Starting phenix.real_space_refine on Sun May 3 00:25:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9on2_70627/05_2026/9on2_70627.cif Found real_map, /net/cci-nas-00/data/ceres_data/9on2_70627/05_2026/9on2_70627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9on2_70627/05_2026/9on2_70627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9on2_70627/05_2026/9on2_70627.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9on2_70627/05_2026/9on2_70627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9on2_70627/05_2026/9on2_70627.map" } resolution = 3.16 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= 0.039 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 12 5.49 5 S 53 5.16 5 C 5859 2.51 5 N 1643 2.21 5 O 1750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9317 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2523 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 307} Chain breaks: 2 Chain: "C" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2470 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 11, 'TRANS': 302} Chain breaks: 2 Chain: "D" Number of atoms: 2288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2288 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 7, 'TRANS': 295} Chain breaks: 2 Chain: "X" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1912 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 5, 'TRANS': 230} Chain breaks: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.80, per 1000 atoms: 0.19 Number of scatterers: 9317 At special positions: 0 Unit cell: (84.39, 85.26, 133.11, 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 53 16.00 P 12 15.00 O 1750 8.00 N 1643 7.00 C 5859 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 321.4 milliseconds 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2206 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 51.1% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.554A pdb=" N LEU A 6 " --> pdb=" O ASP A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 24 through 30 removed outlier: 3.845A pdb=" N PHE A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 39 Processing helix chain 'A' and resid 42 through 58 Processing helix chain 'A' and resid 64 through 71 Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.828A pdb=" N HIS A 79 " --> pdb=" O PHE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 93 Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 147 through 157 Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 186 through 204 removed outlier: 4.576A pdb=" N VAL A 198 " --> pdb=" O VAL A 194 " (cutoff:3.500A) Proline residue: A 199 - end of helix Processing helix chain 'A' and resid 215 through 223 removed outlier: 3.977A pdb=" N PHE A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 250 Processing helix chain 'A' and resid 285 through 291 removed outlier: 3.778A pdb=" N GLN A 291 " --> pdb=" O THR A 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 31 Processing helix chain 'C' and resid 34 through 39 removed outlier: 3.647A pdb=" N LEU C 38 " --> pdb=" O THR C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 53 through 67 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 104 through 111 Processing helix chain 'C' and resid 130 through 143 removed outlier: 4.269A pdb=" N GLN C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 165 through 187 removed outlier: 3.548A pdb=" N GLU C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 197 removed outlier: 4.344A pdb=" N ARG C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 215 through 233 Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 244 through 250 removed outlier: 4.040A pdb=" N PHE C 248 " --> pdb=" O ILE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 277 Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 46 through 62 Processing helix chain 'D' and resid 68 through 79 removed outlier: 3.632A pdb=" N THR D 77 " --> pdb=" O GLU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.946A pdb=" N LYS D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 127 Processing helix chain 'D' and resid 142 through 154 Processing helix chain 'D' and resid 156 through 166 Processing helix chain 'D' and resid 174 through 192 Processing helix chain 'D' and resid 207 through 213 removed outlier: 4.004A pdb=" N VAL D 211 " --> pdb=" O SER D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 240 Processing helix chain 'D' and resid 266 through 271 removed outlier: 3.609A pdb=" N PHE D 270 " --> pdb=" O SER D 267 " (cutoff:3.500A) Processing helix chain 'X' and resid 53 through 67 Processing helix chain 'X' and resid 88 through 100 Processing helix chain 'X' and resid 104 through 113 Processing helix chain 'X' and resid 122 through 140 removed outlier: 3.955A pdb=" N GLU X 134 " --> pdb=" O LEU X 130 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N SER X 135 " --> pdb=" O TYR X 131 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N MET X 136 " --> pdb=" O SER X 132 " (cutoff:3.500A) Processing helix chain 'X' and resid 150 through 153 removed outlier: 3.599A pdb=" N ALA X 153 " --> pdb=" O