cc_start: 0.8091 (pm20) cc_final: 0.7467 (pm20) REVERT: B 254 ASP cc_start: 0.8819 (t0) cc_final: 0.7711 (p0) REVERT: B 256 ARG cc_start: 0.8943 (tpp80) cc_final: 0.8406 (tpt170) REVERT: B 295 ASN cc_start: 0.8575 (m-40) cc_final: 0.8175 (m-40) REVERT: R 143 MET cc_start: 0.8025 (mtt) cc_final: 0.7751 (mtt) REVERT: R 222 ARG cc_start: 0.7421 (ttp80) cc_final: 0.7050 (tmm160) REVERT: R 317 MET cc_start: 0.7542 (tmm) cc_final: 0.7158 (tmm) REVERT: S 51 ILE cc_start: 0.6120 (OUTLIER) cc_final: 0.5665 (mp) REVERT: S 95 TYR cc_start: 0.6816 (m-10) cc_final: 0.6402 (m-10) REVERT: S 219 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.6279 (tt) REVERT: Y 44 HIS cc_start: 0.8145 (m90) cc_final: 0.7265 (m170) outliers start: 31 outliers final: 24 residues processed: 180 average time/residue: 0.0778 time to fit residues: 20.1663 Evaluate side-chains 182 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 219 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 38 optimal weight: 0.0970 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.200933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.129337 restraints weight = 11904.588| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.53 r_work: 0.3369 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9251 Z= 0.171 Angle : 0.682 10.998 12526 Z= 0.340 Chirality : 0.044 0.216 1397 Planarity : 0.004 0.053 1584 Dihedral : 4.227 43.423 1250 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.25 % Allowed : 16.43 % Favored : 80.32 % 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: -0.40 (0.26), residues: 1129 helix: 1.70 (0.27), residues: 400 sheet: -0.79 (0.31), residues: 280 loop : -1.75 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 222 TYR 0.019 0.001 TYR R 27 PHE 0.019 0.001 PHE R 91 TRP 0.022 0.002 TRP B 339 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 ( 9248) covalent geometry : angle 0.68249 / 0.34 (12520) SS BOND : bond 0.00525 / 0.23 ( 3) SS BOND : angle 0.67582 / 0.37 ( 6) hydrogen bonds : bond 0.05058 / 3.36 ( 403) hydrogen bonds : angle 4.55062 / 3.19 ( 1164) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.341 Fit side-chains REVERT: A 38 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8834 (tt) REVERT: A 186 GLU cc_start: 0.7608 (tt0) cc_final: 0.7336 (tm-30) REVERT: A 198 MET cc_start: 0.7997 (mmp) cc_final: 0.7750 (mmm) REVERT: B 10 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7537 (pm20) REVERT: B 121 CYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6822 (m) REVERT: B 175 GLN cc_start: 0.8172 (pm20) cc_final: 0.7540 (pm20) REVERT: B 214 ARG cc_start: 0.8297 (mmm-85) cc_final: 0.7974 (mmm-85) REVERT: B 254 ASP cc_start: 0.8826 (t0) cc_final: 0.7703 (p0) REVERT: B 256 ARG cc_start: 0.8968 (tpp80) cc_final: 0.8423 (tpt170) REVERT: B 259 GLN cc_start: 0.8599 (tp40) cc_final: 0.8004 (tp40) REVERT: B 295 ASN cc_start: 0.8573 (m-40) cc_final: 0.8161 (m-40) REVERT: R 81 MET cc_start: 0.8737 (ttp) cc_final: 0.8363 (ttm) REVERT: R 222 ARG cc_start: 0.7445 (ttp80) cc_final: 0.7083 (tmm160) REVERT: R 317 MET cc_start: 0.7636 (tmm) cc_final: 0.7031 (tmm) REVERT: S 51 ILE cc_start: 0.6275 (OUTLIER) cc_final: 0.5826 (mp) REVERT: S 219 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.6210 (tt) REVERT: Y 44 HIS cc_start: 0.8169 (m90) cc_final: 0.7275 (m170) outliers start: 32 outliers final: 25 residues processed: 176 average time/residue: 0.0795 time to fit residues: 19.9070 Evaluate side-chains 181 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 302 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 219 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.203967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.138116 restraints weight = 11779.732| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 3.46 r_work: 0.3409 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9251 Z= 0.125 Angle : 0.650 11.175 12526 Z= 0.322 Chirality : 0.042 0.189 1397 Planarity : 0.004 0.052 1584 Dihedral : 4.103 41.654 1250 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.74 % Allowed : 16.63 % Favored : 80.63 % 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: -0.27 (0.26), residues: 1129 helix: 1.88 (0.27), residues: 396 sheet: -0.69 (0.31), residues: 278 loop : -1.72 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 222 TYR 0.019 0.001 TYR R 27 PHE 0.017 0.001 PHE R 91 TRP 0.017 0.001 TRP B 339 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 9248) covalent geometry : angle 0.65056 / 0.32 (12520) SS BOND : bond 0.00460 / 0.20 ( 3) SS BOND : angle 0.49406 / 0.26 ( 6) hydrogen bonds : bond 0.04357 / 2.88 ( 403) hydrogen bonds : angle 4.41053 / 3.09 ( 1164) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8769 (tt) REVERT: B 10 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7578 (pm20) REVERT: B 17 GLN cc_start: 0.8937 (pp30) cc_final: 0.8487 (pp30) REVERT: B 121 CYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6857 (m) REVERT: B 254 ASP cc_start: 0.8836 (t0) cc_final: 0.7763 (p0) REVERT: B 256 ARG cc_start: 0.8920 (tpp80) cc_final: 0.8448 (tpt170) REVERT: B 295 ASN cc_start: 0.8540 (m-40) cc_final: 0.8144 (m-40) REVERT: R 81 MET cc_start: 0.8684 (ttp) cc_final: 0.8323 (ttm) REVERT: R 143 MET cc_start: 0.8026 (mtt) cc_final: 0.7758 (mtt) REVERT: S 51 ILE cc_start: 0.6254 (OUTLIER) cc_final: 0.5833 (mp) REVERT: Y 44 HIS cc_start: 0.8138 (m90) cc_final: 0.7225 (m170) outliers start: 27 outliers final: 21 residues processed: 170 average time/residue: 0.0817 time to fit residues: 19.5369 Evaluate side-chains 177 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.202641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.130437 restraints weight = 11787.517| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 3.05 r_work: 0.3436 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9251 Z= 0.143 Angle : 0.675 10.832 12526 Z= 0.335 Chirality : 0.043 0.183 1397 Planarity : 0.004 0.053 1584 Dihedral : 4.128 41.153 1250 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.64 % Allowed : 16.84 % Favored : 80.53 % 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: -0.32 (0.26), residues: 1129 helix: 1.76 (0.27), residues: 400 sheet: -0.75 (0.31), residues: 280 loop : -1.68 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 222 TYR 0.019 0.001 TYR R 27 PHE 0.018 0.001 PHE R 91 TRP 0.018 0.001 TRP B 339 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 9248) covalent geometry : angle 0.67493 / 0.33 (12520) SS BOND : bond 0.00475 / 0.20 ( 3) SS BOND : angle 0.56993 / 0.31 ( 6) hydrogen bonds : bond 0.04651 / 3.08 ( 403) hydrogen bonds : angle 4.44795 / 3.10 ( 1164) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2428.17 seconds wall clock time: 42 minutes 18.29 seconds (2538.29 seconds total)