Starting phenix.real_space_refine on Thu Jul 2 19:56:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/24xy_69904/07_2026/24xy_69904.cif Found real_map, /net/cci-nas-00/data/ceres_data/24xy_69904/07_2026/24xy_69904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/24xy_69904/07_2026/24xy_69904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/24xy_69904/07_2026/24xy_69904.map" model { file = "/net/cci-nas-00/data/ceres_data/24xy_69904/07_2026/24xy_69904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/24xy_69904/07_2026/24xy_69904.cif" } resolution = 3.0 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= 0.000 sd= 1.031 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 60 5.16 5 C 6211 2.51 5 N 1669 2.21 5 O 1812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 9754 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2147 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 13, 'TRANS': 249} Chain breaks: 1 Chain: "A" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1845 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain breaks: 1 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2591 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "G" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 394 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.19, per 1000 atoms: 0.22 Number of scatterers: 9754 At special positions: 0 Unit cell: (84.4254, 127.112, 133.753, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 2 15.00 O 1812 8.00 N 1669 7.00 C 6211 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 36 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS R 116 " - pdb=" SG CYS R 194 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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: 1.00 Conformation dependent library (CDL) restraints added in 358.8 milliseconds 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2314 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 15 sheets defined 32.5% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'R' and resid 40 through 46 removed outlier: 3.901A pdb=" N VAL R 46 " --> pdb=" O ILE R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 69 removed outlier: 3.522A pdb=" N LEU R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 95 removed outlier: 3.567A pdb=" N ILE R 80 " --> pdb=" O SER R 76 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET R 95 " --> pdb=" O ILE R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 105 Processing helix chain 'R' and resid 109 through 116 Processing helix chain 'R' and resid 118 through 147 removed outlier: 3.930A pdb=" N ILE R 122 " --> pdb=" O PHE R 118 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY R 130 " --> pdb=" O THR R 126 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL R 132 " --> pdb=" O TYR R 128 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU R 134 " --> pdb=" O GLY R 130 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS R 144 " --> pdb=" O ASP R 140 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE R 145 " --> pdb=" O ARG R 141 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE R 146 " --> pdb=" O PHE R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 155 Processing helix chain 'R' and resid 156 through 181 removed outlier: 3.904A pdb=" N ALA R 160 " --> pdb=" O LYS R 156 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR R 162 " --> pdb=" O VAL R 158 " (cutoff:3.500A) Proline residue: R 177 - end of helix Processing helix chain 'R' and resid 199 through 235 removed outlier: 3.680A pdb=" N LEU R 203 " --> pdb=" O GLY R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 268 Processing helix chain 'R' and resid 268 through 274 removed outlier: 3.683A pdb=" N HIS R 272 " --> pdb=" O PHE R 268 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 284 removed outlier: 4.205A pdb=" N HIS R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 318 removed outlier: 4.094A pdb=" N ASN R 293 " --> pdb=" O CYS R 289 " (cutoff:3.500A) Proline residue: R 314 - end of helix removed outlier: 4.228A pdb=" N TYR R 317 " --> pdb=" O ASP R 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 95 through 101 removed outlier: 3.532A pdb=" N GLN A 98 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS A 99 " --> pdb=" O TRP A 96 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN A 101 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 164 through 168 removed outlier: 3.784A pdb=" N PHE A 167 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 168 " --> pdb=" O PRO A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 164 through 168' Processing helix chain 'A' and resid 183 through 203 Processing helix chain 'A' and resid 223 through 243 Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.092A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.624A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 76 removed outlier: 3.906A pdb=" N ASP A 85 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL A 86 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 105 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL A 139 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N HIS A 214 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU A 141 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.261A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.537A 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: 3.970A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.569A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.770A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.160A 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: 7.172A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.731A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.564A 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: 6.516A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.630A pdb=" N VAL N 12 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL N 124 " --> pdb=" O ALA N 92 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.535A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 130 Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.674A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 143 through 145 removed outlier: 3.720A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1242 