SER X 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 150 through 153' Processing helix chain 'X' and resid 154 through 162 Processing helix chain 'X' and resid 165 through 188 removed outlier: 5.069A pdb=" N THR X 172 " --> pdb=" O LEU X 168 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU X 173 " --> pdb=" O GLN X 169 " (cutoff:3.500A) Processing helix chain 'X' and resid 228 through 233 Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 181 removed outlier: 5.589A pdb=" N GLY A 136 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N LEU A 254 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL A 210 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE A 256 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE A 212 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N THR A 103 " --> pdb=" O CYS A 255 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN A 257 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU A 105 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE A 102 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU A 296 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N GLU A 104 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA A 298 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA A 106 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG A 295 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG A 313 " --> pdb=" O TYR A 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 85 through 86 removed outlier: 6.225A pdb=" N VAL D 132 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL D 170 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TYR D 134 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN D 131 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 202 " --> pdb=" O ASN D 131 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYS D 201 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL D 246 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL D 203 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N THR D 248 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL D 205 " --> pdb=" O THR D 248 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N HIS D 250 " --> pdb=" O VAL D 205 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 85 through 86 removed outlier: 6.225A pdb=" N VAL D 132 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL D 170 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TYR D 134 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN D 131 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 202 " --> pdb=" O ASN D 131 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYS D 201 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL D 246 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL D 203 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N THR D 248 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL D 205 " --> pdb=" O THR D 248 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N HIS D 250 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N THR D 103 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ASN D 249 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE D 105 " --> pdb=" O ASN D 249 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ILE D 251 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLY D 107 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N ARG D 253 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ARG D 275 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 208 through 212 removed outlier: 5.403A pdb=" N GLU C 154 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR C 283 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR C 120 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU C 313 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLU C 122 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N PHE C 315 " --> pdb=" O GLU C 122 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N CYS C 124 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N TRP C 317 " --> pdb=" O CYS C 124 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ARG C 312 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 340 through 342 Processing sheet with id=AA6, first strand: chain 'D' and resid 66 through 67 removed outlier: 6.513A pdb=" N GLU X 77 " --> pdb=" O LEU X 143 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU X 145 " --> pdb=" O GLU X 77 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASP X 42 " --> pdb=" O LEU X 191 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ALA X 193 " --> pdb=" O ASP X 42 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU X 44 " --> pdb=" O ALA X 193 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N THR X 195 " --> pdb=" O LEU X 44 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N PHE X 46 " --> pdb=" O THR X 195 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE X 43 " --> pdb=" O HIS X 237 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N MET X 239 " --> pdb=" O ILE X 43 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU X 45 " --> pdb=" O MET X 239 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE X 241 " --> pdb=" O GLU X 45 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N HIS X 47 " --> pdb=" O PHE X 241 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N LYS X 243 " --> pdb=" O HIS X 47 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N PHE X 269 " --> pdb=" O CYS X 280 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1353 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: 1.44 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3024 1.34 - 1.46: 1091 1.46 - 1.57: 5256 1.57 - 1.69: 24 1.69 - 1.81: 75 Bond restraints: 9470 Sorted by residual: bond pdb=" O3A ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" O3A ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" O3A ANP A 401 " pdb=" PB ANP A 401 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" O3A ANP X 301 " pdb=" PB ANP X 301 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" N3B ANP X 301 " pdb=" PG ANP X 301 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.76e+01 ... (remaining 9465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 12736 3.55 - 7.10: 70 7.10 - 10.64: 11 10.64 - 14.19: 4 14.19 - 17.74: 4 Bond angle restraints: 12825 Sorted by residual: angle pdb=" PB ANP C 401 " pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 126.95 109.21 17.74 3.00e+00 1.11e-01 3.50e+01 angle pdb=" PB ANP X 301 " pdb=" N3B ANP X 301 " pdb=" PG ANP X 301 " ideal model delta sigma weight residual 126.95 109.46 17.49 3.00e+00 1.11e-01 3.40e+01 angle pdb=" PB ANP D 401 " pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 126.95 109.67 17.28 3.00e+00 1.11e-01 3.32e+01 angle pdb=" PB ANP A 401 " pdb=" N3B ANP A 401 " pdb=" PG ANP A 401 " ideal model delta sigma weight residual 126.95 110.71 16.24 3.00e+00 1.11e-01 2.93e+01 angle pdb=" O1B ANP D 401 " pdb=" PB ANP D 401 " pdb=" O2B ANP D 401 " ideal model delta sigma weight residual 120.08 109.06 11.02 3.00e+00 1.11e-01 1.35e+01 ... (remaining 12820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.65: 5601 34.65 - 69.30: 198 69.30 - 103.95: 16 103.95 - 138.60: 1 138.60 - 173.25: 1 Dihedral angle restraints: 5817 sinusoidal: 2423 harmonic: 3394 Sorted by residual: dihedral pdb=" O1A ANP A 401 " pdb=" O3A ANP A 401 " pdb=" PA ANP A 401 " pdb=" PB ANP A 401 " ideal model delta sinusoidal sigma weight residual 83.11 -90.14 173.25 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1B ANP A 401 " pdb=" N3B ANP A 401 " pdb=" PB ANP A 401 " pdb=" PG ANP A 401 " ideal model delta sinusoidal sigma weight residual 35.15 -71.20 106.35 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" CA ASP X 36 " pdb=" CB ASP X 36 " pdb=" CG ASP X 36 " pdb=" OD1 ASP X 36 " ideal model delta sinusoidal sigma weight residual -30.00 -89.44 59.44 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 5814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1286 0.054 - 0.108: 182 0.108 - 0.162: 28 0.162 - 0.216: 2 0.216 - 0.270: 4 Chirality restraints: 1502 Sorted by residual: chirality pdb=" C3' ANP D 401 " pdb=" C2' ANP D 401 " pdb=" C4' ANP D 401 " pdb=" O3' ANP D 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C3' ANP C 401 " pdb=" C2' ANP C 401 " pdb=" C4' ANP C 401 " pdb=" O3' ANP C 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C3' ANP X 301 " pdb=" C2' ANP X 301 " pdb=" C4' ANP X 301 " pdb=" O3' ANP X 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 1499 not shown) Planarity restraints: 1616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 9 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO A 10 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 10 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 10 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 125 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" C GLY C 125 " 0.029 2.00e-02 2.50e+03 pdb=" O GLY C 125 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA C 126 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 126 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A 127 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 127 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 127 " -0.020 5.00e-02 4.00e+02 ... (remaining 1613 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 293 2.71 - 3.26: 9279 3.26 - 3.81: 15585 3.81 - 4.35: 20348 4.35 - 4.90: 34490 Nonbonded interactions: 79995 Sorted by model distance: nonbonded pdb=" O GLN X 196 " pdb=" OH TYR X 226 " model vdw 2.163 3.040 nonbonded pdb=" O ASP D 206 " pdb=" OG1 THR D 248 " model vdw 2.167 3.040 nonbonded pdb=" OG1 THR D 209 " pdb=" OD1 ASN D 249 " model vdw 2.170 3.040 nonbonded pdb=" OG SER X 242 " pdb=" OG SER X 254 " model vdw 2.190 3.040 nonbonded pdb=" O LEU D 75 " pdb=" OG1 THR D 79 " model vdw 2.192 3.040 ... (remaining 79990 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.180 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.144 9470 Z= 0.268 Angle : 0.733 17.738 12825 Z= 0.313 Chirality : 0.042 0.270 1502 Planarity : 0.003 0.044 1616 Dihedral : 16.725 173.249 3611 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.77 % Favored : 97.14 % Rotamer: Outliers : 0.59 % Allowed : 17.22 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.26), residues: 1155 helix: 1.23 (0.23), residues: 533 sheet: 0.34 (0.38), residues: 208 loop : -0.54 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 279 TYR 0.008 0.001 TYR X 131 PHE 0.008 0.001 PHE D 173 TRP 0.008 0.001 TRP A 288 HIS 0.005 0.001 HIS X 86 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 9470) covalent geometry : angle 0.73344 (12825) hydrogen bonds : bond 0.16169 ( 461) hydrogen bonds : angle 6.76744 ( 1353) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.306 Fit side-chains REVERT: X 192 PHE cc_start: 0.9100 (m-80) cc_final: 0.8788 (m-80) outliers start: 6 outliers final: 2 residues processed: 87 average time/residue: 0.0852 time to fit residues: 10.5819 Evaluate side-chains 79 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain X residue 194 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.124360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.111141 restraints weight = 13122.895| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.26 r_work: 0.3095 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9470 Z= 0.124 Angle : 0.517 6.348 12825 Z= 0.255 Chirality : 0.041 0.168 1502 Planarity : 0.004 0.039 1616 Dihedral : 9.610 170.268 1394 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.51 % Favored : 97.40 % Rotamer: Outliers : 2.85 % Allowed : 15.65 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.25), residues: 1155 helix: 1.29 (0.23), residues: 542 sheet: 0.29 (0.37), residues: 210 loop : -0.58 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 279 TYR 0.011 0.001 TYR X 226 PHE 0.010 0.001 PHE C 346 TRP 0.004 0.001 TRP A 288 HIS 0.006 0.001 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9470) covalent geometry : angle 0.51728 (12825) hydrogen bonds : bond 0.03368 ( 461) hydrogen bonds : angle 5.05416 ( 1353) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.263 Fit side-chains REVERT: A 191 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8013 (mp) REVERT: A 305 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7614 (pp20) REVERT: X 45 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.7742 (tt0) outliers start: 29 outliers final: 12 residues processed: 110 average time/residue: 0.0992 time to fit residues: 15.0660 Evaluate side-chains 88 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 199 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 5 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.122693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.109369 restraints weight = 13231.727| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.25 r_work: 0.3089 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9470 Z= 0.127 Angle : 0.496 5.504 12825 Z= 0.244 Chirality : 0.040 0.158 1502 Planarity : 0.004 0.036 1616 Dihedral : 9.227 173.389 1392 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.77 % Favored : 97.14 % Rotamer: Outliers : 3.15 % Allowed : 15.75 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.25), residues: 1155 helix: 1.34 (0.23), residues: 542 sheet: 0.17 (0.38), residues: 204 loop : -0.64 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 58 TYR 0.009 0.001 TYR A 139 PHE 0.009 0.001 PHE X 80 TRP 0.005 0.001 TRP A 288 HIS 0.006 0.001 HIS X 40 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9470) covalent geometry : angle 0.49624 (12825) hydrogen bonds : bond 0.03267 ( 461) hydrogen bonds : angle 4.89623 ( 1353) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 0.373 Fit side-chains REVERT: A 191 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8091 (mp) REVERT: A 279 ARG cc_start: 0.6143 (ptt-90) cc_final: 0.5585 (ptt-90) REVERT: A 305 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7652 (pp20) REVERT: D 228 MET cc_start: 0.8269 (mmm) cc_final: 0.7993 (mmp) REVERT: X 45 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: X 266 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7232 (ptmm) outliers start: 32 outliers final: 18 residues processed: 102 average time/residue: 0.0963 time to fit residues: 13.6855 Evaluate side-chains 92 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 199 MET Chi-restraints excluded: chain X residue 266 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 3 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.121987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.108559 restraints weight = 13319.104| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.25 r_work: 0.3064 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9470 Z= 0.134 Angle : 0.501 7.308 12825 Z= 0.245 Chirality : 0.041 0.152 1502 Planarity : 0.004 0.044 1616 Dihedral : 9.195 175.108 1392 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.12 % Favored : 96.80 % Rotamer: Outliers : 3.74 % Allowed : 15.35 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.25), residues: 1155 helix: 1.31 (0.23), residues: 542 sheet: 0.18 (0.39), residues: 198 loop : -0.67 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 58 TYR 0.009 0.001 TYR A 139 PHE 0.013 0.001 PHE X 241 TRP 0.006 0.001 TRP A 288 HIS 0.006 0.001 