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: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1569 1.31 - 1.43: 2780 1.43 - 1.56: 5530 1.56 - 1.69: 4 1.69 - 1.82: 86 Bond restraints: 9969 Sorted by residual: bond pdb=" C4 ADP R 901 " pdb=" C5 ADP R 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C PRO A 184 " pdb=" O PRO A 184 " ideal model delta sigma weight residual 1.238 1.178 0.060 1.24e-02 6.50e+03 2.33e+01 bond pdb=" C5 ADP R 901 " pdb=" C6 ADP R 901 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C VAL A 76 " pdb=" O VAL A 76 " ideal model delta sigma weight residual 1.236 1.278 -0.042 1.01e-02 9.80e+03 1.75e+01 bond pdb=" C HIS R 272 " pdb=" O HIS R 272 " ideal model delta sigma weight residual 1.237 1.281 -0.045 1.17e-02 7.31e+03 1.46e+01 ... (remaining 9964 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 12145 2.24 - 4.48: 1197 4.48 - 6.72: 149 6.72 - 8.96: 19 8.96 - 11.20: 4 Bond angle restraints: 13514 Sorted by residual: angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 122.61 130.37 -7.76 1.56e+00 4.11e-01 2.47e+01 angle pdb=" N ASN A 244 " pdb=" CA ASN A 244 " pdb=" C ASN A 244 " ideal model delta sigma weight residual 113.38 107.56 5.82 1.17e+00 7.31e-01 2.47e+01 angle pdb=" N LEU A 245 " pdb=" CA LEU A 245 " pdb=" C LEU A 245 " ideal model delta sigma weight residual 111.11 105.19 5.92 1.20e+00 6.94e-01 2.43e+01 angle pdb=" N ASP B 246 " pdb=" CA ASP B 246 " pdb=" C ASP B 246 " ideal model delta sigma weight residual 112.72 107.16 5.56 1.14e+00 7.69e-01 2.38e+01 angle pdb=" CA ILE R 216 " pdb=" C ILE R 216 " pdb=" O ILE R 216 " ideal model delta sigma weight residual 121.27 116.21 5.06 1.04e+00 9.25e-01 2.37e+01 ... (remaining 13509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 5372 17.13 - 34.27: 438 34.27 - 51.40: 82 51.40 - 68.53: 16 68.53 - 85.66: 13 Dihedral angle restraints: 5921 sinusoidal: 2337 harmonic: 3584 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 138.66 -45.66 1 1.00e+01 1.00e-02 2.89e+01 dihedral pdb=" O1B ADP R 901 " pdb=" O3A ADP R 901 " pdb=" PB ADP R 901 " pdb=" PA ADP R 901 " ideal model delta sinusoidal sigma weight residual -60.00 -144.29 84.29 1 2.00e+01 2.50e-03 2.16e+01 dihedral pdb=" CB CYS R 36 " pdb=" SG CYS R 36 " pdb=" SG CYS R 289 " pdb=" CB CYS R 289 " ideal model delta sinusoidal sigma weight residual 93.00 127.77 -34.77 1 1.00e+01 1.00e-02 1.71e+01 ... (remaining 5918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 854 0.066 - 0.132: 451 0.132 - 0.198: 167 0.198 - 0.264: 40 0.264 - 0.331: 9 Chirality restraints: 1521 Sorted by residual: chirality pdb=" CB VAL N 12 " pdb=" CA VAL N 12 " pdb=" CG1 VAL N 12 " pdb=" CG2 VAL N 12 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA ARG S 179 " pdb=" N ARG S 179 " pdb=" C ARG S 179 " pdb=" CB ARG S 179 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CG LEU A 122 " pdb=" CB LEU A 122 " pdb=" CD1 LEU A 122 " pdb=" CD2 LEU A 122 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 1518 not shown) Planarity restraints: 1713 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS R 198 " -0.028 2.00e-02 2.50e+03 5.54e-02 3.07e+01 pdb=" C LYS R 198 " 0.096 2.00e-02 2.50e+03 pdb=" O LYS R 198 " -0.036 2.00e-02 2.50e+03 pdb=" N GLY R 199 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 289 " 0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C CYS R 289 " -0.073 2.00e-02 2.50e+03 pdb=" O CYS R 289 " 0.027 2.00e-02 2.50e+03 pdb=" N ARG R 290 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 175 " -0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C SER R 175 " 0.070 2.00e-02 2.50e+03 pdb=" O SER R 175 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU R 176 " -0.025 2.00e-02 2.50e+03 ... (remaining 1710 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 809 2.74 - 3.28: 8868 3.28 - 3.82: 15201 3.82 - 4.36: 19238 4.36 - 4.90: 32555 Nonbonded interactions: 76671 Sorted by model distance: nonbonded pdb=" O GLU B 226 " pdb=" NH2 ARG N 98 " model vdw 2.198 3.120 nonbonded pdb=" NE ARG A 94 " pdb=" OD2 ASP B 228 " model vdw 2.199 3.120 nonbonded pdb=" OG SER B 227 " pdb=" O PRO N 100 " model vdw 2.216 3.040 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.221 3.120 nonbonded pdb=" O VAL A 198 " pdb=" OG SER A 201 " model vdw 2.287 3.040 ... (remaining 76666 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: 2.080 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.240 Find NCS groups from input model: 0.060 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:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 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 : 0.010 0.110 9975 Z= 0.728 Angle : 1.387 11.198 13526 Z= 0.944 Chirality : 0.090 0.331 1521 Planarity : 0.011 0.127 1713 Dihedral : 13.495 85.663 3589 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.52 % Favored : 95.24 % Rotamer: Outliers : 0.38 % Allowed : 3.38 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.21), residues: 1218 helix: -2.26 (0.21), residues: 358 sheet: -0.53 (0.28), residues: 317 loop : -1.85 (0.22), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 24 TYR 0.017 0.003 TYR B 59 PHE 0.025 0.003 PHE N 29 TRP 0.034 0.004 TRP A 96 HIS 0.011 0.002 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.01012 / 0.73 ( 9969) covalent geometry : angle 1.38710 / 0.94 (13514) SS BOND : bond 0.00703 / 0.29 ( 6) SS BOND : angle 1.56379 / 1.02 ( 12) hydrogen bonds : bond 0.22720 / 14.96 ( 439) hydrogen bonds : angle 8.45984 / 5.81 ( 1242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 457 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: R 77 THR cc_start: 0.7863 (p) cc_final: 0.7501 (p) REVERT: R 161 LYS cc_start: 0.8335 (mttt) cc_final: 0.8003 (mmtm) REVERT: R 215 PHE cc_start: 0.7596 (t80) cc_final: 0.7350 (t80) REVERT: R 294 GLN cc_start: 0.8052 (mt0) cc_final: 0.7482 (mp10) REVERT: R 312 MET cc_start: 0.7156 (mtp) cc_final: 0.6504 (ppp) REVERT: R 313 ASP cc_start: 0.8566 (t70) cc_final: 0.7778 (m-30) REVERT: A 25 GLU cc_start: 0.7904 (tt0) cc_final: 0.7320 (tp30) REVERT: A 31 ARG cc_start: 0.8150 (ttp-110) cc_final: 0.7855 (ttp-110) REVERT: A 111 ASP cc_start: 0.8616 (t0) cc_final: 0.8404 (t70) REVERT: A 119 GLN cc_start: 0.7995 (tp40) cc_final: 0.7672 (mm-40) REVERT: A 145 LYS cc_start: 0.8277 (mttm) cc_final: 0.8049 (mttt) REVERT: A 239 ASN cc_start: 0.9193 (m-40) cc_final: 0.8956 (m-40) REVERT: B 138 GLU cc_start: 0.7667 (pm20) cc_final: 0.7448 (pm20) REVERT: B 249 THR cc_start: 0.8208 (p) cc_final: 0.7983 (m) REVERT: B 251 ARG cc_start: 0.7622 (mtt180) cc_final: 0.6593 (ttt180) REVERT: B 313 ASN cc_start: 0.9150 (t0) cc_final: 0.8688 (t0) REVERT: B 340 ASN cc_start: 0.7114 (t0) cc_final: 0.6861 (t0) REVERT: G 17 GLU cc_start: 0.7908 (tp30) cc_final: 0.7335 (mm-30) REVERT: G 21 MET cc_start: 0.8179 (mmp) cc_final: 0.7516 (mpp) REVERT: G 38 MET cc_start: 0.7184 (ttt) cc_final: 0.6964 (ttt) REVERT: N 46 GLU cc_start: 0.6795 (mp0) cc_final: 0.6128 (mp0) REVERT: N 80 TYR cc_start: 0.8094 (m-80) cc_final: 0.7890 (m-80) REVERT: N 115 TYR cc_start: 0.9131 (t80) cc_final: 0.8751 (t80) REVERT: S 93 MET cc_start: 0.7979 (tmm) cc_final: 0.7576 (tmm) outliers start: 4 outliers final: 2 residues processed: 460 average time/residue: 0.4764 time to fit residues: 237.6025 Evaluate side-chains 333 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 331 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 301 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 84 ASN ** R 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 206 HIS R 210 ASN R 211 ASN R 309 ASN A 43 ASN A 130 ASN A 214 HIS A 244 ASN S 82 GLN S 159 ASN S 167 GLN S 171 GLN S 174 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.154557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.123158 restraints weight = 14807.334| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.51 r_work: 0.3407 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9975 Z= 0.173 Angle : 0.718 8.236 13526 Z= 0.370 Chirality : 0.046 0.191 1521 Planarity : 0.006 0.059 1713 Dihedral : 5.765 59.429 1355 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.07 % Allowed : 20.64 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.84 (0.23), residues: 1218 helix: 0.16 (0.26), residues: 358 sheet: 0.08 (0.28), residues: 319 loop : -1.41 (0.24), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 168 TYR 0.016 0.002 TYR S 178 PHE 0.025 0.002 PHE R 166 TRP 0.023 0.002 TRP R 205 HIS 0.013 0.002 HIS S 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 9969) covalent geometry : angle 0.71787 / 0.37 (13514) SS BOND : bond 0.00947 / 0.47 ( 6) SS BOND : angle 1.19632 / 0.48 ( 12) hydrogen bonds : bond 0.05232 / 3.42 ( 439) hydrogen bonds : angle 5.16591 / 3.60 ( 1242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 363 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 161 LYS cc_start: 0.8260 (mttt) cc_final: 0.7630 (mmtt) REVERT: R 184 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6923 (mmtm) REVERT: R 215 PHE cc_start: 0.8125 (t80) cc_final: 0.7678 (t80) REVERT: R 216 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8278 (mm) REVERT: R 225 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7805 (tm) REVERT: R 284 ASN cc_start: 0.7259 (m-40) cc_final: 0.7002 (m-40) REVERT: R 312 MET cc_start: 0.6775 (mtp) cc_final: 0.6061 (pp-130) REVERT: R 313 ASP cc_start: 0.8582 (t70) cc_final: 0.7554 (m-30) REVERT: A 25 GLU cc_start: 0.7718 (tt0) cc_final: 0.7055 (tp30) REVERT: A 147 ASP cc_start: 0.7280 (p0) cc_final: 0.6945 (p0) REVERT: A 151 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8133 (mm-30) REVERT: A 183 ASP cc_start: 0.6955 (t70) cc_final: 0.6727 (t0) REVERT: A 239 ASN cc_start: 0.9160 (m-40) cc_final: 0.8945 (m-40) REVERT: B 176 GLN cc_start: 0.9266 (mt0) cc_final: 0.8430 (mt0) REVERT: B 217 MET cc_start: 0.7758 (mmm) cc_final: 0.7551 (pmm) REVERT: B 262 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.8076 (mtp) REVERT: B 270 ILE cc_start: 0.8877 (pt) cc_final: 0.8571 (pp) REVERT: B 312 ASP cc_start: 0.8949 (m-30) cc_final: 0.8677 (m-30) REVERT: N 5 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: N 46 GLU cc_start: 0.6489 (mp0) cc_final: 0.6092 (mp0) REVERT: N 80 TYR cc_start: 0.7392 (m-80) cc_final: 0.7161 (m-80) REVERT: N 115 TYR cc_start: 0.8674 (t80) cc_final: 0.8459 (t80) REVERT: S 82 GLN cc_start: 0.8348 (tp40) cc_final: 0.8129 (tp-100) REVERT: S 93 MET cc_start: 0.7590 (tmm) cc_final: 0.7179 (tmm) REVERT: S 155 HIS cc_start: 0.8795 (t70) cc_final: 0.8556 (t-170) REVERT: S 166 LEU cc_start: 0.8940 (tp) cc_final: 0.8626 (tm) REVERT: S 171 GLN cc_start: 0.8802 (mt0) cc_final: 0.8560 (mm110) outliers start: 54 outliers final: 18 residues processed: 388 average time/residue: 0.4540 time to fit residues: 191.9733 Evaluate side-chains 355 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 332 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 180 ILE Chi-restraints excluded: chain R residue 184 LYS Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 90 optimal weight: 4.9990 chunk 78 optimal weight: 0.0970 chunk 81 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 0.0770 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 206 HIS R 207 GLN A 244 ASN B 340 ASN S 155 HIS S 167 GLN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.154988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.123580 restraints weight = 14808.357| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.52 r_work: 0.3415 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9975 Z= 0.129 Angle : 0.649 9.257 13526 Z= 0.329 Chirality : 0.044 0.185 1521 Planarity : 0.005 0.048 1713 Dihedral : 5.349 56.694 1353 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.97 % Allowed : 24.48 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.25 (0.24), residues: 1218 helix: 1.09 (0.27), residues: 360 sheet: 0.20 (0.29), residues: 323 loop : -1.26 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 214 TYR 0.018 0.001 TYR S 178 PHE 0.017 0.001 PHE R 166 TRP 0.016 0.001 TRP R 205 HIS 0.007 0.001 HIS S 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 9969) covalent geometry : angle 0.64819 / 0.33 (13514) SS BOND : bond 0.00662 / 0.33 ( 6) SS BOND : angle 0.99694 / 0.52 ( 12) hydrogen bonds : bond 0.04453 / 2.92 ( 439) hydrogen bonds : angle 4.74587 / 3.33 ( 1242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 348 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 161 LYS cc_start: 0.8230 (mttt) cc_final: 0.7583 (mmtt) REVERT: R 215 PHE cc_start: 0.8213 (t80) cc_final: 0.7662 (t80) REVERT: R 225 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7781 (tm) REVERT: R 284 ASN cc_start: 0.7256 (m-40) cc_final: 0.7008 (m-40) REVERT: R 312 MET