HIS X 40 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9470) covalent geometry : angle 0.50107 (12825) hydrogen bonds : bond 0.03206 ( 461) hydrogen bonds : angle 4.82656 ( 1353) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 74 time to evaluate : 0.382 Fit side-chains REVERT: A 191 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8080 (mp) REVERT: A 279 ARG cc_start: 0.6045 (ptt-90) cc_final: 0.5400 (ptt-90) REVERT: A 305 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7663 (pp20) REVERT: C 286 MET cc_start: 0.7797 (mmt) cc_final: 0.7092 (mmt) REVERT: D 228 MET cc_start: 0.8294 (mmm) cc_final: 0.8041 (mmp) REVERT: X 45 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: X 147 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8012 (mm) REVERT: X 266 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7221 (ptmm) outliers start: 38 outliers final: 24 residues processed: 106 average time/residue: 0.1009 time to fit residues: 15.2105 Evaluate side-chains 100 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 147 ILE Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 199 MET Chi-restraints excluded: chain X residue 256 VAL Chi-restraints excluded: chain X residue 266 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 72 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.117431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.103974 restraints weight = 13483.099| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.27 r_work: 0.3013 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 9470 Z= 0.197 Angle : 0.564 6.260 12825 Z= 0.276 Chirality : 0.043 0.173 1502 Planarity : 0.004 0.040 1616 Dihedral : 9.544 172.749 1392 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.29 % Favored : 96.62 % Rotamer: Outliers : 4.23 % Allowed : 16.04 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.25), residues: 1155 helix: 1.05 (0.23), residues: 541 sheet: -0.02 (0.38), residues: 200 loop : -0.78 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 58 TYR 0.009 0.001 TYR A 139 PHE 0.017 0.002 PHE X 241 TRP 0.007 0.001 TRP A 288 HIS 0.010 0.001 HIS X 40 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 9470) covalent geometry : angle 0.56353 (12825) hydrogen bonds : bond 0.03723 ( 461) hydrogen bonds : angle 5.03573 ( 1353) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 77 time to evaluate : 0.358 Fit side-chains REVERT: A 63 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7808 (mp) REVERT: A 191 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8069 (mp) REVERT: A 305 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7581 (pp20) REVERT: X 45 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: X 147 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8063 (mm) REVERT: X 266 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7220 (ptmm) outliers start: 43 outliers final: 29 residues processed: 112 average time/residue: 0.1027 time to fit residues: 16.5204 Evaluate side-chains 106 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 71 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 147 ILE Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 199 MET Chi-restraints excluded: chain X residue 256 VAL Chi-restraints excluded: chain X residue 266 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 28 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 0.0270 chunk 91 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN D 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.121949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.108608 restraints weight = 13280.691| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.25 r_work: 0.3080 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9470 Z= 0.104 Angle : 0.481 5.477 12825 Z= 0.236 Chirality : 0.040 0.164 1502 Planarity : 0.004 0.057 1616 Dihedral : 9.049 176.816 1392 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.60 % Favored : 97.32 % Rotamer: Outliers : 3.64 % Allowed : 16.83 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.25), residues: 1155 helix: 1.30 (0.23), residues: 542 sheet: 0.06 (0.39), residues: 198 loop : -0.70 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 58 TYR 0.006 0.001 TYR A 139 PHE 0.016 0.001 PHE X 241 TRP 0.007 0.001 TRP A 288 HIS 0.005 0.001 HIS X 40 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9470) covalent geometry : angle 0.48092 (12825) hydrogen bonds : bond 0.02921 ( 461) hydrogen bonds : angle 4.72582 ( 1353) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 70 time to evaluate : 0.473 Fit side-chains REVERT: A 191 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8078 (mp) REVERT: A 305 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7767 (pp20) REVERT: D 303 THR cc_start: 0.8704 (m) cc_final: 0.8461 (m) REVERT: X 45 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: X 147 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8046 (mm) REVERT: X 266 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7196 (ptmm) outliers start: 37 outliers final: 19 residues processed: 103 average time/residue: 0.1003 time to fit residues: 14.8149 Evaluate side-chains 91 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 147 ILE Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 199 MET Chi-restraints excluded: chain X residue 256 VAL Chi-restraints excluded: chain X residue 266 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 35 optimal weight: 0.0770 chunk 56 optimal weight: 0.9990 chunk 42 optimal weight: 0.0870 chunk 57 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.122972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.109671 restraints weight = 13306.824| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.25 r_work: 0.3093 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9470 Z= 0.107 Angle : 0.487 5.439 12825 Z= 0.235 Chirality : 0.040 0.150 1502 Planarity : 0.004 0.038 1616 Dihedral : 8.954 179.064 1392 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.86 % Favored : 97.06 % Rotamer: Outliers : 3.74 % Allowed : 16.63 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.26), residues: 1155 helix: 1.42 (0.23), residues: 543 sheet: 0.00 (0.39), residues: 203 loop : -0.63 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 58 TYR 0.007 0.001 TYR A 139 PHE 0.008 0.001 PHE X 80 TRP 0.005 0.001 TRP D 314 HIS 0.005 0.001 HIS X 40 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9470) covalent geometry : angle 0.48714 (12825) hydrogen bonds : bond 0.02896 ( 461) hydrogen bonds : angle 4.63429 ( 1353) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 74 time to evaluate : 0.287 Fit side-chains REVERT: A 191 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8097 (mp) REVERT: A 305 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7712 (pp20) REVERT: D 303 THR cc_start: 0.8694 (m) cc_final: 0.8427 (m) REVERT: X 45 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: X 147 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8027 (mm) REVERT: X 241 PHE cc_start: 0.8744 (m-80) cc_final: 0.8522 (m-80) REVERT: X 266 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7283 (ptmm) outliers start: 38 outliers final: 28 residues processed: 105 average time/residue: 0.0939 time to fit residues: 14.2269 Evaluate side-chains 99 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 66 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 147 ILE Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 199 MET Chi-restraints excluded: chain X residue 256 VAL Chi-restraints excluded: chain X residue 266 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 21 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 111 optimal weight: 0.5980 chunk 45 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 chunk 30 optimal weight: 0.0970 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.124072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.110771 restraints weight = 13158.926| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.25 r_work: 0.3107 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9470 Z= 0.104 Angle : 0.486 7.438 12825 Z= 0.235 Chirality : 0.040 0.153 1502 Planarity : 0.004 0.034 1616 Dihedral : 8.843 177.147 1392 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.60 % Favored : 97.32 % Rotamer: Outliers : 3.64 % Allowed : 17.62 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.26), residues: 1155 helix: 1.47 (0.23), residues: 543 sheet: 0.03 (0.39), residues: 203 loop : -0.62 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 58 TYR 0.007 0.001 TYR A 139 PHE 0.009 0.001 PHE X 80 TRP 0.005 0.001 TRP A 288 HIS 0.004 0.001 HIS X 40 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 9470) covalent geometry : angle 0.48625 (12825) hydrogen bonds : bond 0.02775 ( 461) hydrogen bonds : angle 4.57831 ( 1353) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 71 time to evaluate : 0.369 Fit side-chains REVERT: A 191 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8036 (mp) REVERT: A 279 ARG cc_start: 0.6020 (ptt-90) cc_final: 0.5403 (ptt-90) REVERT: A 305 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7671 (pp20) REVERT: D 303 THR cc_start: 0.8641 (m) cc_final: 0.8375 (m) REVERT: X 45 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.7584 (tt0) REVERT: X 147 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.8026 (mm) REVERT: X 266 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7279 (ptmm) outliers start: 37 outliers final: 27 residues processed: 102 average time/residue: 0.1095 time to fit residues: 15.5508 Evaluate side-chains 99 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 147 ILE Chi-restraints excluded: chain X residue 199 MET Chi-restraints excluded: chain X residue 256 VAL Chi-restraints excluded: chain X residue 266 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 55 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 63 optimal weight: 0.0570 chunk 111 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.124121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.110775 restraints weight = 13086.785| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.26 r_work: 0.3094 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9470 Z= 0.107 Angle : 0.505 9.811 12825 