cc_start: 0.6804 (mtp) cc_final: 0.6143 (ppp) REVERT: R 313 ASP cc_start: 0.8490 (t70) cc_final: 0.7513 (m-30) REVERT: A 6 SER cc_start: 0.7635 (OUTLIER) cc_final: 0.7332 (m) REVERT: A 25 GLU cc_start: 0.7724 (tt0) cc_final: 0.7082 (tp30) REVERT: A 35 ARG cc_start: 0.8128 (mtp85) cc_final: 0.7869 (mtm-85) REVERT: A 147 ASP cc_start: 0.7282 (p0) cc_final: 0.6918 (p0) REVERT: A 151 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8211 (mm-30) REVERT: A 183 ASP cc_start: 0.6905 (t70) cc_final: 0.6658 (t0) REVERT: A 239 ASN cc_start: 0.9116 (m-40) cc_final: 0.8882 (m-40) REVERT: B 175 GLN cc_start: 0.8265 (mm-40) cc_final: 0.7935 (mm110) REVERT: B 215 GLU cc_start: 0.8062 (pm20) cc_final: 0.7826 (pp20) REVERT: B 269 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8651 (tp) REVERT: B 301 LYS cc_start: 0.7993 (mmmm) cc_final: 0.7731 (mmmm) REVERT: B 312 ASP cc_start: 0.8956 (m-30) cc_final: 0.8715 (m-30) REVERT: B 323 ASP cc_start: 0.7998 (p0) cc_final: 0.7764 (p0) REVERT: N 5 GLN cc_start: 0.8044 (tp-100) cc_final: 0.7803 (mm-40) REVERT: N 29 PHE cc_start: 0.7978 (t80) cc_final: 0.7643 (t80) REVERT: N 46 GLU cc_start: 0.6472 (mp0) cc_final: 0.6230 (mp0) REVERT: N 80 TYR cc_start: 0.7376 (m-80) cc_final: 0.7163 (m-80) REVERT: S 82 GLN cc_start: 0.8263 (tp40) cc_final: 0.7966 (tp-100) REVERT: S 93 MET cc_start: 0.7649 (tmm) cc_final: 0.7309 (tmm) REVERT: S 166 LEU cc_start: 0.8972 (tp) cc_final: 0.8621 (tm) REVERT: S 171 GLN cc_start: 0.8599 (mt0) cc_final: 0.8364 (mm110) REVERT: S 190 ARG cc_start: 0.8703 (mtm-85) cc_final: 0.8146 (mtm-85) REVERT: S 206 ARG cc_start: 0.8420 (ttm-80) cc_final: 0.7910 (ttm-80) REVERT: S 208 GLU cc_start: 0.8225 (pt0) cc_final: 0.7609 (pm20) outliers start: 53 outliers final: 18 residues processed: 369 average time/residue: 0.4457 time to fit residues: 179.0164 Evaluate side-chains 350 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 329 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 180 ILE Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 267 CYS Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 75 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 103 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 207 GLN R 285 ASN A 43 ASN A 244 ASN S 167 GLN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.151963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120522 restraints weight = 14911.358| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.49 r_work: 0.3391 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9975 Z= 0.131 Angle : 0.634 8.565 13526 Z= 0.321 Chirality : 0.044 0.190 1521 Planarity : 0.005 0.065 1713 Dihedral : 5.135 50.890 1352 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.50 % Allowed : 26.92 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.24), residues: 1218 helix: 1.23 (0.27), residues: 371 sheet: 0.32 (0.29), residues: 312 loop : -1.14 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 214 TYR 0.027 0.002 TYR A 212 PHE 0.021 0.001 PHE R 123 TRP 0.017 0.001 TRP B 169 HIS 0.005 0.001 HIS R 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 9969) covalent geometry : angle 0.63342 / 0.32 (13514) SS BOND : bond 0.00175 / 0.07 ( 6) SS BOND : angle 0.79298 / 0.43 ( 12) hydrogen bonds : bond 0.04090 / 2.65 ( 439) hydrogen bonds : angle 4.50782 / 3.16 ( 1242) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 347 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 38 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8197 (ttp80) REVERT: R 161 LYS cc_start: 0.8314 (mttt) cc_final: 0.7658 (mmtt) REVERT: R 215 PHE cc_start: 0.8289 (t80) cc_final: 0.7611 (t80) REVERT: R 225 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7761 (tm) REVERT: R 312 MET cc_start: 0.6804 (mtp) cc_final: 0.6186 (tmm) REVERT: R 313 ASP cc_start: 0.8464 (t70) cc_final: 0.7540 (m-30) REVERT: A 25 GLU cc_start: 0.7720 (tt0) cc_final: 0.7078 (tp30) REVERT: A 29 LYS cc_start: 0.8538 (tppp) cc_final: 0.8232 (tppp) REVERT: A 159 LYS cc_start: 0.8998 (tppp) cc_final: 0.8626 (tptp) REVERT: A 183 ASP cc_start: 0.6737 (t70) cc_final: 0.6492 (t0) REVERT: A 220 ASP cc_start: 0.7811 (t0) cc_final: 0.7599 (t0) REVERT: A 239 ASN cc_start: 0.9069 (m-40) cc_final: 0.8829 (m-40) REVERT: B 172 GLU cc_start: 0.8937 (tp30) cc_final: 0.8648 (tp30) REVERT: B 175 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8081 (mm110) REVERT: B 176 GLN cc_start: 0.9011 (mt0) cc_final: 0.8561 (mt0) REVERT: B 204 CYS cc_start: 0.8625 (m) cc_final: 0.8249 (m) REVERT: B 215 GLU cc_start: 0.8127 (pm20) cc_final: 0.7400 (pm20) REVERT: B 269 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8630 (tp) REVERT: B 301 LYS cc_start: 0.8088 (mmmm) cc_final: 0.7838 (mmmm) REVERT: B 312 ASP cc_start: 0.8961 (m-30) cc_final: 0.8721 (m-30) REVERT: G 17 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7369 (mm-30) REVERT: G 21 MET cc_start: 0.8332 (mmp) cc_final: 0.7517 (mpp) REVERT: N 46 GLU cc_start: 0.6530 (mp0) cc_final: 0.6284 (mp0) REVERT: S 82 GLN cc_start: 0.8146 (tp40) cc_final: 0.7838 (tp-100) REVERT: S 93 MET cc_start: 0.7711 (tmm) cc_final: 0.7479 (tmm) REVERT: S 126 ILE cc_start: 0.7841 (mm) cc_final: 0.7560 (mm) REVERT: S 166 LEU cc_start: 0.8976 (tp) cc_final: 0.8602 (tm) REVERT: S 171 GLN cc_start: 0.8550 (mt0) cc_final: 0.7997 (mp10) REVERT: S 190 ARG cc_start: 0.8608 (mtm-85) cc_final: 0.7971 (mtm-85) REVERT: S 206 ARG cc_start: 0.8389 (ttm-80) cc_final: 0.7617 (ttm-80) REVERT: S 208 GLU cc_start: 0.8211 (pt0) cc_final: 0.7421 (pm20) outliers start: 48 outliers final: 21 residues processed: 368 average time/residue: 0.4368 time to fit residues: 174.9068 Evaluate side-chains 354 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 330 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 ARG Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 155 LYS Chi-restraints excluded: chain R residue 180 ILE Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 267 CYS Chi-restraints excluded: chain R residue 309 ASN Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 77 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 206 HIS R 207 GLN R 280 HIS R 285 ASN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.146518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.115533 restraints weight = 15240.938| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.47 r_work: 0.3308 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9975 Z= 0.178 Angle : 0.670 9.271 13526 Z= 0.342 Chirality : 0.046 0.183 1521 Planarity : 0.005 0.074 1713 Dihedral : 5.182 49.142 1352 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.72 % Allowed : 25.61 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.07 (0.24), residues: 1218 helix: 1.38 (0.27), residues: 368 sheet: 0.41 (0.29), residues: 318 loop : -1.13 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 214 TYR 0.020 0.002 TYR A 212 PHE 0.024 0.002 PHE R 123 TRP 0.021 0.002 TRP B 169 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 ( 9969) covalent geometry : angle 0.66945 / 0.34 (13514) SS BOND : bond 0.00669 / 0.33 ( 6) SS BOND : angle 0.73687 / 0.39 ( 12) hydrogen bonds : bond 0.04483 / 2.92 ( 439) hydrogen bonds : angle 4.58397 / 3.23 ( 1242) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 347 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 161 LYS cc_start: 0.8384 (mttt) cc_final: 0.7668 (mmtt) REVERT: R 215 PHE cc_start: 0.8148 (t80) cc_final: 0.7663 (t80) REVERT: R 225 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7928 (tp) REVERT: R 312 MET cc_start: 0.6809 (mtp) cc_final: 0.6139 (pp-130) REVERT: R 313 ASP cc_start: 0.8525 (t70) cc_final: 0.7533 (m-30) REVERT: A 25 GLU cc_start: 0.7763 (tt0) cc_final: 0.7088 (tp30) REVERT: A 29 LYS cc_start: 0.8572 (tppp) cc_final: 0.8260 (tppp) REVERT: A 159 LYS cc_start: 0.9037 (tppp) cc_final: 0.8688 (tptp) REVERT: A 183 ASP cc_start: 0.6822 (t70) cc_final: 0.6546 (t0) REVERT: A 220 ASP cc_start: 0.7924 (t0) cc_final: 0.7622 (t0) REVERT: A 239 ASN cc_start: 0.9092 (m-40) cc_final: 0.8878 (m-40) REVERT: A 244 ASN cc_start: 0.9148 (t0) cc_final: 0.8916 (t160) REVERT: B 42 ARG cc_start: 0.8518 (tpp-160) cc_final: 0.8098 (tpp-160) REVERT: B 145 TYR cc_start: 0.8811 (p90) cc_final: 0.8443 (p90) REVERT: B 172 GLU cc_start: 0.9055 (tp30) cc_final: 0.8769 (tp30) REVERT: B 175 GLN cc_start: 0.8523 (mm-40) cc_final: 0.7685 (mp10) REVERT: B 176 GLN cc_start: 0.9133 (mt0) cc_final: 0.8687 (mt0) REVERT: B 204 CYS cc_start: 0.8469 (m) cc_final: 0.8162 (m) REVERT: B 214 ARG cc_start: 0.8882 (ttm110) cc_final: 0.8382 (mtp180) REVERT: B 215 GLU cc_start: 0.8330 (pm20) cc_final: 0.7840 (pm20) REVERT: B 263 THR cc_start: 0.7953 (OUTLIER) cc_final: 0.7638 (m) REVERT: B 269 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8725 (tp) REVERT: B 312 ASP cc_start: 0.8980 (m-30) cc_final: 0.8751 (m-30) REVERT: G 17 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7330 (mm-30) REVERT: G 21 MET cc_start: 0.8377 (mmp) cc_final: 0.7538 (mpp) REVERT: N 46 GLU cc_start: 0.6548 (mp0) cc_final: 0.6239 (mp0) REVERT: N 80 TYR cc_start: 0.7867 (m-80) cc_final: 0.7611 (m-80) REVERT: S 18 ARG cc_start: 0.8299 (ttt-90) cc_final: 0.8090 (ttt-90) REVERT: S 82 GLN cc_start: 0.8283 (tp40) cc_final: 0.7980 (tp-100) REVERT: S 93 MET cc_start: 0.7853 (tmm) cc_final: 0.7610 (tmm) REVERT: S 148 ARG cc_start: 0.7717 (ttm-80) cc_final: 0.7488 (ttp80) REVERT: S 166 LEU cc_start: 0.9003 (tp) cc_final: 0.8584 (tm) REVERT: S 190 ARG cc_start: 0.8577 (mtm-85) cc_final: 0.8366 (mtm-85) outliers start: 61 outliers final: 34 residues processed: 378 average time/residue: 0.4115 time to fit residues: 169.6100 Evaluate side-chains 374 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 337 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 CYS Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 180 ILE Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 267 CYS Chi-restraints excluded: chain R residue 309 ASN Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 189 ASP Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 49 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 80 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 206 HIS R 207 GLN R 285 ASN A 43 ASN A 75 GLN B 44 GLN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.148313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.117279 restraints weight = 14922.402| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 3.48 r_work: 0.3343 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9975 Z= 0.131 Angle : 0.645 9.501 13526 Z= 0.326 Chirality : 0.044 0.178 1521 Planarity : 0.004 0.046 1713 Dihedral : 5.058 49.055 1352 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.88 % Allowed : 29.17 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.22 (0.24), residues: 1218 helix: 1.56 (0.27), residues: 369 sheet: 0.35 (0.29), residues: 308 loop : -0.97 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 214 TYR 0.027 0.002 TYR N 115 PHE 0.018 0.001 PHE R 123 TRP 0.016 0.001 TRP B 332 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 9969) covalent geometry : angle 0.64540 / 0.33 (13514) SS BOND : bond 0.00269 / 0.13 ( 6) SS BOND : angle 0.61946 / 0.29 ( 12) hydrogen bonds : bond 0.03996 / 2.61 ( 439) hydrogen bonds : angle 4.43940 / 3.15 ( 1242) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 344 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 161 LYS cc_start: 0.8377 (mttt) cc_final: 0.7645 (mmtt) REVERT: R 215 PHE cc_start: 0.8128 (t80) cc_final: 0.7624 (t80) REVERT: R 225 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7856 (tp) REVERT: R 312 MET cc_start: 0.6783 (mtp) cc_final: 0.6040 (pp-130) REVERT: R 313 ASP cc_start: 0.8520 (t70) cc_final: 0.7489 (m-30) REVERT: A 25 GLU cc_start: 0.7798 (tt0) cc_final: 0.7138 (tp30) REVERT: A 29 LYS cc_start: 0.8547 (tppp) cc_final: 0.8162 (tppp) REVERT: A 147 ASP cc_start: 0.7773 (p0) cc_final: 0.6951 (p0) REVERT: A 151 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8218 (mm-30) REVERT: A 159 LYS cc_start: 0.9068 (tppp) cc_final: 0.8748 (tptp) REVERT: A 183 ASP cc_start: 0.6671 (t70) cc_final: 0.6140 (t0) REVERT: A 239 ASN cc_start: 0.9097 (m-40) cc_final: 0.8827 (m-40) REVERT: A 244 ASN cc_start: 0.9093 (t0) cc_final: 0.8833 (t160) REVERT: B 42 ARG cc_start: 0.8549 (tpp-160) cc_final: 0.8164 (tpp-160) REVERT: B 145 TYR cc_start: 0.8814 (p90) cc_final: 0.8423 (p90) REVERT: B 172 GLU cc_start: 0.9074 (tp30) cc_final: 0.8802 (tp30) REVERT: B 175 GLN cc_start: 0.8564 (mm-40) cc_final: 0.7732 (mp10) REVERT: B 176 GLN cc_start: 0.9107 (mt0) cc_final: 0.8654 (mt0) REVERT: B 204 CYS cc_start: 0.8525 (m) cc_final: 0.8148 (m) REVERT: B 214 ARG cc_start: 0.8973 (ttm110) cc_final: 0.8530 (mtp180) REVERT: B 217 MET cc_start: 0.7879 (pmt) cc_final: 0.7645 (pmm) REVERT: B 228 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.8126 (m-30) REVERT: B 269 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8748 (tp) REVERT: B 312 ASP cc_start: 0.8965 (m-30) cc_final: 0.8689 (m-30) REVERT: G 21 MET cc_start: 0.8379 (mmp) cc_final: 0.7551 (mpp) REVERT: N 46 GLU cc_start: 0.6567 (mp0) cc_final: 0.6290 (mp0) REVERT: S 82 GLN cc_start: 0.8134 (tp40) cc_final: 0.7829 (tp-100) REVERT: S 93 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7569 (tmm) REVERT: S 166 LEU cc_start: 0.9024 (tp) cc_final: 0.8603 (tm) REVERT: S 171 GLN cc_start: 0.8763 (mm110) cc_final: 0.7675 (mp10) REVERT: S 175 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9125 (tp) REVERT: S 190 ARG cc_start: 0.8522 (mtm-85) cc_final: 0.8192 (mtm-85) REVERT: S 208 GLU cc_start: 0.8251 (pt0) cc_final: 0.7585 (pm20) outliers start: 52 outliers final: 29 residues processed: 369 average time/residue: 0.3557 time to fit residues: 143.4731 Evaluate side-chains 366 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 332 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 CYS Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 180 ILE Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 267 CYS Chi-restraints excluded: chain R residue 309 ASN Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 115 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 84 ASN R 206 HIS R 207 GLN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.148511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.117332 restraints weight = 14780.420| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.47 r_work: 0.3329 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9975 Z= 0.146 Angle : 0.675 10.389 13526 Z= 0.339 Chirality : 0.045 0.175 1521 Planarity : 0.004 0.059 1713 Dihedral : 5.086 49.167 1352 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.07 % Allowed : 29.83 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.22 (0.24), residues: 1218 helix: 1.49 (0.27), residues: 374 sheet: 0.42 (0.29), residues: 308 loop : -0.97 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 214 TYR 0.027 0.002 TYR N 115 PHE 0.022 0.001 PHE R 166 TRP 0.019 0.001 TRP B 332 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 9969) covalent geometry : angle 0.67476 / 0.34 (13514) SS BOND : bond 0.00252 / 0.12 ( 6) SS BOND : angle 0.63936 / 0.31 ( 12) hydrogen bonds : bond 0.04060 / 2.65 ( 439) hydrogen bonds : angle 4.46699 / 3.17 ( 1242) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 339 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 161 LYS cc_start: 0.8347 (mttt) cc_final: 0.7628 (mmtt) REVERT: R 215 PHE cc_start: 0.8163 (t80) cc_final: 0.7638 (t80) REVERT: R 225 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7878 (tp) REVERT: R 312 MET cc_start: 0.6802 (mtp) cc_final: 0.6025 (pp-130) REVERT: R 313 ASP cc_start: 0.8532 (t70) cc_final: 0.7497 (m-30) REVERT: A 25 GLU cc_start: 0.7790 (tt0) cc_final: 0.7130 (tp30) REVERT: A 29 LYS cc_start: 0.8544 (tppp) cc_final: 0.8165 (tppp) REVERT: A 147 ASP cc_start: 0.7776 (p0) cc_final: 0.6998 (p0) REVERT: A 151 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8223 (mm-30) REVERT: A 159 LYS cc_start: 0.9023 (tppp) cc_final: 0.8689 (tptp) REVERT: A 239 ASN cc_start: 0.9100 (m-40) cc_final: 0.8843 (m-40) REVERT: A 244 ASN cc_start: 0.9093 (t0) cc_final: 0.8844 (t160) REVERT: B 42 ARG cc_start: 0.8572 (tpp-160) cc_final: 0.8159 (tpp-160) REVERT: B 59 TYR cc_start: 0.7938 (OUTLIER) cc_final: 0.6886 (m-10) REVERT: B 145 TYR cc_start: 0.8812 (p90) cc_final: 0.8386 (p90) REVERT: B 172 GLU cc_start: 0.9124 (tp30) cc_final: 0.8860 (tp30) REVERT: B 175 GLN cc_start: 0.8577 (mm-40) cc_final: 0.7754 (mp10) REVERT: B 176 GLN cc_start: 0.9075 (mt0) cc_final: 0.8634 (mt0) REVERT: B 204 CYS cc_start: 0.8551 (m) cc_final: 0.8127 (m) REVERT: B 214 ARG cc_start: 0.8849 (ttm110) cc_final: 0.8448 (mtt180) REVERT: B 251 ARG cc_start: 0.7964 (mtt-85) cc_final: 0.7756 (mtt-85) REVERT: B 269 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8722 (tp) REVERT: B 312 ASP cc_start: 0.8946 (m-30) cc_final: 0.8659 (m-30) REVERT: G 17 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7253 (mm-30) REVERT: G 21 MET cc_start: 0.8394 (mmp) cc_final: 0.7555 (mpp) REVERT: G 38 MET cc_start: 0.7005 (ttt) cc_final: 0.6762 (ttt) REVERT: N 46 GLU cc_start: 0.6633 (mp0) cc_final: 0.6329 (mp0) REVERT: S 82 GLN cc_start: 0.8184 (tp40) cc_final: 0.7878 (tp-100) REVERT: S 93 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7673 (tmm) REVERT: S 162 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8046 (mt) REVERT: S 166 LEU cc_start: 0.9057 (tp) cc_final: 0.8640 (tm) REVERT: S 175 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9176 (tp) REVERT: S 190 ARG cc_start: 0.8573 (mtm-85) cc_final: 0.8146 (mtm-85) REVERT: S 208 GLU cc_start: 0.8264 (pt0) cc_final: 0.7605 (pm20) outliers start: 54 outliers final: 36 residues processed: 364 average time/residue: 0.3900 time to fit residues: 154.6126 Evaluate side-chains 372 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 330 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 CYS Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 180 ILE Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 267 CYS Chi-restraints excluded: chain R residue 309 ASN Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 119 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 96 optimal weight: 0.0970 chunk 87 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 84 ASN R 206 HIS R 207 GLN A 43 ASN A 75 GLN B 44 GLN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.148049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.116210 restraints weight = 14843.025| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.54 r_work: 0.3330 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9975 Z= 0.136 Angle : 0.668 9.807 13526 Z= 0.335 Chirality : 0.045 0.254 1521 Planarity : 0.004 0.044 1713 Dihedral : 5.015 49.802 1352 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.88 % Allowed : 31.14 % Favored : 63.