Z= 0.240 Chirality : 0.040 0.149 1502 Planarity : 0.004 0.031 1616 Dihedral : 8.734 175.086 1391 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.77 % Favored : 97.14 % Rotamer: Outliers : 3.25 % Allowed : 18.21 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.26), residues: 1155 helix: 1.47 (0.23), residues: 543 sheet: -0.02 (0.39), residues: 203 loop : -0.62 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 58 TYR 0.007 0.001 TYR A 139 PHE 0.019 0.001 PHE X 241 TRP 0.006 0.001 TRP D 314 HIS 0.005 0.001 HIS X 40 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9470) covalent geometry : angle 0.50505 (12825) hydrogen bonds : bond 0.02799 ( 461) hydrogen bonds : angle 4.57078 ( 1353) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 70 time to evaluate : 0.355 Fit side-chains REVERT: A 191 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8018 (mp) REVERT: A 279 ARG cc_start: 0.6022 (ptt-90) cc_final: 0.5402 (ptt-90) REVERT: A 305 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7756 (pp20) REVERT: D 255 ARG cc_start: 0.7326 (mtt180) cc_final: 0.7123 (mtt180) REVERT: D 303 THR cc_start: 0.8604 (m) cc_final: 0.8331 (m) REVERT: X 45 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.7607 (tt0) REVERT: X 147 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.8008 (mm) REVERT: X 266 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7257 (ptmm) outliers start: 33 outliers final: 26 residues processed: 98 average time/residue: 0.1014 time to fit residues: 14.0373 Evaluate side-chains 102 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 71 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 147 ILE Chi-restraints excluded: chain X residue 256 VAL Chi-restraints excluded: chain X residue 266 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 61 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 50 optimal weight: 0.4980 chunk 91 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.124370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.111021 restraints weight = 13148.863| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.27 r_work: 0.3111 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9470 Z= 0.105 Angle : 0.505 12.460 12825 Z= 0.240 Chirality : 0.040 0.154 1502 Planarity : 0.004 0.031 1616 Dihedral : 8.683 173.739 1391 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.60 % Favored : 97.32 % Rotamer: Outliers : 3.35 % Allowed : 18.31 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.26), residues: 1155 helix: 1.48 (0.23), residues: 543 sheet: 0.02 (0.39), residues: 203 loop : -0.62 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 58 TYR 0.007 0.001 TYR A 139 PHE 0.008 0.001 PHE X 80 TRP 0.007 0.001 TRP D 314 HIS 0.005 0.001 HIS X 40 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9470) covalent geometry : angle 0.50471 (12825) hydrogen bonds : bond 0.02757 ( 461) hydrogen bonds : angle 4.56315 ( 1353) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.361 Fit side-chains REVERT: A 191 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8058 (mp) REVERT: A 305 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7748 (pp20) REVERT: D 303 THR cc_start: 0.8594 (m) cc_final: 0.8319 (m) REVERT: X 45 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.7637 (tt0) REVERT: X 147 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8030 (mm) REVERT: X 266 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7244 (ptmm) outliers start: 34 outliers final: 29 residues processed: 105 average time/residue: 0.1017 time to fit residues: 15.0565 Evaluate side-chains 104 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 70 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 147 ILE Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 256 VAL Chi-restraints excluded: chain X residue 266 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 62 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 9 optimal weight: 0.0970 chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.125168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.111826 restraints weight = 13048.003| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.28 r_work: 0.3121 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9470 Z= 0.103 Angle : 0.514 12.171 12825 Z= 0.243 Chirality : 0.040 0.155 1502 Planarity : 0.004 0.040 1616 Dihedral : 8.616 172.195 1391 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.34 % Favored : 97.58 % Rotamer: Outliers : 3.35 % Allowed : 18.70 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.26), residues: 1155 helix: 1.44 (0.23), residues: 543 sheet: 0.03 (0.39), residues: 203 loop : -0.59 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 58 TYR 0.007 0.001 TYR A 139 PHE 0.010 0.001 PHE X 241 TRP 0.004 0.001 TRP D 314 HIS 0.005 0.001 HIS X 40 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9470) covalent geometry : angle 0.51432 (12825) hydrogen bonds : bond 0.02723 ( 461) hydrogen bonds : angle 4.55604 ( 1353) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2157.53 seconds wall clock time: 37 minutes 48.39 seconds (2268.39 seconds total)