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 (0.24), residues: 1218 helix: 1.61 (0.27), residues: 369 sheet: 0.52 (0.30), residues: 290 loop : -0.91 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 169 TYR 0.020 0.001 TYR A 212 PHE 0.012 0.001 PHE R 123 TRP 0.020 0.001 TRP B 332 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 9969) covalent geometry : angle 0.66854 / 0.34 (13514) SS BOND : bond 0.00250 / 0.12 ( 6) SS BOND : angle 0.60016 / 0.27 ( 12) hydrogen bonds : bond 0.03963 / 2.59 ( 439) hydrogen bonds : angle 4.47518 / 3.18 ( 1242) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 337 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 44 GLN cc_start: 0.8689 (pt0) cc_final: 0.8430 (pp30) REVERT: R 112 ARG cc_start: 0.8634 (tpt170) cc_final: 0.8365 (tpt170) REVERT: R 161 LYS cc_start: 0.8351 (mttt) cc_final: 0.7644 (mmtt) REVERT: R 215 PHE cc_start: 0.8158 (t80) cc_final: 0.7601 (t80) REVERT: R 225 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7870 (tp) REVERT: R 313 ASP cc_start: 0.8529 (t70) cc_final: 0.7472 (m-30) REVERT: A 25 GLU cc_start: 0.7781 (tt0) cc_final: 0.7127 (tp30) REVERT: A 29 LYS cc_start: 0.8583 (tppp) cc_final: 0.8213 (tppp) REVERT: A 147 ASP cc_start: 0.7751 (p0) cc_final: 0.7003 (p0) REVERT: A 151 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8229 (mm-30) REVERT: A 159 LYS cc_start: 0.9072 (tppp) cc_final: 0.8764 (tptp) REVERT: A 239 ASN cc_start: 0.9174 (m-40) cc_final: 0.8890 (m-40) REVERT: A 244 ASN cc_start: 0.9124 (t0) cc_final: 0.8865 (t160) REVERT: B 42 ARG cc_start: 0.8572 (tpp-160) cc_final: 0.8116 (tpp-160) REVERT: B 57 LYS cc_start: 0.8969 (pttm) cc_final: 0.8098 (pttm) REVERT: B 59 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.6817 (m-10) REVERT: B 175 GLN cc_start: 0.8594 (mm-40) cc_final: 0.7817 (mp10) REVERT: B 176 GLN cc_start: 0.9068 (mt0) cc_final: 0.8680 (mt0) REVERT: B 204 CYS cc_start: 0.8443 (m) cc_final: 0.7999 (m) REVERT: B 214 ARG cc_start: 0.9006 (ttm110) cc_final: 0.8532 (ptp-110) REVERT: B 215 GLU cc_start: 0.8403 (pm20) cc_final: 0.7905 (pm20) REVERT: B 269 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8762 (tp) REVERT: G 17 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7289 (mm-30) REVERT: G 21 MET cc_start: 0.8403 (mmp) cc_final: 0.7562 (mpp) REVERT: N 46 GLU cc_start: 0.6612 (mp0) cc_final: 0.6274 (mp0) REVERT: S 82 GLN cc_start: 0.8180 (tp40) cc_final: 0.7872 (tp-100) REVERT: S 93 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7629 (tmm) REVERT: S 162 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8088 (mt) REVERT: S 166 LEU cc_start: 0.9047 (tp) cc_final: 0.8622 (tm) REVERT: S 190 ARG cc_start: 0.8557 (mtm-85) cc_final: 0.8177 (mtm-85) REVERT: S 206 ARG cc_start: 0.8243 (ttm-80) cc_final: 0.7387 (ttm110) REVERT: S 208 GLU cc_start: 0.8253 (pt0) cc_final: 0.7521 (pm20) outliers start: 52 outliers final: 35 residues processed: 361 average time/residue: 0.4036 time to fit residues: 158.8828 Evaluate side-chains 368 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 328 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 CYS Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 180 ILE Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 267 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 189 ASP Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 120 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 chunk 7 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN B 44 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.148781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.117029 restraints weight = 14780.576| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.56 r_work: 0.3342 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9975 Z= 0.134 Angle : 0.703 12.573 13526 Z= 0.350 Chirality : 0.045 0.225 1521 Planarity : 0.004 0.043 1713 Dihedral : 4.963 49.760 1352 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.85 % Allowed : 32.36 % Favored : 63.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 (0.24), residues: 1218 helix: 1.68 (0.27), residues: 369 sheet: 0.58 (0.30), residues: 295 loop : -0.89 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 169 TYR 0.021 0.001 TYR A 212 PHE 0.027 0.001 PHE R 166 TRP 0.019 0.001 TRP B 332 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 9969) covalent geometry : angle 0.70280 / 0.35 (13514) SS BOND : bond 0.00229 / 0.11 ( 6) SS BOND : angle 0.58424 / 0.28 ( 12) hydrogen bonds : bond 0.03865 / 2.52 ( 439) hydrogen bonds : angle 4.46623 / 3.16 ( 1242) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 338 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 44 GLN cc_start: 0.8633 (pt0) cc_final: 0.8412 (pp30) REVERT: R 112 ARG cc_start: 0.8651 (tpt170) cc_final: 0.8397 (tpt170) REVERT: R 161 LYS cc_start: 0.8339 (mttt) cc_final: 0.7620 (mmtt) REVERT: R 215 PHE cc_start: 0.8187 (t80) cc_final: 0.7518 (t80) REVERT: R 225 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7793 (tm) REVERT: R 313 ASP cc_start: 0.8537 (t70) cc_final: 0.7436 (m-30) REVERT: A 25 GLU cc_start: 0.7789 (tt0) cc_final: 0.7138 (tp30) REVERT: A 29 LYS cc_start: 0.8595 (tppp) cc_final: 0.8235 (tppp) REVERT: A 147 ASP cc_start: 0.7741 (p0) cc_final: 0.7047 (p0) REVERT: A 151 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8221 (mm-30) REVERT: A 159 LYS cc_start: 0.9009 (tppp) cc_final: 0.8694 (tptp) REVERT: A 239 ASN cc_start: 0.9161 (m-40) cc_final: 0.8901 (m-40) REVERT: A 244 ASN cc_start: 0.9088 (t0) cc_final: 0.8847 (t160) REVERT: B 42 ARG cc_start: 0.8592 (tpp-160) cc_final: 0.8129 (tpp-160) REVERT: B 57 LYS cc_start: 0.8924 (pttm) cc_final: 0.7986 (pttm) REVERT: B 59 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.6792 (m-10) REVERT: B 175 GLN cc_start: 0.8618 (mm-40) cc_final: 0.7844 (mp10) REVERT: B 176 GLN cc_start: 0.9048 (mt0) cc_final: 0.8681 (mt0) REVERT: B 195 ASP cc_start: 0.8722 (t0) cc_final: 0.8141 (m-30) REVERT: B 204 CYS cc_start: 0.8373 (m) cc_final: 0.7929 (m) REVERT: B 214 ARG cc_start: 0.8981 (ttm110) cc_final: 0.8579 (ptp-110) REVERT: B 215 GLU cc_start: 0.8447 (pm20) cc_final: 0.7927 (pm20) REVERT: B 262 MET cc_start: 0.8632 (mmm) cc_final: 0.8198 (tpp) REVERT: B 269 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8744 (tp) REVERT: G 21 MET cc_start: 0.8393 (mmp) cc_final: 0.7553 (mpp) REVERT: N 46 GLU cc_start: 0.6601 (mp0) cc_final: 0.6214 (mp0) REVERT: N 87 LYS cc_start: 0.7986 (mptm) cc_final: 0.7671 (mptt) REVERT: S 82 GLN cc_start: 0.8160 (tp40) cc_final: 0.7857 (tp-100) REVERT: S 93 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7672 (tmm) REVERT: S 162 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8079 (mt) REVERT: S 166 LEU cc_start: 0.9052 (tp) cc_final: 0.8639 (tm) REVERT: S 190 ARG cc_start: 0.8595 (mtm-85) cc_final: 0.8324 (mtm-85) REVERT: S 206 ARG cc_start: 0.8224 (ttm-80) cc_final: 0.7576 (ttm110) REVERT: S 208 GLU cc_start: 0.8222 (pt0) cc_final: 0.7527 (pm20) outliers start: 41 outliers final: 31 residues processed: 359 average time/residue: 0.4356 time to fit residues: 170.8070 Evaluate side-chains 360 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 324 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 CYS Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 180 ILE Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 83 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 0.0020 chunk 96 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 4 optimal weight: 0.5980 chunk 118 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN A 75 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 237 ASN N 82 GLN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.149546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.118404 restraints weight = 14993.987| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.55 r_work: 0.3343 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9975 Z= 0.134 Angle : 0.708 12.420 13526 Z= 0.349 Chirality : 0.046 0.289 1521 Planarity : 0.004 0.043 1713 Dihedral : 4.937 50.266 1352 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.03 % Allowed : 32.65 % Favored : 63.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 (0.24), residues: 1218 helix: 1.62 (0.27), residues: 374 sheet: 0.59 (0.30), residues: 295 loop : -0.87 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 290 TYR 0.020 0.001 TYR A 212 PHE 0.013 0.001 PHE R 123 TRP 0.019 0.001 TRP B 332 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 9969) covalent geometry : angle 0.70818 / 0.35 (13514) SS BOND : bond 0.00241 / 0.11 ( 6) SS BOND : angle 0.55871 / 0.27 ( 12) hydrogen bonds : bond 0.03858 / 2.52 ( 439) hydrogen bonds : angle 4.42858 / 3.13 ( 1242) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 333 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 44 GLN cc_start: 0.8655 (pt0) cc_final: 0.8429 (pp30) REVERT: R 112 ARG cc_start: 0.8658 (tpt170) cc_final: 0.8411 (tpt170) REVERT: R 161 LYS cc_start: 0.8348 (mttt) cc_final: 0.7633 (mmtt) REVERT: R 215 PHE cc_start: 0.8191 (t80) cc_final: 0.7509 (t80) REVERT: R 225 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7804 (tm) REVERT: R 313 ASP cc_start: 0.8490 (t70) cc_final: 0.7331 (m-30) REVERT: A 25 GLU cc_start: 0.7775 (tt0) cc_final: 0.7130 (tp30) REVERT: A 29 LYS cc_start: 0.8575 (tppp) cc_final: 0.8226 (tppp) REVERT: A 147 ASP cc_start: 0.7717 (p0) cc_final: 0.6989 (p0) REVERT: A 151 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8205 (mm-30) REVERT: A 239 ASN cc_start: 0.9149 (m-40) cc_final: 0.8842 (m-40) REVERT: A 244 ASN cc_start: 0.9064 (t0) cc_final: 0.8852 (t160) REVERT: B 42 ARG cc_start: 0.8590 (tpp-160) cc_final: 0.8171 (tpp-160) REVERT: B 57 LYS cc_start: 0.8832 (pttm) cc_final: 0.7786 (pttm) REVERT: B 59 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.6816 (m-10) REVERT: B 137 ARG cc_start: 0.7460 (tpt-90) cc_final: 0.7154 (tpp-160) REVERT: B 172 GLU cc_start: 0.9119 (tp30) cc_final: 0.8889 (tp30) REVERT: B 175 GLN cc_start: 0.8632 (mm-40) cc_final: 0.7874 (mp10) REVERT: B 176 GLN cc_start: 0.9049 (mt0) cc_final: 0.8685 (mt0) REVERT: B 204 CYS cc_start: 0.8354 (m) cc_final: 0.7927 (m) REVERT: B 214 ARG cc_start: 0.8973 (ttm110) cc_final: 0.8570 (ptp-110) REVERT: B 215 GLU cc_start: 0.8487 (pm20) cc_final: 0.7964 (pm20) REVERT: B 262 MET cc_start: 0.8677 (mmm) cc_final: 0.8210 (tpp) REVERT: B 269 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.8732 (tp) REVERT: G 17 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7274 (mm-30) REVERT: G 21 MET cc_start: 0.8374 (mmp) cc_final: 0.7547 (mpp) REVERT: N 46 GLU cc_start: 0.6532 (mp0) cc_final: 0.6155 (mp0) REVERT: S 82 GLN cc_start: 0.8139 (tp40) cc_final: 0.7830 (tp-100) REVERT: S 93 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7651 (tmm) REVERT: S 162 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8048 (mt) REVERT: S 166 LEU cc_start: 0.9050 (tp) cc_final: 0.8633 (tm) REVERT: S 190 ARG cc_start: 0.8581 (mtm-85) cc_final: 0.8335 (mtm-85) REVERT: S 206 ARG cc_start: 0.8250 (ttm-80) cc_final: 0.7601 (ttm110) REVERT: S 208 GLU cc_start: 0.8251 (pt0) cc_final: 0.7574 (pm20) outliers start: 43 outliers final: 32 residues processed: 355 average time/residue: 0.3808 time to fit residues: 148.0127 Evaluate side-chains 368 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 331 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 CYS Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 180 ILE Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 28 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 41 optimal weight: 0.0970 chunk 110 optimal weight: 5.9990 chunk 76 optimal weight: 0.0670 chunk 109 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN B 44 GLN N 82 GLN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.149663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.118341 restraints weight = 14941.980| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.52 r_work: 0.3352 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9975 Z= 0.131 Angle : 0.714 12.409 13526 Z= 0.351 Chirality : 0.046 0.303 1521 Planarity : 0.004 0.043 1713 Dihedral : 4.879 49.969 1352 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.94 % Allowed : 32.83 % Favored : 63.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 (0.24), residues: 1218 helix: 1.70 (0.27), residues: 374 sheet: 0.63 (0.31), residues: 294 loop : -0.84 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 290 TYR 0.019 0.001 TYR A 212 PHE 0.026 0.001 PHE R 166 TRP 0.020 0.001 TRP B 332 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 9969) covalent geometry : angle 0.71451 / 0.35 (13514) SS BOND : bond 0.00224 / 0.10 ( 6) SS BOND : angle 0.55712 / 0.29 ( 12) hydrogen bonds : bond 0.03792 / 2.48 ( 439) hydrogen bonds : angle 4.42952 / 3.14 ( 1242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3938.12 seconds wall clock time: 67 minutes 43.69 seconds (4063.69 seconds total)